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  • Molekel - Message forums

    Discussion forums: Help

    Expanded view | Monitor forum | Save place

    Welcome to Help
    Submitted by Unset; posted on Wednesday, September 13, 2006
    Welcome to Help
    Have Problem Opening Multi-Structure xyz File in Windows Vista
    Submitted by Lee; posted on Thursday, February 22, 2007
    When I opened multi-structure xyz file, molekel quits after reading the structures. This is what Visual Studio 2005 gives when debugging: Unhandled exception at 0x00000000 in Molekel.exe: 0xC0000005: Access violation reading location 0x00000000. Any thought? Thanks!
    Re: Have Problem Opening Multi-Structure xyz File in Windows Vista
    Submitted by Ugo Varetto; posted on Monday, March 05, 2007
    Actually we have not tested yet Molekel on Vista, we'll start testing after the OpenGL drivers get better; the NVIDIA forceware driver released on March 2 2007 supporting VISTA is still beta.
    How display MO from G03 computation.
    Submitted by Vincent Thery; posted on Monday, February 12, 2007
    Hello, Since the new version of MOLEKEL (5.1), I cannot display the MO from Gaussian computation. Before (4.3 version) I used the Gfprint keyword, but now it does'nt work. Which G03 keyword should I use now? I specify that I run calculation on an Altix 350 (OS: Suze 10 ) and i display the results (with MOLEKEl) on a PC under FC5. Thank for your help. Best regards
    Re: How display MO from G03 computation.
    Submitted by Ugo Varetto; posted on Monday, March 05, 2007
    Not sure about what's going on since the code for reading Gaussian files didn't change (src/old/readgauss.cpp) and I haven't seen your data, but do you have the "ATOMIC CENTER" | "ATOMIC ORBITAL" | "GAUSSIAN FUNCTIONS" table in the file ? You can try to use the "gfoldprint pop=full" option.
    Re: How display MO from G03 computation.
    Submitted by Amos Anderson; posted on Tuesday, April 03, 2007
    hello -- looking through quite a few different molecular visualization programs, i found molekel, and i'm quite excited about the possibilities. my goal is to not only be able to visualize the molecule, but to be able to see the molecular orbitals as well, and of the programs i've been looking at, it appears molekel has the best chance of being useful in this regard. however, i can't figure out how to get it to work! the code I use most often is Jaguar, so that's what i want to figure out how to connect to molekel in order to see MOs. 1) I can output Gaussian 92 input files. However, it appears that molekel can only read gaussian 98 or 03. The error messsage I get refers to "Molekel 4.6 read_gauss() function" 2) I can output a "molden orbitals file", to which Jaguar gives the extenstion ".molf", but I the error message now refers to a "Molekel 4.6 read_molden() function" Do you have any recommendations? thanks! Amos.
    Re: How display MO from G03 computation.
    Submitted by Molekel Admin; posted on Friday, August 10, 2007
    Hi, the molden file should be ok, on Windows you need to convert the file to Windows format using e.g. unix2dos. Can you please upload send the molden file to molekel AT cscs DOT ch or upload it to ftp://ftp.cscs.ch/in/put/abc/molekel. Thank you
    Relative atoms size
    Submitted by Valentin Ananikov; posted on Monday, April 02, 2007
    Hi! "Ball and wire" or "Ball and stick" display of transition metal complex shows the metal (Pd, Pt, etc.) even smaller than the Hydrogen atoms. This apparently results in unrealistic picture - metal atom should have larger diameter. How to change this? Using "Atom scaling" does not help, since it changes the size of all atoms, while I need to increase the diameter of one atom, while keeping the diameters of other atoms unchanged. Thanks! Regards, Valentin Ananikov.
    Viewing ADF t41 surface files
    Submitted by Jason Durivage; posted on Sunday, April 15, 2007
    In the previous version Molekel (4.3) there was a way to view t41 surface files on xyz files. Is this possible in Molekel 5.1? If it is, how do I do it? Thanks in advance for all your help. Cheers, Jason Durivage
    Re: Viewing ADF t41 surface files
    Submitted by Ugo Varetto; posted on Tuesday, May 22, 2007
    Hi, not sure I understand, cannot you simply display at the same time a molecule read from an xyz file and a surface computed from a t41 file ? If you do not want to display the atoms read from the t41 file you can set the size of atoms and bonds to zero. Note that we added preliminary t41 support in Molekel 5.1.1 so you cannot do that with previous versions.
    Re: Viewing ADF t41 surface files
    Submitted by Jason Durivage; posted on Tuesday, June 12, 2007
    Thanks for your reply. In Molekel 4.3.2, the way I would plot my orbitals would be to open the xyz file, then go to the surfaces menu and load the .t41 that I wanted. I just tried Molekel 5.1.1. I am able to get a surface but I can see the different phases. Any help would be appreciated.
    Trouble compiling on Linux x86_64
    Submitted by Peter Ruprecht; posted on Thursday, May 24, 2007
    Hi, I'm trying to compile molekel 5.1.1 on RedHat Enterprise Linux 4.5 (64-bit.) I think I have all of the prerequisite packages working successfully, but I get an error when running "gmake" to build molekel: [ 54%] Building CXX object CMakeFiles/Molekel.dir/utility/OBMSMSFormat.o /usr/local/src/molekel/molekel-5.1/src/utility/OBMSMSFormat.cpp: In member function `virtual bool OBMSMSFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)': /usr/local/src/molekel/molekel-5.1/src/utility/OBMSMSFormat.cpp:111: error: `ostream' was not declared in this scope /usr/local/src/molekel/molekel-5.1/src/utility/OBMSMSFormat.cpp:111: error: `os' was not declared in this scope make[2]: *** [CMakeFiles/Molekel.dir/utility/OBMSMSFormat.o] Error 1 make[1]: *** [CMakeFiles/Molekel.dir/all] Error 2 make: *** [all] Error 2 I'm not much of a C++ programmer, so if anyone could give any suggestions about what I can do to fix this, please let me know. -Peter Ruprecht U of Colorado
    Trouble compiling on Linux x86_64
    Submitted by Peter Ruprecht; posted on Thursday, May 24, 2007
    Hi, I'm trying to compile molekel 5.1.1 on RedHat Enterprise Linux 4.5 (64-bit.) I think I have all of the prerequisite packages working successfully, but I get an error when running "gmake" to build molekel: [ 54%] Building CXX object CMakeFiles/Molekel.dir/utility/OBMSMSFormat.o /usr/local/src/molekel/molekel-5.1/src/utility/OBMSMSFormat.cpp: In member function `virtual bool OBMSMSFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)': /usr/local/src/molekel/molekel-5.1/src/utility/OBMSMSFormat.cpp:111: error: `ostream' was not declared in this scope /usr/local/src/molekel/molekel-5.1/src/utility/OBMSMSFormat.cpp:111: error: `os' was not declared in this scope make[2]: *** [CMakeFiles/Molekel.dir/utility/OBMSMSFormat.o] Error 1 make[1]: *** [CMakeFiles/Molekel.dir/all] Error 2 make: *** [all] Error 2 I'm not much of a C++ programmer, so if anyone could give any suggestions about what I can do to fix this, please let me know. -Peter Ruprecht U of Colorado
    Re: Trouble compiling on Linux x86_64
    Submitted by Ugo Varetto; posted on Wednesday, June 06, 2007
    Hi, which version of OpenBabel are you using ? this is a compilation error I got while testing with OpenBabel 2.1, you shouldn't be getting it with OB 2.0.x. This should be fixed in the current /trunk source tree. If you want to fix it yourself simply open OBMSMSFormat.cpp and add the following code just after the other #include statements: #include <iostream> using namespace std;
    Reading GAMESS output files (*.out)
    Submitted by Adam Jara; posted on Thursday, June 21, 2007
    I'm having trouble loading GAMESS output files with the newest version of Molekel (5.1.1.4). The program gives me the following error message: ("I/O" Error: Cannot read *.out with OpenBabel.) Is there a certain format my GAMESS output file must take. The file I'm attempting to open is the result of a successful geometry optimization and I have not altered the file in any way. Thanks, Adam Jara
    Reading GAMESS output files (*.out)
    Submitted by Adam Jara; posted on Thursday, June 21, 2007
    I'm having trouble loading GAMESS output files with the newest version of Molekel (5.1.1.4). The program gives me the following error message: ("I/O" Error: Cannot read *.out with OpenBabel.) Is there a certain format my GAMESS output file must take. The file I'm attempting to open is the result of a successful geometry optimization and I have not altered the file in any way. Thanks, Adam Jara
    Re: Reading GAMESS output files (*.out)
    Submitted by Ugo Varetto; posted on Thursday, June 28, 2007
    Hi, can you please send us the file ? (I'm assuming you are selecting the GAMESS format in the 'open file' dialog). Unfortunately bioinformatics.org does not allow attachments, you can put the file on a writable ftp directory here: ftp.cscs.ch/in/put/abc/uvaretto
    Re: Reading GAMESS output files (*.out)
    Submitted by Duncan Wild; posted on Friday, July 06, 2007
    Hi there, I am a new user of Molekel, and I am also having trouble with loading GAMESS output files. None of mine work! Did you find an answer to this previous post? I am using Molekel version 5.1.1.4 under Windows XP professional. For more info, I have been using WinGAMES which was built with the Cygwin compiler. This is not PC GAMESS. At the start I was getting an OpenBabel error, however now I get an I/O error that says "Cannot read C:/... with Molekel 4.6 read_gamess() function" Your help would be greatly appreciated, as from the outside looking in the program looks great! Thanks in advance Dr. Duncan Wild..
    Re: Reading GAMESS output files (*.out)
    Submitted by Duncan Wild; posted on Friday, July 06, 2007
    I hope you don't mind, however I just uploaded an example of a GAMESS output file that I am trying to load. Also, more info. I have been choosing the "gam" option when trying to load the files into Molekel. Thanks again, Duncan Wild
    Re: Reading GAMESS output files (*.out)
    Submitted by Adam Jara; posted on Tuesday, July 24, 2007
    I've uploaded the .out file to the ftp site. I've been able to successfully load the .out file with other programs such as MolPlt. Thanks, Adam Jara
    Saving molekel files
    Submitted by T.Pedersen; posted on Thursday, July 19, 2007
    Hi, I was wondering what format to save Molekel files in? 5.1.1 doesn't seem to have a default format - like 4.3 has. Since it can take some time to display electron density surfaces it would be nice to be able to save one's work. Any ideas would be appreciated. Cheers.
    Re: Saving molekel files
    Submitted by Molekel Admin; posted on Thursday, July 19, 2007
    Hi, actually we started looking into that a while ago, one of the problem is that saving all the information (settings + mesh data) to one single file may result in huge file sizes, it's a problem to deal with versions and it's not easy to extend; so we are thinking of saving the entire workspace to a user specified directory with: - one file per molecule containing molecule structure information - one file per surface containing surface geometry and rendering properties - one file per molecule containing per-molecule settings (animation mode, rendering properties etc.) - one workspace.molekel file containing a list of all the surfaces/molecules/settings files Molecules will be saved in one of the standard molecular file formats (probably just a copy of the original file). Meshes will be saved in a standard format like OBJ or other standard. Since however this change is going to take some time we decided to postpone it until after the release of Molekel 5.2.
    Saving molekel files
    Submitted by T.Pedersen; posted on Thursday, July 19, 2007
    Hi, I was wondering what format to save Molekel files in? 5.1.1 doesn't seem to have a default format - like 4.3 has. Since it can take some time to display electron density surfaces it would be nice to be able to save one's work. Any ideas would be appreciated. Cheers.
    Molekel quits on me in Windows XP
    Submitted by Ian Konen; posted on Friday, August 03, 2007
    I have had no luck with Molekel 5.1.1 or 5.2 in Windows XP. I've tried a couple of different Gaussian .log files (G03 and G98) and a .xyz file, and they all cause Molekel to quit as soon as I load. I'm pretty sure it's not the file format, because if I purposely mess up the input file, I get an error message about openbabel (and the program stays open). But with a working input file, it just quits with no explanation other than the XP dialog telling me Molekel has unexpectedly quit. Has anyone else been able to get it to work in XP?
    Re: Molekel quits on me in Windows XP
    Submitted by Molekel Admin; posted on Friday, August 10, 2007
    Hi, what graphics card do you have ? is it an ATI ? Note sure what it is, but in case it's the graphic driver you can set the value of two environment variables as follows: * COIN_FULL_INDIRECT_RENDERING=0 * COIN_FORCE_GL1_0_ONLY=1 before launching Molekel to disable the use of advanced OpenGL features.
    Re: Molekel quits on me in Windows XP
    Submitted by Ian Konen; posted on Monday, August 13, 2007
    Hey, thanks for the help. I do have an ATI card, and that did fix it. Actually, it still runs without setting the "COIN_FULL_INDIRECT_RENDERING" variable, so it looks like all I need is set COIN_FORCE_GL1_0_ONLY=1 I have no idea what that means, but hopefully it rules out 50% of the possible problems :-)
    Re: Molekel quits on me in Windows XP
    Submitted by Antony Memboeuf; posted on Tuesday, September 18, 2007
    Hello !! I've exactly the same problem as the one Ian Konen described above (the same sudden quitting way with the windows error message, and I also have ATI graphic card and a lot of fancy Open GL, 3D accelerator, ...), but I don't really understand what I should do to solve it ... I mean how do I set up that value COIN_FORCE_GL1_0_ONLY=1 is a mystery for me !!!! thanks in advance for your help !! Antony Memboeuf (a new Molekel user)
    Re: Molekel quits on me in Windows XP
    Submitted by Molekel Admin; posted on Tuesday, February 19, 2008
    To set the environment variables permanently on Windows XP right-click on My Computer then select the Advanced tab and click on the Environment Variables button.
    Gaussian 03 support
    Submitted by Molekel Admin; posted on Tuesday, August 14, 2007
    I'm forwarding a message received from a Molekel user which explains how to configure Gaussian 03 to output basis set information in a format that Molekel understands: ... "I found a solution, which you please may pass to other molekel users. To get basis set printed in a suitable form by gaussian03 use iop(3/24=1) instead of gfprint"
    Viewing molecular orbitals from Molden files.
    Submitted by Molekel Admin; posted on Thursday, August 16, 2007
    Viewing molecular orbitals read from Molden files can be a problem in case the basis set elements are not in the same order as the atoms. This behavior is going to change in the next release of Molekel and a fix has already been committed. In the meantime if you need to visualize molecular orbitals read from Molden you could simply reorder the atoms in the Molden file in the same order as the basis set elements. E.g. In case the atoms are ordered like this: [Atoms] Angs C 1 6 0.0000000000 0.0000000000 0.0000000000 H 2 1 0.0000000000 0.0000000000 1.0856415283 H 3 1 0.0000000000 1.0343722180 -0.3297423077 H 4 1 -0.9307128069 -0.4512369987 -0.3298275233 C 5 6 1.2066572971 -0.7558134495 -0.5524694437 H 6 1 1.2067585831 -1.7901882479 -0.2227929118 H 7 1 2.1373286719 -0.3044302328 -0.2226968903 H 8 1 1.2065923496 -0.7556902812 -1.6381205626 And the basis set is: [GTO] 1 0 ... 5 0 ... 2 0 ... 3 0 ... 4 0 ... 6 0 ... 7 0 ... 8 0 ... If you change to: [Atoms] Angs C 1 6 0.0000000000 0.0000000000 0.0000000000 C 2 6 1.2066572971 -0.7558134495 -0.5524694437 H 3 1 0.0000000000 0.0000000000 1.0856415283 H 4 1 0.0000000000 1.0343722180 -0.3297423077 H 5 1 -0.9307128069 -0.4512369987 -0.3298275233 H 6 1 1.2067585831 -1.7901882479 -0.2227929118 H 7 1 2.1373286719 -0.3044302328 -0.2226968903 H 8 1 1.2065923496 -0.7556902812 -1.6381205626 ... [GTO] 1 0 ... 2 0 ... 3 0 ... 4 0 ... 5 0 ... 6 0 ... 7 0 ... 8 0 ... It should work.
    How do I change the orbital colors?
    Submitted by Benj FitzPatrick; posted on Thursday, August 16, 2007
    Using the recent post for viewing orbitals in molden format I can now get sensible looking pictures, but I was wondering if there was a way to change the default colors for the orbitals?
    Re: How do I change the orbital colors?
    Submitted by Molekel Admin; posted on Friday, August 24, 2007
    Hi, we replied to the other message you sent to the 'Open Discussion' forum. The colors are currently fixed, we do plan to make colors configurable but I'm not sure if it will be on a per-surface, per-molecule or application-level basis. Thank you
    Screen refresh trouble
    Submitted by Nato Shkwa; posted on Monday, August 27, 2007
    I am experiencing a trouble in screen refreshing with Molekel ver 5 and 5.2.. The installatoin completed just fine, and the program started up just nicely. Molekel read GamessUS log file, and it showed MO surface perfectly, but the problem started here. When I rotate the molecule by the mouse, Molekel does not erace the previous surface, and draws a new surface on it. So, as you move the mouse, the screen is smeared over with uneraced surfaces. The system I use is Fedora Core 5. The above trouble was seen in both KDE and GNOME environments. Does anyone know a remedy for this? I would appreciate your help. Nato
    crash when reading molden file
    Submitted by Markus Doerr; posted on Thursday, September 20, 2007
    Hi, when trying to read a molden file (generated from turbomole data by tm2molden) molekel crashes with the following error messages: [ATOMS] section read! *** glibc detected *** bin/Molekel: free(): invalid next size (normal): 0x086097b0 *** ======= Backtrace: ========= [...] There is nothing special with the molekel file except that it contains f basis functions (TZVPP basis set). Also the ordering of the basis functions is the same as that of the atoms. I am using molekel 5.2 on a Linux x86_64 system, but I get the same error with molekel 5.1 and even with the old molekel 4.3. Can anybody give me a hint what the cause of this problem is? Thanks in advance Markus
    crash when reading molden file
    Submitted by Markus Doerr; posted on Thursday, September 20, 2007
    Hi, when trying to read a molden file (generated from turbomole data by tm2molden) molekel crashes with the following error messages: [ATOMS] section read! *** glibc detected *** bin/Molekel: free(): invalid next size (normal): 0x086097b0 *** ======= Backtrace: ========= [...] There is nothing special with the molekel file except that it contains f basis functions (TZVPP basis set). Also the ordering of the basis functions is the same as that of the atoms. I am using molekel 5.2 on a Linux x86_64 system, but I get the same error with molekel 5.1 and even with the old molekel 4.3. Can anybody give me a hint what the cause of this problem is? Thanks in advance Markus
    molecular orbitals generated with gaussian
    Submitted by anna amat alberti; posted on Tuesday, December 11, 2007
    i have a problem visualizing the cube files generated with gaussian'03. i'm using molekel_macos_5.2.0 and i can't use the Electron Density utility. i can get into the option from the surface menu but all the options from the Electron Density menu appear unabled. i have no problem using Grid Data but i would like to do as in the old version of molekel where i can add or subtract orbitals, use both signs.... can anybody help me? thanks!
    Re: molecular orbitals generated with gaussian
    Submitted by Molekel Admin; posted on Tuesday, January 08, 2008
    The reason for which the Electron Density is not accessible is that no electron density data is available. Data in the .cube files can be anything e.g. electrostatic potential; all you have in .cube files is a 3d grid of float values, that's it. Regarding using +/- signs in the current version of Molekel, you can simply reload a second copy of the molecule and generate a new surface specifying a different isovalue. While this is definitely a workaround it's also quite handy because you can e.g. use one molecule to render all the surfaces with positive isovalues, another to render all the surfaces with negative isovalues and then toggle the visibility of each molecule to display only the surfaces with a specific isovalue.
    View Molecular elecrostatic potential
    Submitted by e y; posted on Thursday, January 24, 2008
    Hello I have a gamess .out file. I open it with MOLEKEL and try to visualize the molecular elec. potential. when I hit surfaces button I select electron density, then I see alpha orbitals of the molecule. I then check molecular electrostatic potential map. but the "generate" button is inactive. How can I view it? thank you I am using MOLEKEL 5.1 for windows. esra
    Re: View Molecular elecrostatic potential
    Submitted by Molekel Admin; posted on Tuesday, February 05, 2008
    Hi, you also need to select the orbital surface you want to generate. The 'generate' button is enabled only after a specific orbital is selected.
    Re: View Molecular elecrostatic potential
    Submitted by e y; posted on Wednesday, February 06, 2008
    Thanks for the reply. My output file contains 232 atoms and a lot of orbitals. and to draw one of the orbitals takes 30 min. I was wondering if there is another way. Thank you
    Re: View Molecular elecrostatic potential
    Submitted by Molekel Admin; posted on Tuesday, February 12, 2008
    I'm afraid there is not much we can do for now. Could you please tell us which system are you running Molekel on ? (Processor, memory, OS). Also it would be great if you could upload the data here: ftp://ftp.cscs.ch/in/put/abc/molekel I'm thinking that we could use your data as test data for profiling the application since all the Gaussian, GAMESS, ADF and Molden files we are using for testing are pretty small. We are working on parallel implementations for some of the algorithms so this will change in the future but it will require a multicore CPU and/or a cluster system and/or a fast graphics card (if we decide to implement something on the GPU). Thank you P.S. Just a little insight of what's going on: Whenever you hit the 'Generate' button Molekel generates a 3D grid and for each point in the grid it computes the electron density which is basically a weighted sum of of exponentials and an electrostatic potential value which is another weighted sum of functions similar to 1/r. Both sums are a function of the number of atoms and atom types; usually when you have more than 30 atoms it can really get slow.
    Problems opening Molekel 5.3.0
    Submitted by Jason Durivage; posted on Wednesday, February 27, 2008
    When I try to open Molekel 5.3.0, it automatically crashes. I'm on an Intel-based MacBook Pro running OS X 10.5.2. The graphics card in the computer is an ATI RadeonX1600 that has 256MB of dedicated video RAM. Do you have any suggestions on why the program is crashing and any possible fixes. Thanks, Jason Durivage
    Re: Problems opening Molekel 5.3.0
    Submitted by Jason Durivage; posted on Wednesday, February 27, 2008
    Just a quick other note. I haven't had any problems with the other versions of Molekel 5.x. Jason Durivage
    Re: Problems opening Molekel 5.3.0
    Submitted by Molekel Admin; posted on Monday, March 03, 2008
    Chances hare there are some problems finding the Qt libraries, we had issues with the Mac build script which didn't properly set some dependencies in some of the dynamic libraries. Try the version here: ftp://ftp.cscs.ch/out/molekel/molekel_5.3/molekel_MacOS_5_3_0_i386.dmg.zip
    Re: Problems opening Molekel 5.3.0
    Submitted by Jason Durivage; posted on Wednesday, March 05, 2008
    Thanks for the link. The program opened up and worked fine.
    opening .mkl file
    Submitted by Herbert Fruchtl; posted on Monday, March 03, 2008
    When I try to open an mkl file (created by ORCA's orca_2mkl utility, with the express purpose of viewing with MOLEKEL), I get the following error: Cannot read file: /home/hf63/Dendrimers_2/Charges_and_geometries/POSS-vbp0-zindo.mkl with OpenBabel Is this format not supported (the ORCA manual advertises the utility program explicitly for using MOLEKEL), or do I have to open it some other way? Thanks in advance, Herbert
    Re: opening .mkl file
    Submitted by Molekel Admin; posted on Tuesday, March 04, 2008
    You should use Molekel 4.3 to visualize .mkl files.
    Re: opening .mkl file
    Submitted by greib; posted on Thursday, July 10, 2008
    Well is it possible to convert any .mkl files to one of the new openbabel formats? I have lots of .mkl files but would like to use the new features and even if I had to convert them it would be easier than rebuilding new files from scratch. Thanks in advance for any info or script to achieve this.
    export image
    Submitted by jose ceron; posted on Wednesday, March 05, 2008
    Hi everybody, I have a problem when I export MO image generated by Molekel. I've tried do it with "save image" and "save to" but the resolution is very poor with both and I don't know how I can change the picture size. Any suggestions will be welcome! Thanks, Jose
    Changing Atoms Colors in Molekel
    Submitted by Dr. Matteo Cavalleri; posted on Thursday, March 20, 2008
    Hey! In the documentation is briefly mentioned how to change atoms colors, by editing a text file as the one provided in the /data directory. The problem is that file is just a list of numbers of difficult comprehension, I have problems to associate them to any specific element. Could you provide me with a couple of brief examples on how to use this file to change elements colors in Molekel (e.g. to change Si color to yellow)? Also it could be nice as future features to have a simple menu way to do this (as it is already possible for the background), as well as for the surface/orbitals colors, in this aspect Molden 4.3 was superb! Thank you and Keep up the good work, Matteo
    Re: Changing Atoms Colors in Molekel
    Submitted by Molekel Admin; posted on Monday, March 31, 2008
    Hi, the sample file lists one atom color per line. The line number matches the atomic number e.g. 8th line -> atomic number 8. Colors are encoded as red, green and blue values between 0 and 1. To change the Si color simply go to line 14 and change the rgb values.
    Re: Changing Atoms Colors in Molekel
    Submitted by Dr. Matteo Cavalleri; posted on Monday, March 31, 2008
    Great! Thank you!
    build on ubuntu-amd64
    Submitted by Claudio Marinelli; posted on Wednesday, March 26, 2008
    Dear all, while compiling on amd64 laptop with ubuntu 7.10 i get an error regarindg openbabel during the linking step. This happens with the pre-installed openbabel-2.0 as well as with the 2.1.1 I compiled myself. Should I build 2.0 or 2.1 with special options? The error is this: Linking CXX executable dist/bin/Molekel CMakeFiles/Molekel.dir/utility/System.o: In function `GetTemporaryFileName(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': System.cpp:(.text+0x43e): warning: the use of `tmpnam' is dangerous, better use `mkstemp' CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OpenBabel::OBMoleculeFormat::WriteChemObject(OpenBabel::OBConversion*)': OBGaussianCubeFormat.cpp:(.text._ZN9OpenBabel16OBMoleculeFormat15WriteChemObjectEPNS_12OBConversionE[OpenBabel::OBMoleculeFormat::WriteChemObject(OpenBabel::OBConversion*)]+0x19): undefined reference to `OpenBabel::OBMoleculeFormat::WriteChemObjectImpl(OpenBabel::OBConversion*, OpenBabel::OBFormat*)' CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*)': OBGaussianCubeFormat.cpp:(.text._ZN9OpenBabel16OBMoleculeFormat14ReadChemObjectEPNS_12OBConversionE[OpenBabel::OBMoleculeFormat::ReadChemObject(OpenBabel::OBConversion*)]+0x19): undefined reference to `OpenBabel::OBMoleculeFormat::ReadChemObjectImpl(OpenBabel::OBConversion*, OpenBabel::OBFormat*)' collect2: ld returned 1 exit status make[2]: *** [dist/bin/Molekel] Error 1 make[1]: *** [CMakeFiles/Molekel.dir/all] Error 2 make: *** [all] Error 2
    Re: build on ubuntu-amd64
    Submitted by Molekel Admin; posted on Monday, March 31, 2008
    Hi, how are you building OpenBabel (static or dynamic) ? you need to build it as a dynamic library.
    Re: build on ubuntu-amd64
    Submitted by Claudio Marinelli; posted on Monday, March 31, 2008
    I'm now at work, and cannot check but it should be dynamic. The configure of opebabel ny dedafult shuld build dynamic and static libs (--enable-shared[=PKGS] build shared libraries [default=yes]). I cannot think of anyone reason to have build static libs but maybe I need to specify --enable-shared. Anyway I have tried the repository version of Ubuntu (ver 2.0.2, and it should be dynamic) with the same error. Anyway I'll try to rebuild openbabel with explicit --enable-shared and tell you the outcome. Thanks
    Re: build on ubuntu-amd64
    Submitted by Claudio Marinelli; posted on Monday, March 31, 2008
    hi, i tried to reinstall using openbabel-2.0.2 (Ihave read on this forum to use 2.0.x rather than 2.1.x) with --enable-shared but without success; the error is: CMakeFiles/Molekel.dir/MolekelMolecule.o: In function `MolekelMolecule::GetGridLabels() const': MolekelMolecule.cpp:(.text+0x2859): undefined reference to `OpenBabel::OBMol::GetData(char const*)' CMakeFiles/Molekel.dir/MolekelMolecule.o: In function `MolekelMolecule::HasGridData() const': MolekelMolecule.cpp:(.text+0x7a04): undefined reference to `OpenBabel::OBMol::HasData(char const*)' MolekelMolecule.cpp:(.text+0x7a1d): undefined reference to `OpenBabel::OBMol::HasData(char const*)' CMakeFiles/Molekel.dir/MolekelMolecule.o: In function `MolekelMolecule::GetGridDataStepSize(double*) const': MolekelMolecule.cpp:(.text+0x7acc): undefined reference to `OpenBabel::OBMol::GetData(char const*)' MolekelMolecule.cpp:(.text+0x7b6f): undefined reference to `OpenBabel::OBMol::GetData(char const*)' CMakeFiles/Molekel.dir/MolekelMolecule.o: In function `MolekelMolecule::GetGridDataNumSteps(int*) const': MolekelMolecule.cpp:(.text+0x7c72): undefined reference to `OpenBabel::OBMol::GetData(char const*)' MolekelMolecule.cpp:(.text+0x7ccf): undefined reference to `OpenBabel::OBMol::GetData(char const*)' CMakeFiles/Molekel.dir/MolekelMolecule.o: In function `MolekelMolecule::GetGridDataMin(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const': MolekelMolecule.cpp:(.text+0x7d86): undefined reference to `OpenBabel::OBMol::GetData(char const*)' CMakeFiles/Molekel.dir/MolekelMolecule.o:MolekelMolecule.cpp:(.text+0x7dec): more undefined references to `OpenBabel::OBMol::GetData(char const*)' follow CMakeFiles/Molekel.dir/utility/OBGaussianCubeFormat.o: In function `OBGridData::OBGridData()': OBGaussianCubeFormat.cpp:(.text._ZN10OBGridDataC1Ev[OBGridData::OBGridData()]+0x12): undefined reference to `OpenBabel::OBGenericData::OBGenericData()' CMakeFiles/Molekel.dir/utility/OBT41Format.o: In function `OBT41Data::OBT41Data()': OBT41Format.cpp:(.text._ZN9OBT41DataC1Ev[OBT41Data::OBT41Data()]+0x12): undefined reference to `OpenBabel::OBGenericData::OBGenericData()'
    Molekel 5.3 Win32 crashes when rendering grid data
    Submitted by James; posted on Thursday, April 10, 2008
    Hi, Molekel 5.3 crashes every time when I try to render a Gaussian cube file. For example, loading the example h20-dens.cube file from the Molekel data directory and using Surfaces|Grid Data with default options causes the program to crash with a fatal error message about libvtkrendering.dll. Thanks James
    Re: Molekel 5.3 Win32 crashes when rendering grid data
    Submitted by Molekel Admin; posted on Thursday, May 08, 2008
    We've experienced this problem with very old graphics cards or Intel mobile graphics cards. This problem has been fixed as of revision 570 so any new builds from revisions >= 570 should not have this issue.
    Molekel 5.3 doesn't start
    Submitted by Mihai Medeleanu; posted on Friday, April 11, 2008
    I'm using Molekel (32 bit) on PCLinuxOS. The last version does not start and send the error: "Floating point exception" Any ideas? Thanks.
    Re: Molekel 5.3 doesn't start
    Submitted by Molekel Admin; posted on Thursday, May 08, 2008
    This looks like a problem with libc, no idea though, it will probably go away if you build the program from source on your platform. We can only test on SuSE and RedHat distributions.
    Viewing Orbitals calculated with Turbomole
    Submitted by Katharina Hunger; posted on Friday, May 16, 2008
    Hello everybody, I optmized the geometry of my molecule with Turbomole and now would like to have a look at the orbitals. Can anybody tell me, what to do? I can`t load the mos-file, because molekel only shows files with file-endings... Thanks, Katharina
    Trouble in MEP scalar bar
    Submitted by Baifan Wang; posted on Thursday, June 12, 2008
    The MEP scalar bar seems to adapt the molecular electrostatic potential automatically. Is there an option that can change the scalar of the MEP scalar bar manually£¿
    Re: Trouble in MEP scalar bar
    Submitted by Molekel Admin; posted on Monday, June 16, 2008
    Scalar bar values do indeed automatically adapt to the data range; you can currently change the center point and interval range only when using the plane probe widget (display the plane probe widget then drag the mouse pointer on the plane while keeping the right mouse button down).
    Grid Surfaces
    Submitted by Eduard Matito; posted on Saturday, June 14, 2008
    Hi, I'm using molekel 5.3 for Mac. I have two files with cube structure (from non-commercial program). One contains a grid of points and values, and the second information regarding which point belongs to which part of the surface. I would like to picture these surfaces with different colors, for which I need to map the second file into the first. How can I do this in the current version of Molekel? Such possibility existed for Molekel 4.1. I loaded separately both files and then I chose "Grid Value", automatically surface was colored by different regions. Either a way to solve this issue for Molekel5.3 or a version of Molekel4.1 for Mac (or with the source code so that I can compile it there) would solve my problem. Many thanks in advance, Eduard PS/ Please contact me by e-mail: ematito@gmail.com
    Molekel 5.3 crashes when opening a file
    Submitted by Noah Silas; posted on Thursday, June 26, 2008
    I'm attempting to install the prebuilt Molekel 5.3 for Linux x86_32 on Ubuntu 7.04. The program will run, but after loading a data file will crash when attempting to draw it. Here are the errors that appear: Coin error in SoType::createType(): a type with name ``SFDouble'' already created Coin error in SoType::createType(): a type with name ``MFDouble'' already created Molekel: ../../../src/glue/gl.c:2179: cc_glglue_instance: Assertion `glGetError() == 0x0 && "GL error when calling glGetString() -- no current GL context?"' failed. Also, here is a gdb backtrace, if that helps. Program received signal SIGABRT, Aborted. [Switching to Thread -1266567472 (LWP 10420)] 0xffffe410 in __kernel_vsyscall () (gdb) bt #0 0xffffe410 in __kernel_vsyscall () #1 0xb4971df0 in raise () from /lib/tls/i686/cmov/libc.so.6 #2 0xb4973641 in abort () from /lib/tls/i686/cmov/libc.so.6 #3 0xb496b43b in __assert_fail () from /lib/tls/i686/cmov/libc.so.6 #4 0xb6f477db in cc_glglue_instance (contextid=0) at ../../../src/glue/gl.c:2179 #5 0xb6f8bf94 in sogl_glue_instance (state=0x851a1b0) at ../../../src/misc/SoGL.cpp:85 #6 0xb6ea77e5 in SoGLTexture3EnabledElement::updategl (this=0x82ea478) at ../../../../src/elements/GL/SoGLTexture3EnabledElement.cpp:154 #7 0xb6ea7977 in SoGLTexture3EnabledElement::init (this=0x82ea478, stateptr=0x851a1b0) at ../../../../src/elements/GL/SoGLTexture3EnabledElement.cpp:83 #8 0xb6fc209b in SoState (this=0x851a1b0, theAction=0x852d4c4, enabledelements=@0x84f3c7c) at ../../../src/misc/SoState.cpp:161 #9 0xb6dfe4f8 in SoAction::getState (this=0x852d4c4) at ../../../src/actions/SoAction.cpp:1033 #10 0xb6dfe786 in SoAction::apply (this=0x852d4c4, root=0x852df20) at ../../../src/actions/SoAction.cpp:543 #11 0x080cd388 in vtkSoMapper::Draw () #12 0xb615f89c in vtkOpenGLPolyDataMapper::RenderPiece () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #13 0xb60c80a7 in vtkPolyDataMapper::Render () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #14 0xb614a173 in vtkOpenGLActor::Render () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #15 0xb602bd65 in vtkActor::RenderOpaqueGeometry () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #16 0xb6030bf9 in vtkAssembly::RenderOpaqueGeometry () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #17 0xb60df73f in vtkRenderer::UpdateGeometry () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #18 0xb616ce57 in vtkOpenGLRenderer::DeviceRender () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #19 0xb60e1595 in vtkRenderer::Render () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #20 0xb60de1bb in vtkRendererCollection::Render () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #21 0xb60eeb53 in vtkRenderWindow::DoStereoRender () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #22 0xb60ee99d in vtkRenderWindow::DoFDRender () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #23 0xb60ef9c5 in vtkRenderWindow::DoAARender () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #24 0xb60edc53 in vtkRenderWindow::Render () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #25 0xb618b1e4 in vtkXOpenGLRenderWindow::Render () from /home/software/molekel-5.3/lib/libvtkRendering.so.5.1 #26 0x0808b616 in MainWindow::MoleculeLoaded () #27 0x0808c704 in MainWindow::LoadMolecule () #28 0x080956bb in MainWindow::LoadFileSlot () #29 0x0814b035 in MainWindow::qt_metacall () #30 0xb768e870 in QMetaObject::activate () from /home/software/molekel-5.3/lib/libQtCore.so.4 #31 0xb768eacf in QMetaObject::activate () from /home/software/molekel-5.3/lib/libQtCore.so.4 #32 0xb79f57c1 in QAction::triggered () from /home/software/molekel-5.3/lib/libQtGui.so.4 #33 0xb79f647f in QAction::activate () from /home/software/molekel-5.3/lib/libQtGui.so.4 #34 0xb7d35432 in QToolButton::nextCheckState () from /home/software/molekel-5.3/lib/libQtGui.so.4 #35 0xb7c89bcf in ?? () from /home/software/molekel-5.3/lib/libQtGui.so.4 #36 0xb7c89e22 in QAbstractButton::mouseReleaseEvent () from /home/software/molekel-5.3/lib/libQtGui.so.4 #37 0xb7d3551c in QToolButton::mouseReleaseEvent () from /home/software/molekel-5.3/lib/libQtGui.so.4 #38 0xb7a45771 in QWidget::event () from /home/software/molekel-5.3/lib/libQtGui.so.4 #39 0xb7c890a5 in QAbstractButton::event () from /home/software/molekel-5.3/lib/libQtGui.so.4 #40 0xb7d34e04 in QToolButton::event () from /home/software/molekel-5.3/lib/libQtGui.so.4 #41 0xb79fbe60 in QApplicationPrivate::notify_helper () from /home/software/molekel-5.3/lib/libQtGui.so.4 #42 0xb79fe8e3 in QApplication::notify () from /home/software/molekel-5.3/lib/libQtGui.so.4 #43 0xb7a5754e in ?? () from /home/software/molekel-5.3/lib/libQtGui.so.4 #44 0xb7a56b5f in QApplication::x11ProcessEvent () from /home/software/molekel-5.3/lib/libQtGui.so.4 #45 0xb7a79c4b in ?? () from /home/software/molekel-5.3/lib/libQtGui.so.4 #46 0xb751edf2 in g_main_context_dispatch () from /usr/lib/libglib-2.0.so.0 #47 0xb7521dcf in ?? () from /usr/lib/libglib-2.0.so.0 #48 0x081bfb10 in ?? () #49 0x00000000 in ?? () Thank you for any assistance you can offer. ~Noah
    Viewing vibrational modes from GAMESS output
    Submitted by Corey James Fugate; posted on Wednesday, July 02, 2008
    I've been trying to get Molekel 5.3 (on my Macbook 10.5) to animate the vibrational modes of a small molecule from a GAMESS output file. It won't open log files or out files, so I simply renamed the file with the .gam or the .gamout extension. Both will open, however I can only see the first few vibrational modes (which are worthless). Any help I could get would be great.
    Spin Density and Bonds
    Submitted by Cedric Desplanches; posted on Monday, July 07, 2008
    Hello, I have two different questions about things I used to know how to do in the Molekel 4 version but that I do not know in version 5: - how is it possible to draw spin density - how is it possible to draw "manually" a bond (often automatic settings do not draw some metal-carbon or metal-nitrogen bonds) With my best wishes,
    Drawing bonds in Molekel 5.3.0.6
    Submitted by David McKay; posted on Tuesday, July 29, 2008
    Hi, I am using Molekel 5.3.0.6 to produce images of orbitals (G03 log file as input). These look great, however there are bonds missing from my molecule - is there a function to add these in (such as 'Bond Attributes' - 'Add Bond' in version 4.3)? If not is there an alternative file format I can convert my G03 output to which will alleviate this problem? Cheers, Dave
    NBO visualization with Molekel 5,3,0,6
    Submitted by Rachel Crespo Otero; posted on Friday, August 01, 2008
    Is it possible visualize the NBO orbitals (from gaussian) with Molekel 5.3.0.6? How I can do it? I want to know also how I can visualize spin densities? Thank in advance Rachel
    Surface Colors (Electronic Density Visualization)
    Submitted by Dr. Matteo Cavalleri; posted on Monday, August 11, 2008
    Using Molekel 5.2.0.5 it is not possible to change/choose the color of the surfaces (both signs) when visualizing orbitals from a calculations. The colors of + and - surfaces cannot be changed from the blue and greenish, which make them very difficult to distinguish especially when the orbital figures is printed in black and white (against a white background, as in a publication). Is there a way (e.g. editing a ascii file as one does for changing element colors) to choose the surface colors in the visualization of orbitals? Is it possible to do that in the 5.3 version? Best Regards and Thank you for the hard work, Matteo
    Geometry analysis
    Submitted by Tomas Österman; posted on Sunday, November 23, 2008
    I always need to click on one extra atom to get the distance, angle or dihedral angle when analysing my calculated geometries (i.e. 3, 4 and 5 atoms respectively). If I do not do this, I am not able to click on the command of interest in the analysis menu. Is this the correct behaviour of Molekel 5.3.0.6? If yes, how do I know which bond or angle that is actually being measured? If no, what can I do to fix the problem? I have Windos XP and I am using Gaussian03 to perform the calculations.
    read larger gaussian files
    Submitted by torsten; posted on Wednesday, December 10, 2008
    hi. molekel crashs down when we try to read a rather large gaussian output file (300 atoms, 20 MB). smaller gaussian output files work well. is there anything we could do, to be able to load also larger files? thank you!
    Re: read larger gaussian files
    Submitted by Molekel Admin; posted on Monday, February 16, 2009
    Hi, it would help if you could put the file you are not able to read here: ftp://ftp.cscs.ch/in/put/abc/molekel/ so that we can have a look at was causes the crash. Thank you
    Define/Rotate plane probe
    Submitted by E. C. Beret; posted on Thursday, March 26, 2009
    Hello everybody, How can one define which plane is used to probe a grid file? I can generate the data from the grid file, display the plane and move it along the axis perpendicular to it, but I need to rotate it. How can this be done? Thanks, Eli
    Re: Define/Rotate plane probe
    Submitted by Molekel Admin; posted on Wednesday, April 01, 2009
    Hi, to rotate the plane click on the plane borders with the middle mouse button then move the mouse while holding the button down. Best Regards
    Molekel Installation Problem
    Submitted by Bhaskar Chilukuri; posted on Wednesday, September 09, 2009
    Hi all, I got Molekel installed on my Windows PC, but when try to open it after installation, the following error message pops up "This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix the problem." I tried installing it over and over but the problem remains to be the same. I really appreciate any reply.
    Re: Molekel Installation Problem
    Submitted by Molekel Admin; posted on Thursday, September 10, 2009
    Hello, which graphics cards do you have ?
    Trouble Opening GAMESS output file
    Submitted by Constantine Mavromichalis; posted on Saturday, September 19, 2009
    Running the GAMESS (April 11, 2008 version) I get my results in .out files. Molekel will not open these .out files. Looking: http://molekel.cscs.ch/wiki/pmwiki.php/ReferenceGuide/FileFormats It says GAMESS output is .gam or .gamout; which I have not heard of. If I rename my output files to this then it gives me "Cannot read: C:/Filename.gam with Molekel 4.6 read_gamess() function." As far as I know the standard output for GAMESS on the systems I worked the output files is with .out extension. Has anyone had a similar problem or know a fix for this?
    Re: Trouble Opening GAMESS output file
    Submitted by Constantine Mavromichalis; posted on Saturday, September 19, 2009
    Nevermind I solved my problem. Anyone interested I used Unix2Dos to convert the file to work correctly with Molekel on Windows, then renamed the .out files to .gam.
    5.4 cannot parse g09 vibrational data
    Submitted by Benj FitzPatrick; posted on Friday, October 30, 2009
    Molekel 5.4 can open geometry optimization/frequency calculation files from g09, but when I try to use it to visualize the normal modes it shows no motion at all. I think this might be from changes in how the vibrational data is written b/c gaussview3 can't parse the vibrational data in g09 log files. I've tried the linux, windows, and osx versions, all with the same results.
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