[cmview-users] Problem running various pdb files+dssp error

M. F. mfaridun at yahoo.com
Mon Jun 17 09:00:55 EDT 2013


Hi Jose,

Thanks for the tip. I had written down the directory as ../dssp-2.1.0/dssp and it was working, which was because mkdssp command could run. I don't know what happened after I installed the cmview again, but it was not working, and in one of the blind tries, I changed the directory to what you saw.

So, I again corrected it to what you said but it is not working. 
No DSSP executable found.

I read somewhere mac 10.6.8 has a problem with dssp but I cannot that information back to see if there was a solution given. Maybe I am making some mistake or forgot a step about making executable dssp?

Best regards,
Maryam


________________________________
 

From: Jose Duarte <jose.duarte at psi.ch>

To: M. F. <mfaridun at yahoo.com> 
Cc: "cmview-users at bioinformatics.org" <cmview-users at bioinformatics.org> 
Sent: Wednesday, June 12, 2013 12:42 PM
Subject: Re: [cmview-users] Problem running various pdb files+dssp error
 


From your original output:

...
Using DSSP executable ../dssp-2.1.0/src
...

There seems to be 2 problems: you need to make the path absolute
      (it has to be the full path starting with "/" instead of "..") and
      then you need to point to the dssp executable file (it looks like
      you are pointing to the source folder). In Linux it looks like:
      /opt/programs/dssp/dssp

Hope it helps

Jose



On 06/12/2013 12:10 PM, M. F. wrote:


>
>Dear Jose,
>
>Thanks I added chain A as you said and it works. I am happy
          that it helped to find out about the bug. 
>
>
>
>
>
>One more problem that I have and I do not know how to solve it, is about running dssp. I don't know what directory I should put in the configure file for the dssp file. I had done it once and it was working but now I can't make the same configure file again! Could you give me a hint? I will appreciate it a lot? Or is it a bug that dssp is not running, since I read something about it while I was looking through the problem.
>
>Cheers
>Maryam
>
>
>________________________________
> From: Jose Duarte <jose.duarte at psi.ch>
>To: M. F. <mfaridun at yahoo.com> 
>Cc: cmview-users at bioinformatics.org 
>Sent: Monday, June 10, 2013 6:10 PM
>Subject: Re: [cmview-users] Problem running various pdb files+dssp error
> 
>
>
>Thanks a lot for sending the file. So I've managed to track it down to a problem with the chain code used for the ATOM lines (your file has an empty chain code) and the one used for the SEQRES lines (chain code A). It is a bug in CMView: it does not match the 2 sequences up and then tries to guess a sequence from the residue numbers in ATOM lines, instead of using the SEQRES one.
>
>In any case the problem is solved if you use the
                    chain code A for your ATOM lines (replacing the
                    blank in column 22), then you get the correct
                    contact map displayed. Also I've noticed that your
                    coordinates end at TYR 226, but the SEQRES sequence
                    has a few more residues. It would be good if you
                    also removed those from SEQRES so that you don't
                    have a few trailing unobserved (empty coordinates)
                    residues.
>
>We'll try to fix the bug at some point, but that
                    will take some time as at the moment we are bit
                    short of time.
>
>Cheers
>
>Jose
>
>
>
>On 06/10/2013 05:10 PM, M. F. wrote:
>
>Dear Jose,
>>
>>Unfortunately it didn't work. Could you please
                      take a look at the attached file? 
>>
>>Thanks a lot in advance
>>
>>
>>
>>
>>
>>
>>________________________________
>> From: Jose Duarte <jose.duarte at psi.ch>
>>To: cmview-users at bioinformatics.org 
>>Sent: Friday, June 7, 2013 12:06 PM
>>Subject: Re: [cmview-users] Problem running various pdb files+dssp error
>> 
>>
>>
>>Hi Maryam
>>
>>I would say that this is a known
                                  problem with the program that doesn't
                                  cope well when the sequence numbering
                                  starts at a high number. If I
                                  understand from the output you show,
                                  your model is based on PDB code 2kun,
                                  isn't it? I've tried the original 2kun
                                  PDB file and it worked alright.
>>
>>My guess is that in your case it
                                  doesn't work because there is no
                                  SEQRES records indicating what the
                                  exact sequence is for the PDB file. Do
                                  you have SEQRES records in your file?
                                  If not you can add them from the
                                  original PDB file and try it again.
                                  Another way to solve the issue is to
                                  renumber your residue serials in the
                                  ATOM lines to start at 1. 
>>
>>Let us know if that helps. If not it
                                  would be useful to have a look at your
                                  PDB file to be able to track down
                                  exactly what went wrong with the
                                  program.
>>
>>Cheers
>>
>>Jose
>>
>>
>>
>>On 06/06/2013 10:19 AM, M. F. wrote:
>>
>>Hi there,
>>>
>>>I have been struggling with running
                                    cmview now for awhile, I am very
                                    happy to findout about this group
                                    and ask my question here. 
>>>
>>>I have changed my generated pdb file
                                    format, already for several times
                                    and it is still giving a weird sort
                                    of graph and loosing some info
                                    probably. This is the error I get
                                    and the result image is attached.
                                    Please let me know if you need more
                                    info. Thanks in advance!
>>>
>>>
>>>Maryam% cmview.sh
>>>Starting CMView 1.1.1
>>>Loading configuration file
                                      cmview.cfg
>>>Using temporary directory
                                      /var/folders/JN/JNvt1vfbH4CRpqOfuMtdQk+++TI/-Tmp-/
>>>Connecting to PyMol...
>>>Starting PyMol...
>>>Connected.
>>>Using DSSP executable
                                      ../dssp-2.1.0/src
>>>Loading from Pdb file
>>>Filename:   
                                      /Users/Maryam/Desktop/10ns-3.pdb
>>>Model serial:    1
>>>Chain code:    NULL
>>>Contact type:    Ca
>>>Dist. cutoff:    8.0
>>>Min. Seq. Sep.:    none
>>>Max. Seq. Sep.:    none
>>>(Re)assigning secondary structure
                                      using DSSP
>>>Failed to assign secondary
                                      structure: Cannot run program
                                      "../dssp-2.1.0/src": error=13,
                                      Permission denied
>>>Warning: 89 unobserved or
                                      non-standard residues
>>>Warning: Chain NULL is now called
                                      A
>>>Contact map 2kunA loaded.
>>>
>>>
>>>
>>>
>>>
>>>
>>>_______________________________________________
cmview-users mailing list cmview-users at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/cmview-users 
>>
>>_______________________________________________
>>cmview-users mailing list
>>cmview-users at bioinformatics.org
>>http://www.bioinformatics.org/mailman/listinfo/cmview-users
>>
>>
>>
>
>
>
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