Dear Dan, Glad it worked. Sorry about the Y-axis scroll bar. Right now the scroll bars are mapped to the nested rotations, rather than to the relevant mouse coordinates. I will look at making the scroll bars more intuitive. Regards, Herbert At 1:26 PM +0100 4/23/06, Dan Bolser wrote: >Herbert J. Bernstein wrote: >>Dear Dan, >> >> Thank you for reporting this bug in RasMol. I have prepared a >>patch and a few binaries at: >> >> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.3.1/ >> >>The binaries were produced from the RasMol_2.7.3 kit with the patches >>mouserun2.patch, ztrl.patch, distfix.patch applied. At the moment >>there are slackware 10.1 versions with and without xforms and with >>and without shared memory (useful when using another machine as >>the X-windows display), Mac OS X X11 and classic versions, and MS >>Windows versions. If you need another flavor of binary, let me >>know and we'll work on it. >> >> Comments and suggestions would be appreciated. There are some >>drastic changes coming for support of WPDB, Russian (from Gregory >>A. Pozhvanov), Japanese (from Mamoru Yamanishi) and OpenGL (from >>Vassil Litchev and Enno Fennema) and it would be helpful to have >>2.7.3 stable before we move up to 2.7.4. > >Hi, thanks very much for the speedy patch! I tried >'rasmol_NOXF_SHM_32BIT' on Linux 2.6.16-1.2069_FC4 i686 athlon i386 >GNU/Linux, and it worked great. > >I had a quick look at 1c8d and measured the size of the internal >cavity from between 130 to 150 Ang., and the outer diameter from >between 230 and 280 Ang. (roughly). > >I still find the y-axis scroll bar behaves a little bit strangely >(regarding mouserun2.patch), with unusual 'retrograde' motion when I >expected smooth rotation in the y-axis. > >I am not sure how to 'probe' the other new features, so other than >that everything seemed to work fine in general. > > >Thanks very much for all the suggestions from the list regarding the >problem below. I really appreciate the feedback I got from everyone >both on and off the list. > >All the best, >Dan. > > >> Regards, >> Herbert >> >> >>At 12:57 PM +0100 4/20/06, Dan Bolser wrote: >> >>>Hi, I am trying to get some rough estimates for the overall >>>diameter and cavity size of the following 5 structures... >>> >>>1c8d (diameter = ~200A from the literature) >>>1stm >>>1hqk >>>1jh5 (diameter = ~ 200A from the literature) >>>1c8n (diameter = ~ 280A from the literature) >>> >>>Specifically 1stm and 1hqk, for which I can't find an estimate in >>>the literature (admittedly only after a quick look). >>> >>>I decided to tried using Rasmol, starting with 1c8d. I quickly >>>found that I couldn't get the structures from the PQS, which >>>showed the correct structure (60-mer) but the link to the file was >>>broken. Conversely, the pdb-beta site appeared not to know about >>>the correct biological assembly (showing only the ASU), but gave >>>me the correct (60 subunit file) anyway. >>> >>>Using the 'pick distance' feature in Rasmol proved to be a bit >>>buggy, sometimes returning a 'nan' distance at the terminal >>>(apparently labeled correctly on the structure) but worse, >>>sometimes returning a distance that seemed far too small (giving >>>values in the range of 30 to 60 A instead of 100 to 200 A by eye). >>> >>>Computationally what I would like to do is fit a sphere (or an >>>ellipse, whichever is smaller) to the structure and minimize the >>>size of the sphere to enclose something like 95-99% of the atoms. >>>Is there any tool that I can use to do this? >>> >>>I am not even sure if this description makes sense, but I want to >>>avoid just returning the maximum distance between any two atoms, >>>which probably isn't a fair 'rough estimate' of the diameter of >>>the above molecules. >>> >>>Does anyone happen to know (approximately) the external and >>>internal diameter of these molecules? Or a (free) package that >>>lets me find them? >>> >>>Thanks for any suggestions, >>> >>>Dan. >>> >>> >>>_______________________________________________ >>>Molvis-list mailing list >>>Molvis-list at bioinformatics.org >>>https://bioinformatics.org/mailman/listinfo/molvis-list >> >> >> > >_______________________________________________ >Molvis-list mailing list >Molvis-list at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/molvis-list -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 Office: +1-631-244-3035 Lab (KSC 020): +1-631-244-3451 yaya at dowling.edu =====================================================