Problem with a script calculating distance between residues in a single pdb file with several models
Dear all, Here is a single pdb file called modetest_14.pdb. It contains 6 structures: 1 protein MutS (only chain B) with 5 different conformations + another protein MutL (chains A and B). In Chimera, the protein with the 5 different conformations is displayed as model 0.1 to 0.5. The other protein is model 0.6. I would like to calculate the distance between the residue 239 of MutS chain B (for the 5 conformations) and the residue 169 of MutL chain A. I wrote this script which reports this error message: expected an indented block (scriptdistance.py, line 4) *from chimera import runCommand as rc rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\New_filtering\Eucl_Dist_S246-L297\Top solutions\SL0265B\dockLH248\NMA\Test\modetest_14.pdb") for i in range(1, 6): rc("distance #0.%d:239.B@N #0.6:169.A@N" % i)* May you tell me what is wrong? the script correctly opens the file so I suppose it is the python string #0.%d (intended to specify 0.1, 0.2,... 0.5)!? Thanks for your help Damien
Hi Damien, Python uses indentation for "for" loops and other code blocks. So you just need to indent the rc(...) line in the for loop by one or more spaces. If you end up adding more lines inside the "for" loop they all have to be indented by the same number of spaces. Tom
Dear all,
Here is a single pdb file called modetest_14.pdb. It contains 6 structures: 1 protein MutS (only chain B) with 5 different conformations + another protein MutL (chains A and B).
In Chimera, the protein with the 5 different conformations is displayed as model 0.1 to 0.5. The other protein is model 0.6.
I would like to calculate the distance between the residue 239 of MutS chain B (for the 5 conformations) and the residue 169 of MutL chain A.
I wrote this script which reports this error message: expected an indented block (scriptdistance.py, line 4)
*from chimera import runCommand as rc rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\New_filtering\Eucl_Dist_S246-L297\Top solutions\SL0265B\dockLH248\NMA\Test\modetest_14.pdb") for i in range(1, 6): rc("distance #0.%d:239.B@N #0.6:169.A@N" % i)*
May you tell me what is wrong? the script correctly opens the file so I suppose it is the python string #0.%d (intended to specify 0.1, 0.2,... 0.5)!?
Thanks for your help
Damien
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Dear Chimera-developers We noticed a problem with saving images using Chimera, namely, when one saves image under Windows (see attached file), there is a visible grid present on the beads. This does not happen when one uses linux version. On windows I am using version 1.5.3 (build 33475). On linux i have 1.5 (build 32133). regards Alex ---------------------------------------------------------------------- Alexander V. Shkumatov, Ph.D. Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY tel: +49 40 89902 178 Building 25A Notkestraße 85 fax: +49 40 89902 149 22603 Hamburg, Germany email: ashkumat@embl-hamburg.de ----------------------------------------------------------------------
Hi Alex, I tried to generate the problem you describe on a Windows box here in the lab and it worked fine. So I have two generic pieces of advice that may solve the problem: 1) Make sure you have the most current driver for your graphics card installed. 2) If you have multisampling turned on (Favorites->Side View, Effects tab) try turning it off. If neither of these help, please use Help->Report a Bug to submit a bug report. That method will give us a lot more info about your system hardware and software configuration. Also if you can please attach a session file to generate the image with and details about what your settings were in the image-save dialog. Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Aug 8, 2011, at 7:38 AM, Alex Shkumatov wrote:
Dear Chimera-developers
We noticed a problem with saving images using Chimera, namely, when one saves image under Windows (see attached file), there is a visible grid present on the beads. This does not happen when one uses linux version.
On windows I am using version 1.5.3 (build 33475). On linux i have 1.5 (build 32133).
regards Alex
---------------------------------------------------------------------- Alexander V. Shkumatov, Ph.D. Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY tel: +49 40 89902 178 Building 25A Notkestraße 85 fax: +49 40 89902 149 22603 Hamburg, Germany email: ashkumat@embl-hamburg.de ----------------------------------------------------------------------
<image.tif>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Eric Basically, the problem appears when one is using old Win machines. On the new one (win and linux) it all works fine. Thanks for your help anyway! Alex On 08.08.2011 21:11, Eric Pettersen wrote:
Hi Alex, I tried to generate the problem you describe on a Windows box here in the lab and it worked fine. So I have two generic pieces of advice that may solve the problem:
1) Make sure you have the most current driver for your graphics card installed. 2) If you have multisampling turned on (Favorites->Side View, Effects tab) try turning it off.
If neither of these help, please use Help->Report a Bug to submit a bug report. That method will give us a lot more info about your system hardware and software configuration. Also if you can please attach a session file to generate the image with and details about what your settings were in the image-save dialog. Thanks!
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
-- ---------------------------------------------------------------------- Alexander V. Shkumatov, Ph.D. Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY tel: +49 40 89902 178 Building 25A Notkestraße 85 fax: +49 40 89902 149 22603 Hamburg, Germany email: ashkumat@embl-hamburg.de ----------------------------------------------------------------------
participants (4)
-
Alex Shkumatov -
Damien Larivière -
Eric Pettersen -
Tom Goddard