May 2015 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Inter-molecular H-bonds between water molecules not displayed in per-frame script
by George Green 20 Nov '15

20 Nov '15

Hi, I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below: Water molecules are residues :159-162 I would be very grateful for any assistance. :) sg ################################################ #################### # per-frame H-bond repr bs :158 color hot pink :158 color byhet :158 # disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162 disp :WAT # select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select select :90 ################################################

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layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

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Re: [Chimera-users] Request for axes measurements
by Elaine Meng 14 Jun '15

14 Jun '15

Hi, You’re welcome, but I don’t have any further details than what is already given in the manual: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> It’s recommended you send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of me directly, in case others may be able to provide better answers! Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 31, 2015, at 6:26 PM, Jayaraman T <jram(a)pusan.ac.kr> wrote: > > Hi Elaine Meng, > Yes i could figure now the axes as well as angle measurements between them and thanks for your timely help. > > I would be happy if you could tell me the principle on which these axes are calculated. I have noticed that it's from Eigen vector values that are calculated for the coordinates of the set of atoms. > > I'm really interested on the backend for this calculation particularly, might help a bit progressing more for my research. > > Thanks again.

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Python code problem
by Mahendra B Thapa 29 May '15

29 May '15

Dear Chimera users, The command I used was chimera --nogui test.py I tried two codes (following previous posts and tutorials in chimera) in 'test.py' as follows (i) import os from chimera import runCommand as rc from chimera import replyobj rc("open " + 'test.pdb') for i in [2011,2420]: rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) *This code gave the result as expected*: Executing test.py... Opening test.pdb... 60 models opened Distance between #0.2:2010.B@CB and #0.1:2011.B@CB: 72.346 Distance between #0.2:2010.B@CB and #0.1:2420.B@CB: 92.979 Executed test.py (ii) import os from chimera import runCommand as rc from chimera import replyobj rc("open " + 'test.pdb') for i in range(2011,2420): rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) *This code gave the result as* ' You selected %d.' % numSelected) MidasError: Exactly two atoms/axes/planes must be selected. You selected 1. Error while processing test.py: MidasError: Exactly two atoms/axes/planes must be selected. You selected 1. File "/opt/UCSF/Chimera64-1.5.3/share/Midas/__init__.py", line 1266, in distance ' You selected %d.' % numSelected) What could be the error this code? Only difference between two codes is: "for * i in [2011,2420]:" & "for i in range(2011,2420):"* That is, I am interested to use range operator in 2nd case instead of two values as in the 1st case. Thank you for help, Mahendra Thapa University of Cincinnati,OH

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Ramachandran plot for a selection
by Elena Lilkova 28 May '15

28 May '15

Dear Chimera community, First I would like to just say that I am new to Chimera. I made a MD simulation of a protein using NAMD. Now I am interested in generating a Ramachandran plot for the whole trajectory, but only for a specific selection of my protein, namely three specific residues. I fail to succeed. Could anyone probably suggest a solution? Elena Lilkova elilkova(a)phys.uni-sofia.bg PhD student, Atomic Physics Department, Faculty of Physics, University of Sofia "St. Kliment Ohridski" 5 James Bourchier Blvd. 1164 Sofia, Bulgaria Elena Lilkova elilkova(a)phys.uni-sofia.bg PhD student, Atomic Physics Department, Faculty of Physics, University of Sofia "St. Kliment Ohridski" 5 James Bourchier Blvd. 1164 Sofia, Bulgaria

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Distances in biological assembly
by Mahendra B Thapa 27 May '15

27 May '15

Dear Chimera users The biological assembly of a virus in pdb format consists of 60 models; each model with 3 chains :A, B and C. I am interested to find atoms within 4 angstroms of the atom, say CA atom of residue 2059 of chain B of model 2. The chimera crashed in graphical interface (it could be due to size of the pdb file.), so I used the following command [ http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-November/002069.html ]: chimera --nogui file_test.cmd > data_rest.log where 'file_test.cmd' consists of open test.pdb findclash #2:2059.B@CA overlap -4 hbond 0 The output file 'data_rest.log' consisted of Opening test.pdb... 60 models opened Opened test.pdb containing 60 models, 677040 atoms, and 89700 residues No contacts No contacts *I want to know whether I have used right chimera command /code. *Any suggestion might help me. Thank you, Mahendra Thapa University of Cincinnati,OH

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scale bar
by Dmitry 27 May '15

27 May '15

Dear developers, How are you? I have a question about scale bar. I am not completely sure that the scale bar I drew is correct. What are the scale settings for drawing the scale bar? By the default the scale bar is in Angstroms isn’t it? In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/Å/etc) Is there the same possibility in Chimera? Thank you Sincerely, Dmitry

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Starting multiple copies of Chimera on Mac
by Tom Goddard 26 May '15

26 May '15

It is possible to run multiple copies of the same Chimera on a Mac. Here’s how. From a Terminal (/Applications/Utilities/Terminal) type the command open -n -a Chimera The -n option tells the Mac to start another copy of the application. If you prefer to start the second copy by clicking an icon then you can make that icon using /Applications/Automator, choose to make an Application, select Run Shell Script, enter the command open -n -a Chimera as the script to run, then File / Save… to save this application as “Chimera+” or whatever you want to call it. This icon always starts a new copy of Chimera so you can have as many running as you like. Tom

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