July 2014 - 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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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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Delphi electrostatic potential visualization
by Joshua Broyde 04 Aug '14

04 Aug '14

Hi, My name is Joshua Broyde, and I am a big fan of Chimera. I have recently been using Chimera to visualize Delphi outputs (i.e. .phi files).As per your advice here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-March/000710.html I have been using Delphi itself and visualizing the output in Chimera, rather than using the DelphiController within Chimera. Chimera seems to not consistently be able to visualize the output of Delphi on the surface of the proteins. After coloring 2 different protein models with the delphi electrostatic output, I tried to color the third protein surface I was examining with the Delphi output, and Chimera simply colored it gray. To double check that this was not a Delphi problem, I then took this protein structure and created a separate chimera session with it, and then Chimera was able to visualize the Delphi output on the protein surface. Is this a bug or something? Is there a way around this? I want to be able to visualize many Delphi outputs at once on Chimera. Thanks so much, you guys are great! Sincerely, Joshua Broyde

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Setup for 3D workstations?
by Kenward Vaughan 30 Jul '14

30 Jul '14

Hello all, I apologize if this is skewed for the list; please correct me if so. I am putting together a proposal to set up a 3D/computational lab at our school for the STEM area, with Chimera at the top of the list of applications using it. The general idea is to have 10 workstations and one workstation-server (the server side being used for computational work), with students at each station doing their own things. Does anyone have an idea of the best setup for each station with respect to hardware for viewing in 3D?? I expect our Dell-camp school to go with something like an Inspiron T5610, using an nVidia K4000 card. I was thinking that the nVidia 3D vision system made sense, but honestly don't know if that would work with 10 different ones going at once. I am unfamiliar with other options. Would someone help me with this? There would be two or three students at each station, FWIW. Am I out in left field in my thinking? Cheers, Kenward -- In a completely rational society, the best of us would aspire to be *teachers* and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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About MD movie problem
by rama david 30 Jul '14

30 Jul '14

Dear Friends, I completed the simulation of peptide ligand and receptor in gromacs. I want to make the simulation movie. I am using latest version of chimera. I also converted the trajectory files into single pdb movie in gromacs. I did following process: 1. Through tool----> Md movie-- I choose the gromacs option and load the tpr and trr/xtc files. But the software shows that the memory is not enough. ( Frame 4000 and atoms 8000) 2. For second time I chose the PDB option for Mdvie. I load the PDB & now I am getting following message : Residue 4.C not in the first model on line 17718 of Md.pdb file. I am pasting the few lines of md.pdb starting from line 17718 ATOM 8852 N NH2 C 4 61.241 96.447 51.027 1.00 0.00 ATOM 8853 H1 NH2 C 4 61.539 97.208 50.457 1.00 0.00 ATOM 8854 H2 NH2 C 4 61.923 95.899 51.517 1.00 0.00 END Could you please help me in the above problem, I will be a very thankful to you for your help. This is very Important movie for my work. I am looking for reply, With best Wishes Rama David

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Changing Structure/Sequence Associations by a command
by Marek Basler 28 Jul '14

28 Jul '14

Hi, I'd like to be able to change an association between a sequence in a multiple sequence alignment and an opened structure model by a chimera command. I have a model that is a multimer and I'd like to color code one of its subunits according to its sequence conservation ... but I need to reassign the automatic association that Chimera does after opening of a fasta file. Any idea? Thank you!! Best regards, Marek

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[External] import error from module: Togl
by Mike Sivley 25 Jul '14

25 Jul '14

I apologize in advance if this becomes too system-specific, as I believe an automatic update of our server's python libraries may be to blame for this error. However, my hope is that others may have run into the issue as well and have already found a solution. I have a python/chimera script that generates Chimera scenes with various annotations assigned to residues in a protein structure. This script worked without issue for several weeks. I returned from a week of vacation and now the script fails with the following error: ImportError: No module named Togl File "/ant2/Bush_eQTL/sivleyrm/bin/UCSF-Chimera64-2014-05-13/share/chimera/tkgui.py", line 73, in <module> import Togl Togl appears to be a deprecated library, so my best guess is that it was removed during some automatic update (possibly of PyOpenGL?) applied to our servers. However, Chimera is distributed with its own python executable and libraries, so I'm unsure how this type of change could have affected it. I am using the nightly headless linux build of Chimera from 05-13-2014. I have reinstalled chimera from the original .bin file, and I have also installed the most recent nightly headless build. Neither resolved the issue. I'm additionally confused because the exception is raised by tkgui.py, which by naming convention seems like it shouldn't even be called given that I am passing the "--nogui --silent --script" parameters to chimera. The specific call to chimera is this: chimera --nogui --silent --script 'lib/PDBMapVisualize.py 1hho 1 maf temp/61098856282.TEMP 1.000000 0.000000 data/rcsb/biounit/coordinates/all/1hho.pdb1.gz results/pdbmap_1kg_1hho_20140725-11 -' Where lib/PDBMapVisualize.py is my script and everything following are arguments to that script. Nothing about this call or the script it is calling have changed between when chimera ran successfully and now. Any help or advice in resolving this issue would be greatly appreciated. Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University Medical Center

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distance between two residues in multiple pdb files
by Mahendra B Thapa 24 Jul '14

24 Jul '14

Dear Chimera users, One of the ways to find distance between two residues (say, residue no 10 and residue no 15 of a pdb file) is the use of command 'distance' in the command line of Chimera. How can I use the command 'distance' for a multiple pdb files (say, 20 pdb files which are generated by simulation of a protein)? I mean, may I need some scripts for looping? Any other alternatives will also help me a lot. Thank you, Mahendra Thapa University of Cincinnati,OH

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DNA nucleotide bases representation as long sticks
by roz orchidea 23 Jul '14

23 Jul '14

Dear all, I am trying to make nice DNA images with Chimera. I would like to have my nucleotide bases shown as long sticks like in this image: http://www.nature.com/cr/journal/v23/n2/images/cr2012170f1.jpg Does anybody know how to do that? Thanks in advance for you answer! Alexandra

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