August 2015 - Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] [Chimera-users] Query related to chimera
by Elaine Meng 31 Aug '15

31 Aug '15

Dear Akalesh Kumar Verma, Sorry no, Chimera does not do protein-protein docking calculations. 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 Aug 30, 2015, at 3:02 PM, Akhilesh Verma <akhileshverma07(a)gmail.com> wrote: > > Dear Manager, > Is it possible to do Protein protein docking using chimera program? > Your response will be highly appreciated. > Thanking you. > -- > Sincerely yours, > Akalesh Kumar Verma

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Center of rotation:
by Dougherty, Matthew T 24 Aug '15

24 Aug '15

I need to change the center of rotation at every frame. I am using from chimera import viewer cam = chimera.viewer.camera cmd = 'cofr fixed %s,%s,%s' %(cam.eyePos(0)) chimera.runCommand(cmd) which generates a message in the reply log Center of rotation: 564.31 -345.208 699.718 How can I disable this message in the reply log? Or is there another method I should use (eg, hack the cofr command)? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [chimera-dev] distance measurements
by Eric Pettersen 21 Aug '15

21 Aug '15

You run a python file simply by opening it, either with the “open” command or with File->Open. Another option here, since you aren’t creating images or doing anything graphical, is to run it entirely from the command line and not even bring up the graphical interface: chimera —nogui DistSing.py Looking at your script, it mostly looks good except the for the writing to the file. It looks like you give two ‘{}’s in the format string but then provide 4 arguments to the format() call. I think those have to match, though I’m no format() guru. —Eric > On Aug 21, 2015, at 11:18 AM, Feixia <feixia.chu(a)unh.edu> wrote: > > Thank you, Eric. > > I got a prototype program based on your suggestions (see attachment). But, I can't get it to run. I tried the 'Tools / General Controls / IDLE Python shell" by enter "import DistSing.py". The error message I got, "ImportError: No module named DistSing.py". > > I have Python27, and Chimera 1.7. Any suggestion to move forward? I ended PDB downloading at ~107,000 entires when most of the rest structures are gigantic ribosome, virus etc. Thanks. > > Feixia > > > On Thu, 20 Aug 2015 15:35:55 -0400, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > Probably the simplest way is to just see if you wound up with multiple models or not (i.e. len(openModels.list(modelTypes=Molecule)) > 1). If you just want to use one model per entry regardless of it being NMR or not, don’t loop over the model list but just use the first model in it, i.e. instead of: > > for mol in openModels.list(modelTypes=[Molecule]): > indented analysis code > > use: > > mol = openModels.list(modelTypes=[Molecule])[0] > unindented analysis code > > —Eric > >> On Aug 19, 2015, at 9:10 PM, Feixia <feixia.chu(a)unh.edu <mailto:feixia.chu@unh.edu>> wrote: >> >> Thank you, Eric! >> I am still downloading PDB files through Bio.python. I am just interested in the overall distance distribution of residues, say Lys alpha carbon. NMR entries might end up over-representing due to their multiple models. Thank you for pointing it out. Is there a quick way to distinguish crystal structures from NMR structures? >> >> Best, >> Feixia >> >> On Wed, 19 Aug 2015 14:17:35 -0400, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> >> Hi Feixia, >> You could certainly use Chimera to do that. You need to know some Python. Take a look at the Programmer’s Guide: >> >> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> >> >> In particular, the “basic primer” discusses how to loop over files in a directory and do things to them one by one. >> Here’s some example code for printing the lysine CA-CA distances for a single open file. You could take that and move it into the loop described in the basic primer — customizing it as you wish… >> >> from chimera import openModels, Molecule >> # opening NMR files can produce multiple models, so use a loop... >> for mol in openModels.list(modelTypes=[Molecule]): >> lysCas = [a for a in mol.atoms if a.name == “CA” and a.residue.type == “LYS”] >> for i, ca1 in enumerate(lysCas): >> for ca2 in lysCas[i+1:]: >> print mol.name, ca1, ca2, ca1.coord().distance(ca2.coord()) >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >>> On Aug 18, 2015, at 8:36 AM, Feixia <feixia.chu(a)unh.edu <mailto:feixia.chu@unh.edu>> wrote: >>> >>> Hi there, >>> >>> I am interested in retrieving distance information from large dataset in an automatic fashion. For instance, can we use Chimera to get the distances between lysine alpha-carbons of current PDB entries. Presumably, we can download all PDB structures on our local desktop, and just call functions one structure at a time. I wonder if we can do that with Chimera. Your advice will be highly appreciated. >>> >>> Best, >>> Feixia >>> >>> >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > > > -- > Feixia Chu, Ph.D. > Associate Professor > Molecular, Cellular & Biomedical Sciences > University of New Hampshire > Gregg Hall, Rm436 > 35 Colovos Rd > Durham, NH 03824 > Tel 603 862 2436 > <DistSing.py>

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distance measurements
by Feixia 20 Aug '15

20 Aug '15

Hi there, I am interested in retrieving distance information from large dataset in an automatic fashion. For instance, can we use Chimera to get the distances between lysine alpha-carbons of current PDB entries. Presumably, we can download all PDB structures on our local desktop, and just call functions one structure at a time. I wonder if we can do that with Chimera. Your advice will be highly appreciated. Best, Feixia -- Feixia Chu, Ph.D. Associate Professor Molecular, Cellular & Biomedical Sciences University of New Hampshire Gregg Hall, Rm436 35 Colovos Rd Durham, NH 03824 Tel 603 862 2436

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extracting statistics from an existing fitlist
by Dan Lin 11 Aug '15

11 Aug '15

Hello: I'm trying to extract the statistics from a previously run fitmap global search to a text file. Is there a way to find the objects that all the information is stored in so I can write a script to write it out? I've been trying to dig through the code to find out where it is stored, but have not had any luck. Thanks for the help!

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