- Chimera-dev - RBVI Mailing Lists

Model panel rename
by Dougherty, Matthew T 15 Oct '15

15 Oct '15

I would like to tie a USB foot pedal to the model panel rename button. I can get the foot pedal signal into my chimera extension. From an extension, what would be the easiest way to Python code the activation of the model panel button? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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adding an exporter
by Dougherty, Matthew T 25 Sep '15

25 Sep '15

I have modified the collada exporter to work with blender to the point I need to fork it off. I want to call it Blender, as opposed to the existing Collada exporter and overwrite that code. It is mostly the collada chimera exporter, but has additional UI inputs to make it better integrate with blender. How do I register it so it lists like the other scene exporters? Is it entirely within the existing collada code extension, or is there another call or init that needs to be made outside the collada extension directory? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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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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Enhancing the command-line
by Tom Goddard 15 Jul '15

15 Jul '15

Hi Joshua, We are ahead of you. In Chimera 2 which is not yet released we have put in support for command completion, command keyword completion, it should be able to give you the whole syntax of the command in the status line. It doesn’t do this yet but it is supposed to have those capabilities. We haven’t discussed improved command history search but I agree that would be handy, to for instance bring back your last command starting with “surf”. Could these features be put in Chimera 1? I don’t think we will do it because we are putting all effort on Chimera 2 and plan a first release with very minimal capabilities this Fall. We’d be happy to help you add these things to Chimera 1. The command-line user interface is in chimera/share/Midas/midas_ui.py and uses the Tk window toolkit. This would be the place where you would bind the tab key or other special keys that for instance do history search. We don’t have detailed Chimera 1 programming API documentation, just a few tutorials http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> and nothing that describes command-line code. A basic problem is that Chimera 1 only knows the command names. There is no table of keyword arguments that a command takes so you couldn’t provide any detailed help on tab completion. It doesn’t seem very useful to complete just the command name. To get programming help use the chimera-dev mailing list. The Chimera developers here, Eric, Conrad, Greg and I will answer any technical questions through that list. Tom > On Jul 15, 2015, at 10:40 AM, Broyde, Joshua E. wrote: > > Dear Tom, > I hope you are well. I have a general question/issue regarding the Chimera user interface that I wanted to discuss with you. > The Chimera GUI user interface is extremely intuitive and well done, but I was wondering if it would be possible to beef up the command-line user interface? For example, it would be nice if there was tab completion within the command-line interface For example, if a user typed "mat" and then a tab, the command line could show "match", "matchmaker", "matrixcopy" ,""matrixget", and "matrixset". Other features could include a more robust history search, for example. > > These kind of things are implemented in other command-line interfaces for other resources, such as Bash, iPython, and Rstudio. > > This is something that I was thinking of doing myself to make my work more efficient, except that I don't know where to begin from a programatic perspective. Are there any files/directories or things I should know about how the command-line works internally in Chimera that would help for implementing this? Is there a point person at RBVI I could contact to ask questions regarding this? I need to generally know more about the internal guts of the CLI of Chimera before beginning. > > Of course, if I produce something useful, I will share it with you so you can share it with the general Chimera community. > > Sincerely, > Joshua Broyde

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chimera extensions
by Dougherty, Matthew T 06 Jul '15

06 Jul '15

How can I reload an extension when chimera is running? At the present, after I modify python code I restart chimera for the s/w changes to take effect. Is there a way through idle, etc, that I can cause user code modifications to load without restarting chimera? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Packaging an extension... Error
by MARYAM ARAB 15 Jun '15

15 Jun '15

Dear Developers, Hi, I have a C++ program and I want to package it under the tools menu. I made a dll from my program. My dll gets two input ( pdb name and volum density level ,) and generate the output. when I save the python codes to execute my dll in the chimera IDLE, every thing works well and my program starts working and generates the output. here is the code that I ran in the IDLE: import ctypes dll = ctypes.CDLL('tracer_v2.dll') dll.calc.argtypes = [ctypes.c_char_p, ctypes.c_double] dll.calc.restype = ctypes.c_int print(dll.calc('1733_H',3)) The problem that I faced is that when I add an extension button to the chimera and wants to call my function (calc('1733_H', 3) ) from there, I get an error: WindowsError Exception in Tk callback Function: <function command at 0x0D1A89B0> (type: <type 'function'>) Args: () Traceback (innermost last): File "C:\Program Files (x86)\Chimera 1.10.1\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files (x86)\Chimera 1.10.1\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "Z:\Tracer_Chimera\GUI\TracerUI\gui.py", line 43, in Apply TracerUI.mainchain() File "Z:\Tracer_Chimera\GUI\TracerUI\__init__.py", line 9, in mainchain dll = ctypes.CDLL('tracer_v2.dll') File "C:\Program Files (x86)\Chimera 1.10.1\bin\lib\ctypes\__init__.py", line 365, in __init__ self._handle = _dlopen(self._name, mode) WindowsError: [Error 126] The specified module could not be found Would you please help me know how I can fix it? Thanks, Maryam Arab Research Assistant Old Dominion University

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