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BioPython on Mac OS X
by Mateusz Dobrychłop 14 Aug '14

14 Aug '14

Dear Chimera Team, I'm currently trying to install BioPython using Chimera's Python copy on Mac OS X. Thanks to the Chimera Programming FAQ, I've already managed to install BioPython succesfully on Ubuntu, but on Mac OS X I get the following error: Error while importing Combine from /Applications/Chimera.app/ Contents/Resources/share: Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/extension/base.py", line 349, in _importExtension __import__(module) File "/Applications/Chimera.app/Contents/Resources/share/Combine/ChimeraExtension.py", line 32, in <module> balloon="Combine molecular models into new model", moleculesOnly=True) File "/Applications/Chimera.app/Contents/Resources/share/ModelPanel/base.py", line 40, in addButton "Button named '%s' already exists" % name KeyError: "Button named 'copy/combine...' already exists" Error while importing Ramachandran from /Applications/Chimera.app/ Contents/Resources/share: Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/extension/base.py", line 349, in _importExtension __import__(module) File "/Applications/Chimera.app/Contents/Resources/share/ Ramachandran/ChimeraExtension.py", line 29, in <module> ModelPanel.addButton("Ramachandran plot...", emo.modelPanelCB) File "/Applications/Chimera.app/Contents/Resources/share/ModelPanel/base.py", line 40, in addButton "Button named '%s' already exists" % name KeyError: "Button named 'Ramachandran plot...' already exists" running install running build running build_py running build_ext Error while processing 'setup.py install': TypeError: argument of type 'NoneType' is not iterable File "/Applications/Chimera.app/Contents/Resources/frameworks/ Python.framework/Versions/2.7/lib/python2.7/_osx_support.py", line 185, in _find_appropriate_compiler if 'llvm-gcc' in data: See reply log for Python traceback. Is there anything I can do to solve this problem? Best, Mateusz

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Re: [chimera-dev] [Chimera-users] Feature request
by Elaine Meng 11 Aug '14

11 Aug '14

Dear Xavier, I personally don’t recommend the Chimera/Povray approach… my neon/conic suggestion is better-looking, but not as easy as the feature you request. There is limited programmer time, so I can’t say it will happen, but we can put it on the list of requests. You can enable showing backbone atoms at the same time as ribbon with command “ribbackbone” — then try displaying the carbonyls. You may also need to unchain (avoid drawing long bonds between different carbonyls, e.g. command: setattr m autochain 0). However, the default ribbon path is smoothed, so in some places the backbone atoms will appear to be floating away from the ribbon. You can try reducing that problem by using a different method to calculate the ribbon path, for example, with command: ribspline cardinal smooth strand …but see the manual for other command options and parameters. The cardinal spline tries to follow CA positions, so it is still possible you won’t be able to totally eliminate spaces between ribbon and C atoms. It may be necessary to show the C atoms as balls (slightly larger than stick-ends) to obscure the gapping. The ribbackbone and ribbon path issues are discussed in more detail here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo…> I hope this helps, Elaine On Aug 11, 2014, at 1:48 AM, F.Xavier Gomis-Rüth <xgrcri(a)ibmb.csic.es> wrote: > Dear Elaine & Eric, > thanks again for your and Eric's suggestions. The issue is that the POV-Ray rendering is not as attractive as the CHIMERA rendering. > Would it be possible to kindly and humbly request that this minor feature be implemented at a certain time point in a new version > of the program :-) ? > Another issue I have currently problems with: > it would be very helpful to be able to display the main-chain carbonyls sticking out from the ribbon at the right place. I tried with the > licorize option of the ribbon trace but it was not solving the problem. This is particularly helpful when representing e.g. metal-binding sites. > Thanks again for your help and dedication to constantly improve this fantastic program. > Best wishes, > Xavier > > On 1/8/14 9:11 PM, Elaine Meng wrote: >> A few caveats of the Povray approach: >> In my tests (current daily build), it always makes cylinders with the same aspect ratio regardless of whether I am showing the lines as dotted or dashed in Chimera. Also, it is hard to tell they are cylinders unless you make the linewidth fairly large. >> >> Elaine >> >> On Aug 1, 2014, at 11:28 AM, Eric Pettersen >> <pett(a)cgl.ucsf.edu> >> wrote: >> >> >>> Hi Xavier, >>> In addition to Elaine's neon suggestion, if when you save an image you change the rendering from "Chimera" to "POV-Ray" then any dashed or dotted lines will be converted into equivalent cylinders and spheres in the POV-Ray image. I've attached an image that shows how a distance looks. >>> >>> --Eric >>> >>> > > -- > <fxgr_signanew.jpg> _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Feature request
by "F.Xavier Gomis-Rüth" 01 Aug '14

01 Aug '14

Dear CHIMERA team, I moved from SETOR to CHIMERA for preparing nice protein structure images for publication already some time ago and am totally happy. Thre is, however, one single feature that was possible in SETOR but I still miss in CHIMERA: to draw pseudobonds as dashed sticks or small spheres. Is it be really not possible to implement this nuisance? I known Elaine negatively answered a similar question some time ago within the BB but I would herewith strike a blow for it again. Best wishes and thanks for maintaining and devloping such a fantastic program, Xavier --

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how to write documentation for an extension
by Jan Kosinski 25 Jul '14

25 Jul '14

Hi, I wrote a custom extension and now I want to create a documentation page that upon clicking a Help button opens a web page similarly to some other Chimera tools. Is there any html template, style guide or any important instructions I should follow for implementing it? Thanks in advance, Jan

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warped dome
by Dougherty, Matthew T 24 Jun '14

24 Jun '14

I was able to fish out the Paul Bourke warp dome python code from blender. I should be able to get it into a form that could be put into chimera. Would like to discuss how this might be passed off into official releases. Also, the material science lab at Carnegie Mellon is replicating my 9ft lab dome, which uses spherical mirror to create the warped dome. The full fisheye is critical for getting chimera output into regular permanent planetariums doing animation. The warp dome would be critical for interactive lab research. As an aside, Marc DeGraef has also been developing and HDF5 format for their EM & Xray datasets. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Does chimera support molecules from MMTK
by Jean-Didier Maréchal 18 Jun '14

18 Jun '14

Dear all, I would like to avoid gaff assignation with the dock prep interface (basically, I need to work with some organometallic compounds) and I was wondering if chimera accepts MMTK molecules ( as can be found in lib/site-packages/MMTK/Database/Molecules). I believe this would be of the best way to expand the force field inside chimera. Cheers, JD

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Impossible to download Chimera Source Code
by Alfonso Avino 03 Jun '14

03 Jun '14

Hi, I get this error downloading the source code of the last Chimera: svn: REPORT of '/svn/chimera/!svn/vcc/default': Could not read response body: connection was closed by server (http://svn.cgl.ucsf.edu) Thanks for your help. -- Alfonso Avino Informatica IBMB-CSIC C/ Baldiri Reixac 15, 3 A17 08028, Barcelona, España Tel. (+34)934020244

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Plugin installation from a web link
by Alex 03 Jun '14

03 Jun '14

Hello Chimera developers, If I remember well, during a visit in your lab in January, Conrad Huang showed me a way to package a Python plugin that can be installed just by opening the package with Chimera. Do you have an example? I found something vaguely related here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.h… But I don't see how to include commands to copy libraries or python modules into the lib or share directories, or to make sure Chimera can remember where to find the files in the future. Many thanks for your help, Alex

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(no subject)
by maryam.khoshnejat 03 Jun '14

03 Jun '14

hello could you help me? i should model specific mutant residue of protein . i have PDB file and rotamer of mutant residue how can i find coordination of mutant residue based on backbone and CB coordination of native residue , rotamer and atom bonding distance i need a code for finding coordination of mutant residue regards

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how to remove chimera file load history?
by Dennis N Bromley 12 May '14

12 May '14

Hi all, Whenever I try and load a file into chimera, it tries to open the windows file load dialog in the last directory I loaded a file from (I guess that is what is happening, at any rate). But that directory now has around 10K pdb files in it and chimera hangs trying to enumerate them all (maybe due to windows/samba/etc). As a result, I can no longer even use chimera because it hangs every time I try and load a file. Is there a way to clear this so that I can load files again? thanks! -denny-

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