August 2014 - Chimera-dev - RBVI Mailing Lists

where to find public doc on Chimera test suite
by Jan Kosinski 19 Aug '14

19 Aug '14

Hi, I would like to create some unit tests for my extension. I found example tests in Chimera trunk that use "Chimera test suite" but I would like to have a look at the documentation. Apparently the doc is present at https://www.cgl.ucsf.edu/intranet/chimera-testsuite/README.html ( found the url at http://svn.cgl.ucsf.edu/svn/chimera/trunk/test/README) but I cannot access it due to password protection. Is there any public doc for Chimera test suite? Thanks, Jan

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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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Chimera-dev August 2014