November 2014 - Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] Getting distance values from runCommand
by Tom Goddard 18 Nov '14

18 Nov '14

Hi Alex, The Chimera 1 code should have a routine for finding the minimum distance between atoms, but it just isn’t written very well (I wrote that code). Chimera users who are not programming have always been our highest priority. But in Chimera 2 we are putting much more effort into the programming interfaces to encourage outside developers. We do not expect to have a release for some time (maybe a year). It will be open source. Tom On Nov 18, 2014, at 2:49 AM, Alex Voronov <alexey.voronov(a)gmail.com> wrote: > Hi Tom, > > After your explanation I understand that I'd have to implement some higher level measurement logic relying only on the distance between two atoms, and your example of handling selection and coordinates is very helpful! I looked earlier at measure/measure.py, but have not found a function that I can use out-of-the-box, now I understand why. > > It is great to hear that you are planning a new release. Will it be open source too? If you plan a beta release, I can volonteer to test some new features ;) > > Best Regards, > Alex > > On Tuesday, November 18, 2014, Tom Goddard <goddard(a)sonic.net> wrote: > Hi Alex, > > The “measure distance” code is the measure() function in > > chimera/share/Measure/measure.py > > It handles distances between atoms and also surfaces and can handle multiple distance calculations and prints the result but unfortunately does not return it as a Python value. I’ve attached some Python code to find the minimum distance between two sets of atoms. > > Unfortunately the Chimera Python programming interface is not documented. The programmer’s guide on the Chimera web side documentation page may be of some use, especially the examples, > > http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html > > and also the Chimera Python scripts on the Chimera developer web site can be of some use > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > Many of the simpler Chimera commands are in > > chimera/share/Midas/__init__.py > > To find others you can search all the Python under chimera/share for “addCommand(“ (for example on Linux or Mac shell command find . -type f -exec grep -nH -e "addCommand(" {} +) giving the attached file of command names and modules where the code is located. > > In our next generation Chimera we are making full reference documentation for Python programming. > > Tom >

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Re: [chimera-dev] [Chimera-users] Reading Chimera source ...?
by Tom Goddard 17 Nov '14

17 Nov '14

Hi Boris, Unfortunately Python programming in Chimera is not well documented. The “sel” variable means Selection, they are defined in chimera/share/selection/__init__.py. An example using Chimera selections is giving in the chimera-dev mailing list post http://plato.cgl.ucsf.edu/pipermail/chimera-dev/2014/001157.html with Python code http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/atomdist.py Tom On Nov 14, 2014, at 8:27 PM, Boris Steipe wrote: > Hi - > > I'm new to writing Chimera code; I've started poking around in the sample scripts and the modules but and I find it a bit slow to find my way around. For example I would like to perform some simple calculations on the coordinates of a set of selected atoms, and I see many functions that take a "sel" argument, but I can't seem to find documentation on exactly what that argument is expected to contain, or the function that would return such a selection list (is it even a list) of objects. I'm sure if I spend more time, through trial and error and dir() and grep, I'll eventually figure it out, but I wonder if there isn't a more principled approach - a document on the big picture of how the code is structured, and/or a searchable list of all functions? What's the best strategy to start reading and coding Chimera scripts? > > Thanks! > Boris > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Getting distance values from runCommand
by Alex Voronov 17 Nov '14

17 Nov '14

Hi, I'm measuring distance between two points. The measurement goes well and I get a correct value in the viewport. I would like to get the same value into a Python variable. Is it possible? I'm thinking about a code like this: d = chimera.runCommand('distance #1 #2') However, it seems to be impossible to get any value from runCommand, I always get None... Even parsing the log that appears in IDLE from commands 'distance #1 #2' or 'measure distance #1 #2' would sort-of work, but I don't know how to capture the log either... Is there a way to get values into variables from 'measure distance'? Thank you! Alex

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Chimera Python programming
by Tom Goddard 14 Nov '14

14 Nov '14

Hi Nicolas, Yes, I am the right person to ask about Python programming with Chimera. Tom Ferrin, the head of our lab doesn’t do much programming these days. The good news is that all of the Chimera capabilities are accessible from Python, and all the those Python modules have the code included in the Chimera distribution. The bad news is we don’t have good programming documentation. You can look at our Programmer’s Guide under the Documentation link on the Chimera page http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> but there is not much there. The Examples link which gives some programming examples might be the most useful part, but it doesn’t cover working with density maps. The Python scripts page on the Chimera developer site is a good source of example Python code that manipulates density maps http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> You ask how to use Chimera from your system Python. That is difficult. The Chimera distribution includes its own Python (version 2.7) and it include about 40 third party Python modules many compiled C code built for this specific Python. If your system Python is different in any way it will fail to work with those modules (e.g. I think our Python has a special option for unicode handling compiled in). Unfortunately the reality is Python is not very portable once you are using binary compiled C modules. But the normal solution is to just run the Chimera Python. This is troublesome though when you want to combine Chimera with other Python third-party packages that are not part of Chimera. The usual solution is to just install those extra packages into the Chimera Python. To run a Python script in Chimera just open it in Chimera (e.g. File / Open, or the Chimera open command, or start it from a shell “chimera myscript.py” or “chimera —nogui myscript.py” if you don’t need the graphical user interface). Let me know if there are more specific questions I can help with, or you can ask at chimera-dev(a)cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> and that way any of the Chimera programmers could answer your questions. Tom > On Nov 14, 2014, at 5:12 AM, Nicolas LEMERCIER wrote: > > Hello Thomas, > > I have been using Chimera for several years now. I writing a workflow to automatically treat my datas in cryoelectron tomography. The code is in Python 2.7.6 and I would like to launch chimera command directly from python without using the embedded version to intregrate in my workflow. I did not find the way to do this. Iguess it should be possible. > I send an e-mail to Thomas Ferrin a few days ago but I think you could help me more efficiently as you developped the volume viewer in chimera > Could you explain me how to control chimera from system python? > > Thanks a lot > > Best regards > > Nicolas > > Nicolas LEMERCIER, PhD > > Integrative Structural Biology Center > Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) > 1 rue Laurent Fries > 67404 Illkirch FRANCE

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Chimera-dev November 2014