- Chimera-dev - RBVI Mailing Lists

About Backbone Dependent Library
by ylei＠ecs.umass.edu 16 Sep '09

16 Sep '09

Hi all I am currently working on a project, which needs to rebuild the statistics using modified protein structures, say, some other set of proteins. There is one quick question about interpreting the BBDep Library. What's the exact definition of the fourth column "N" in the library file format? I thought for each residue within some (phi,psi) angle pair bin, it is the total number of sidechains found in all of the 850 proteins. However, I checked ASN and GLN these two types of amino acids using "Chimera" to return the (phi,psi) dihedral angles for each ASN and GLN residue among 850 proteins with tens of exceptions which have no dihedral angles returned from Chimera(I just ignore them). Then, I count the number of sidechains for each (phi,psi) bin(10*10 degree). It turned out that this number is not consistent with the "N" value in BBDep. e.g. For ASN at bin (phi=-70,psi=-40), Chimera returns 372 sidechains in total from those 850 proteins, while BBDep says 2348. The difference is so large and very common over almost all the bins. I thought probably there might be some stupid errors in my understanding of the "N" value, but could you point that out for me? Or, did Dunbrack guys use another set of proteins other than those 850 ones? Best regards and thanks, Yang Lei Electrical & Computer Engineering University of Massachusetts, Amherst

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suggestion for feature addition to chimera
by Rocco Varela 09 Sep '09

09 Sep '09

Hello, I have a small suggestion for an additional feature for Chimera that I think would be useful. I often look at structures of multiple small molecules, some artificial and some real, and I noticed something interesting with the way Chimera writes mol2 files. Here is Scenario 1: 1) I open a mol2 file that contains multiple molecules flagged as "separate" MOLECULEs. 2) I save the loaded file as mol2 and select "a single file [combined @ MOLECULE section]" for the "Save multiple models in" option. 3) After saving and reloading this new mol2 file that now has a single MOLECULE section, all the "names" of the previous molecules have been lost. (ex. s-030, s-048, s-055, etc...) Instead in the SUBSTRUCTURE section "UNK0" is used. It would useful if Chimera could name the components of the new single molecule with the proper names. I could easily write a script to fix this after the fact but I thought it might be a useful option for other people too? Scenario 2: 1) Same as 1 above. 2) Now I want to save all the MOLECULEs in the file as separate mol2 files but with the proper "names" that are listed in the original file loaded. Currently the only option is to provide a common name and to append the "model number". It would be nice if we were allowed to NOT provide a common name and allow it to name all the files according to the molecule "names" not model numbers. Thanks for your time :-) Rocco

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problems with xformCoord and coord
by Elisabeth Ortega 09 Sep '09

09 Sep '09

Dear All, I'm doing a script change the coordinates x,y,z for one molecule to move it using xformCoord coordinate system but my script doesn't work very well. My function looks like: atom.setCoord(a.coord()-0.1*(vector(x,y,z))) How can I write it in xformCoord? a.setCoord doesn't return to me xformCoord even if I write all the variables using xformCoord. In other words, I'm asking about the "translation" of the function atom.setCoord() in xformCoord coordinates. Thank You -- Elisabeth Ortega Carrasco Universitat Autónoma de Barcelona (Spain) eortega(a)klingon.uab.es

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Suggestion: define selection name for startup chimera
by Jean Didier Pie Marechal 09 Sep '09

09 Sep '09

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suggestiion 2: altLoc attribute for residues
by Jean Didier Pie Marechal 08 Sep '09

08 Sep '09

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timeline for python2.6 in Chimera on OS X?
by Mark Moll 08 Sep '09

08 Sep '09

On OS X 10.6 (Snow Leopard) the default python version is 2.6. Python 2.5 is also available, but is kind of hacky. Part of the problem is that python2.5 doesn't compile as a framework. Another (possibly related) problem is that Tk depends on Carbon (at least the "native" version does) and Carbon no longer exists in 10.6. See http://bugs.python.org/issue6802 for details. I'm relying both on MacPorts and Chimera for dependencies, so I need them to be in sync (for example, boost.python built against python2.6 won't work with Chimera's python2.5). I could try to hack around the python2.5 problems on 10.6, but it'd be nice if I could drop in python2.6 in Chimera and everything would "just work." This is unlikely going to be the case, so I was wondering if the Chimera team already has a switch to python2.6 planned in its development roadmap. -- Mark

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OT: off-screen app on OSX
by Randy Heiland 04 Sep '09

04 Sep '09

Hi folks, Off-topic, but would one of you have any insight as to why a new vis app I built/ran on OSX appears partly off-screen (off the top). I was thinking that maybe I've seen this same behavior at times with Chimera, but can't recall the circumstances. Fwiw, the app is from vtkedge.org. I'm exchanging emails with one of the developers who has admitted that they haven't done testing on OSX yet. thanks, Randy

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Re: [chimera-dev] [Chimera-users] Ignored settings
by Eric Pettersen 24 Aug '09

24 Aug '09

Hi Mark, I don't know how you're opening these molecules but if you're using the "open" command then providing the "noprefs" keyword will prevent smart display. Also, if you are using openModels.open() or openModels.add() then there is a 'noprefs' keyword that you could specify as False. The 'noprefs' keyword for the open command has been around for awhile, but that keyword is new for the openModels functions, so if your plugin needs to work with a variety of Chimera versions either you will need to introspect the openModels function (using Python's inspect module, probably the getargspec function) or check chimera.version. I actually recommend the inspect approach since the format of chimera.version has changed over time, so inspect is more bulletproof. Using that setAttr command for stickScale works for me. You are aware that stickScale defaults to 1, right? There will be some minimal speed advantage to using direct Python calls to runCommand (elimination of some of the text parsing), but I would only expect the difference to be noticeable if we are talking about thousands of calls to the functions. I guess I'm referring to the type of code you sent, where the Midas-module equivalent function is called (so only the parsing is eliminated). There certainly could be more savings in some cases where the generic Midas-module code is replaced by special-purpose code. --Eric On Aug 24, 2009, at 11:42 AM, Mark Moll wrote: > Eric, > > I'm observing some odd behavior with a recent daily build (build > 28565) that may be related to this. I am working on a plugin that > creates new models. *After* the chimera models have been created, > the plugin runs a number of Midas commands in the python code: > > Midas.undisplay('element.H') > Midas.represent('stick','#') > Midas.represent('bs','@ca') > Midas.color('byhetero','#') > Midas.setAttr('m','stickScale',1,'#') > Midas.setAttr('m','ballScale',.35,'#') > > This doesn't seem to have the desired effect. Turning off "smart > initial display" works a little better, but the stickScale command > still has no effect... > > (BTW, is there any speed advantage to using python commands rather > than runCommand statements?) > -- > Mark > > >

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Crash on Ubuntu
by Svetlana Lockwood 12 Aug '09

12 Aug '09

I am just wondering if anybody has used successfully Chimera on Ubuntu. I downloaded and installed it ok, launch - ok, but then while opening (or fetching) a file - oops! Chimera disapears (program closes). Any ideas why or how to fix this? Meanwhile I'm using it on a PC - and scripting on there is not a fun. Cheers,

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Rotation of a single submolecule in a mol2
by christopher lau 08 Aug '09

08 Aug '09

Hi, I am currently working on a project to modify the ViewDock program to work on a Tiled Wall Display. I am reluctant to require the user to download the daily build to allow use of molecule specific rotations in my TDW ViewDock program. I was wondering if there was a way from the Command Line to rotate a single molecule, say #0.1, without rotating all the molecules in model #0. If it is possible to inactivate all the submodels except for #0.1, I can use the rotation commands (roll, rock, turn) to rotate a single submolecule. I know that I can split the submolecules into individual molecules and apply the rotations in this manner, but that would make the data handling very difficult. I was having problems learning how to deactivate models using the select command with the current stable version of chimera. I was wondering if anyone had any insight on this problem. I would prefer to not require the daily build and would not want to use the split command line command to separate the submolecules into separate molecules for rotation. Thanks for your help, Chris

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