December 2007 - Chimera-dev - RBVI Mailing Lists

add h
by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

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SimpleSession.sesRepr()
by Eric Pettersen 20 Dec '07

20 Dec '07

Hi all, For anyone saving data into session files, I've implemented a sesRepr () function for use in place of repr() for large data objects (ones whose repr() would be hundreds or thousands of characters). sesRepr () inserts newlines periodically [where possible] so that the resulting session file has a better chance of being viewable in an editor or sent through various mailers without corruption. sesRepr() will also frequently make the representation smaller despite the additional newlines since it passes float values through the "%g" format which will often trim their representation by half a dozen characters or so. I thought pprint.pformat() would do the job but it adds a _lot_ of whitespace to the repr if there are nested compound objects (e.g. a dictionary whose values are lists). You access sesRepr() (as of tomorrow's daily build) with: from SimpleSession import sesRepr --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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modified chimera to use an unmodified Python
by Greg Couch 19 Dec '07

19 Dec '07

It will be available in tomorrow's daily builds. So in principle, it will be possible to run chimera inside another Python program by doing "import chimeraInit; chimeraInit.init(eventloop=False)". You should also incorporate into the other program's Python library the bug fixes chimera has in its Python library. This is a development version of chimera and might have major bugs in it. If you get any tracebacks that have the word "metatype" in them, please send them to me ASAP. - Greg

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Re: [chimera-dev] printing "zone" search
by Eric Pettersen 14 Dec '07

14 Dec '07

Hi Ryan, The difference is that when you print a list, the residues in the list are shown with repr(). When you print a residue directly, it is shown with str(). Quoting the Python Tutorial, the difference between str() and repr() is: "The str() function is meant to return representations of values which are fairly human-readable, while repr() is meant to generate representations which can be read by the interpreter..." Since there is no representation of a Residue object that can be directly read by the interpreter, you get the output you saw when printing the list. The result of str() when you directly print the residue is controlled by the "Atomspec display style" preference in the General preferences category (Favorites->Preferences). It seems you have that preference set to "command-line specifier". If you change it to "simple" instead you will get output like "LYS 12.A" etc. Alternatively you could use the chimeraLabel function, e.g.: print chimera.misc.chimeraLabel(r, style="simple") Programmer documentation for Chimera is considerably less complete than user documentation. My best advice is to read through some of the Programmer's Examples (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/ index.html) and look through the Programmer's FAQ (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html). If you know that some Chimera tool does something similar to what you want then browse through its source code. If you don't know Python that well you might want to work through the Python Tutorial if you have time (http://www.python.org/doc/current/tut/tut.html). And feel free to ask questions; we're happy to help. --Eric On Dec 14, 2007, at 4:55 PM, Ryan wrote: > Hi Eric, thanks for your help. I'm getting closer to achieving the > results i'd like. > > So i've been able to properly select the residues within a specified > radius of my ligand, but am a little confused as to how Chimera > handles the selection list. If i try: > > print chimera.selection.currentResidues() > > i get a list like this: > >> [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at >> 0x578cbfb0>, ... ] > > but if i try: > > for x in chimera.selection.currentResidues(): > print x > > i get output that is much closer to what i'm looking for: > >> #0:499 >> #0:496 >> ... > > What is the reason for the difference between these two forms of > output that seem to be accessing the same list? Also, is there a way > i can get more detailed output with residue names and numbers, such as > ['#0:TYR499','#0:TRP496',...]? > > Sorry if these questions are answered elsewhere, but i could not find > the answers online. Is there a document out there that can teach me > how to better master the Chimera Python modules for scripting? I'm no > Python expert -- i've so far only been learning things as i need them. > Thanks again, > > ryan >

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Re: [chimera-dev] [Chimera-users] printing "zone" search
by Eric Pettersen 14 Dec '07

14 Dec '07

On Dec 14, 2007, at 8:23 AM, Ryan wrote: > I am actually currently interested in doing something similar to > Francesco's previous question about writing out a list of residue > names within a certain zone of a ligand -- however i would like to > do this from a Python script. > > I tried to find the zone selection command to use in a script, but > could not. Would it be easiest to just use the runCommand('z<') > function to select a zone? Using runCommand() would be by far the easiest and is what I would recommend. Nonetheless, there are alternatives. I've appended a script that finds all NZ atoms of lysines that are within 8 angstroms of an NZ of a different lysine. It calls into the underlying chimera.specifier.zone() function since it needs to do additional processing to exclude each lysine's own NZ atom when examining the zones for NZs within 8 angstroms. If efficiency is important (and it doesn't sound like it really is from your description) you would want to consider using the _closepoints module to quickly eliminate most atoms that aren't in the zone, but then you have to process the remainder to ensure that they meet the zone criteria (some remaining ones won't). Look at the start of the detectClash() function in DetectClash/__init__.py for an example. > Also, when the zone is selected, are the selected residue names > stored in a list? If so, how can i access this list to print out > the residue names into an output file of my own? chimera.selection.currentResidues() returns such a list. --Eric

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how to export the volume data which is stored in the memory?
by Zhiheng Yu 03 Dec '07

03 Dec '07

Hi, I loaded some volume data (mrc files) into Chimera remotely from a network hard drive. Unfortunately, the network hard drive crashed so I can not access those mrc files anymore. But in Chimera which was started before the drive crash, I still have the volume data and am still able to manipulate them. Apparently, these are stored in the memory. Does anyone know how can I export these data onto a hard drive. I tried "save as" but there is an I/O error since the computer was simply trying to duplicate data from the crashed drive. Any suggestion is appreciated. Thanks, Zhiheng

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Chimera-dev December 2007