February 2008 - 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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Re: [chimera-dev] [Chimera-users] list of atoms attributes
by Eric Pettersen 01 Apr '08

01 Apr '08

On Feb 22, 2008, at 7:28 AM, Jean-Didier Maréchal wrote: > Hi again, > > When using the python shell, I am often struggling to find the > attribute for the atoms I work on. > for at my list with the selected atoms, I caught that at[i].name gives > the atom name of the entry at[i], at[i].residue provides with the name > residue.chain, etc. > > Where can I find in the programmer's guide the full list of available > attributes? What would be the way to ask for the serialNumber from the > IDLE? > > Thanks lot > JD Hi JD, dir(a) will list the attributes of 'a'. help(a) will produce documentation for the attributes of 'a' that come from the C++ layer (but not ones that were added in the Python layer). 'a' could be a class rather than an instance. For example, help(chimera.Atom) lists the methods/attributes of Atom and provides some info about them. We do what we can to keep the programmer's guide up to date, but for attributes (since they get added/changed pretty frequently) it is better to query with help()/dir() than to fall back on the relatively static programmer's guide documentation. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [chimera-dev] [Chimera-users] Driving matchAtoms from the IDLE
by Eric Pettersen 22 Feb '08

22 Feb '08

On Feb 22, 2008, at 3:45 AM, Jean-Didier Maréchal wrote: > Hi Guys, > > I'd like to superpose two inorganic complexes using two differently > "ordered" atom sets. My compound has quite similar substructures but I > am sure at all what is the best "ordered" selection of atom pairs to > align. Therefore, I'd like to make a "extensive" search (with an > heuristic approach to define...) passing by the idle. I am > unfortunately > missing something before getting to this point! > > Lets say that I just want to align the nitrogen atoms of the my two > structures. I have: > > import chimera > import numpy > from chimera import match > from chimera import runCommand > runCommand("select #1@N=") > an1=chimera.selection.currentAtoms() > runCommand("select #0@N=) > an2=chimera.selection.currentAtoms() > chimera.match.matchAtoms(an1,an2) > > And then it's when I am already stuck! > > the resulting prompt does not provide mistake an gives: > chimera.match.matchAtoms(an1,an2) > (<_chimera.Xform object at 0x9463ef8>, 0.034256915079603358) > > But how this results can be send to the graphical window? I guess I > have > to use the Xform object, but I can not clearly understand how to do > this. > > Thanks for any help! > > JD Hi JD, I'm not 100% certain what your goal is, but you could just run the match command directly: from chimera import runCommand runCommand("match #1@N= #0@N=") If you need access to the RMSD of the match, you could call the underlying match() function: from Midas import match mobileAtoms, refAtoms, rmsd = match("#0@N=", "#1@N=") which will also superimpose the structures. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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change hand ?
by stefan.backstrom＠medchem.umu.se 15 Feb '08

15 Feb '08

Hi. Is it possible to flip the hand of a cryo-EM map in chimera ? Best wishes, Stefan Bäckström Medical Biochemistry and Biophysics Umeå University Sweden

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Chimera-dev February 2008