[Chimera-users] access to pdb parser

Thu Feb 1 03:46:10 PST 2007

Hi Eric,

Well, the truth is that these are two good news. Most likely I didn't explain myself correctly. In reality, for practical reasons, I'd like to use only chimera for the teaching. So, I am planning to only use its internal python shell for python applications. Therefore the tips you gave me are perfect. 

Thanks a lot for the help!  
Cheers

JD

Dr. Jean-Didier Maréchal
Professor Lector
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdonyola (Barcelona)
Tel: +34.935814988
e-mail: JeanDidier.Marechal at uab.es

----- Missatge original -----
De: Eric Pettersen <pett at cgl.ucsf.edu>
Data: Dimecres, Gener 31, 2007 10:31 pm
Assumpte: Re: [Chimera-users] access to pdb parser

> Hi JD,
> 	I have good news and I have bad news.  The good news it that using 
> 
> PDBio to do what you want is pretty easy.  The bad news is that you 
> 
> can't use it in a generic Python shell, only in Chimera's own 
> Python  
> shell.  This is because we use a modified version of Python so that 
> 
> the types we define in the C++ layer (Molecule, etc.) can have  
> attributes added to them in the Python layer -- otherwise they 
> would  
> behave like the built-in Python types (dict, list. etc.) that can't 
> 
> have arbitrary attributes added to them.  We intend to improve our  
> own code to make modifying Python unnecessary, but haven't gotten 
> to  
> it so far.
> 	Nonetheless, you can basically use Chimera in place of a Python  
> interpreter.  "chimera --nogui script.py" will execute the Python  
> script named script.py without bringing up the Chimera interface.   
> Also, you can start Chimera normally and bring up the graphical  
> interface to its interactive Python shell, IDLE (under Tools-
> >General  
> Controls) and type Python commands to that.
> 	Here's a session of me using PDBio in IDLE.  I've added some 
> comments.
> >>> from chimera import PDBio  # import PDBio
> >>> pdbio = PDBio()  # create a PDBio instance
> >>> mols = pdbio.readPDBfile("/mol/pdb/gc/pdb1gcn.ent")  # read a  
> PDB file given its file name
> >>> m = mols[0]  # readPDBfile() returned a list of models (NMR 
> can  
> have many) so get the model itself
> >>> m.pdbHeaders["HEADER"]  # each model will have a pdbHeaders  
> dictionary, keyed by the record type, the values will be a list of  
> strings -- the PDB records
> ['HEADER    HORMONE                                 17-OCT-77    
> 1GCN      1GCN   3']
> >>>
> 
> --Eric
> 
> On Jan 31, 2007, at 12:42 PM, Jean Didier Pie Marechal wrote:
> 
> > Hi Eric,
> >
> > Yes, that would be better to explain more what I'd like to do.
> >
> > I am planning to give a practical on computational (bio)chemistry 
> 
> > in my department next year. I'd stongly like to have the students 
> 
> > using chimera and python as their main tools (though both are 
> tools  
> > I am in process of learning :-)).
> >
> > One of the "simple things" I have in mind, is to obtain pdb infos 
> 
> > directly from the shell e.g list the SEQRES entry or access to 
> the  
> > resolution (REMARK 2), the crystallization conditions  etc. The  
> > students will be chemists and I think that from a didactic point 
> of  
> > view, obtaining infos from the python shell would be better that  
> > reading the pdb files, especially if we want to compare different 
> 
> > structures e.g. Writing a comand that gives you ALL the 
> resolutions  
> > of the 10 structures you loaded would be interesting. I looked at 
> 
> > the PDBio, but I can see how to catch REMARKS infos.
> >
> > I'd really like to have this work going on, but as you can see, I 
> 
> > am a bit lost in where to begin.
> >
> > Any help to tell me where to start would be fantastic!
> >
> > Cheers
> >
> > JD
> >
> >
> >
> >
> > Dr. Jean-Didier Maréchal
> > Professor Lector
> > Unitat de Química Física
> > Departament de Química
> > Universitat Autònoma de Barcelona
> > Edifici C.n.
> > 08193 Cerdonyola (Barcelona)
> > Tel: +34.935814988
> > e-mail: JeanDidier.Marechal at uab.es
> >
> > ----- Missatge original -----
> > De: Eric Pettersen <pett at cgl.ucsf.edu>
> > Data: Dimarts, Gener 30, 2007 1:25 am
> > Assumpte: Re: [Chimera-users] access to pdb parser
> >
> >> Hi JD,
> >> 	Chimera does its PDB parsing in the C++ layer (the PDBio class in
> >>
> >> the Python layer).  There is a file named PDB.py in the mmCIF-
> >> parsing
> >> module, but it's not for parsing PDB files.  Perhaps if you
> >> described
> >> why you need Python PDB parsing I could suggest options -- using
> >> PDBio possibly being one of them.
> >>
> >> --Eric
> >>
> >>                         Eric Pettersen
> >>                         UCSF Computer Graphics Lab
> >>                         pett at cgl.ucsf.edu
> >>                         http://www.cgl.ucsf.edu
> >>
> >> On Jan 29, 2007, at 1:49 PM, Jean Didier Pie Marechal wrote:
> >>
> >>> Hello everyone,
> >>>
> >>> a short question. What is the right call for importing the
> >>> pdbparser module in the chimera python shell? I found the PDB.py
> >>
> >>> module in the site-package mmlib, but I don't know how to import
> >> it...>
> >>> Thanks a lot,
> >>>
> >>> JD
> >>>
> >>>
> >>> Dr. Jean-Didier Maréchal
> >>> Professor Lector
> >>> Unitat de Química Física
> >>> Departament de Química
> >>> Universitat Autònoma de Barcelona
> >>> Edifici C.n.
> >>> 08193 Cerdonyola (Barcelona)
> >>> Tel: +34.935814988
> >>> e-mail: JeanDidier.Marechal at uab.es
> >>>
> >>>
> >>> _______________________________________________
> >>> Chimera-users mailing list
> >>> Chimera-users at cgl.ucsf.edu
> >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >>
> >>
> >
> >
> 
> 