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.

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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@uab.es

----- Missatge original ----- De: Eric Pettersen <pett@cgl.ucsf.edu> Data: Dimarts, Gener 30, 2007 1:25 am Assumpte: Re: [Chimera-users] access to pdb parser

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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@cgl.ucsf.edu http://www.cgl.ucsf.edu

On Jan 29, 2007, at 1:49 PM, Jean Didier Pie Marechal wrote:

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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

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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@uab.es

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