Dear all, I have a mol2 file and I would like to generate an input for an external program using chimera. For a great ease in practicability, I would like the mol2 order to be kept. I used the following artefact to get to what I want: def input(molecule): ##for compatibility with mol2 atom ordering I use the doble loop as follow ##makes the writing substantially slower, but yet the compatibility with mol2 format seems absolute. for i in range(len(molecule.atoms)): for atoms in molecule.atoms: if atoms.serialNumber == i: text=str(atoms.element)+"-"+str(atoms.gaffType)+"-"+str(atoms.charge)+" "+str(atoms.flex)+" "+str(atoms.coord()) +"\n" filename.write(text) i=i+1 I think I could order directly the writing in function of the serialNumber (which is preserved regarding the mol2) file. But how could I do this? Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: chimera-dev-request@cgl.ucsf.edu Data: Dilluns, Octubre 26, 2009 8:00 pm Assumpte: Chimera-dev Digest, Vol 69, Issue 1

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Today's Topics:

1. thank you so much (Corey Fugate) 2. Re: thank you so much (Eric Pettersen)

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Message: 1 Date: Fri, 23 Oct 2009 16:57:11 -1000 From: Corey Fugate <fugate@hawaii.edu> To: chimera-dev@cgl.ucsf.edu Subject: [chimera-dev] thank you so much Message-ID: <D445EAAC-78D8-4394-85E0-997DBED43CD8@hawaii.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed

I started using Chimera a few weeks ago. It is wonderful, I love it.

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Message: 2 Date: Mon, 26 Oct 2009 11:03:55 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> To: Corey Fugate <fugate@hawaii.edu> Cc: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] thank you so much Message-ID: <26F83250-86D7-4E19-8B17-304418C8169D@cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii"; Format="flowed"; DelSp="yes"

So glad you like it. And always struggling to make it better. Thanks! :-)

--Eric

Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

On Oct 23, 2009, at 7:57 PM, Corey Fugate wrote:

...

I started using Chimera a few weeks ago. It is wonderful, I love it. _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev