Dear all, Sorry to bother you again with a similar kind of question, but I'd like my script to stock in an array the three resulting vectors of the new implemented calculation of the axes for a given set of selected atoms. The truth is that I find the right python call for the axis function. I imported StructMeasure and tried different ways around but I can't find my way through. I don't know if I don't give the wrong arguments or have the wrong syntaxes. Thanks a lot for any help, JD -----Mensaje original----- De: chimera-dev-bounces@cgl.ucsf.edu [mailto:chimera-dev-bounces@cgl.ucsf.edu] En nombre de chimera-dev-request@cgl.ucsf.edu Enviado el: jueves, 06 de noviembre de 2008 21:00 Para: chimera-dev@cgl.ucsf.edu Asunto: Chimera-dev Digest, Vol 58, Issue 2 Send Chimera-dev mailing list submissions to chimera-dev@cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev or, via email, send a message with subject or body 'help' to chimera-dev-request@cgl.ucsf.edu You can reach the person managing the list at chimera-dev-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-dev digest..." Today's Topics: 1. atom spec. in BNF (David A. C. Beck) 2. Re: atom spec. in BNF (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Wed, 5 Nov 2008 14:03:02 -0800 (PST) From: "David A. C. Beck" <dacb@u.washington.edu> Subject: [chimera-dev] atom spec. in BNF To: chimera-dev@cgl.ucsf.edu Message-ID: <Pine.LNX.4.64.0811051401230.9881@homer23.u.washington.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Does anyone have BNF notation for the atom specification 'language' used by Chimera? Thanks, - David -- David A. C. Beck, Ph.D. dacb@u.washington.edu Valerie Daggett Laboratory University of Washington, Seattle ------------------------------ Message: 2 Date: Wed, 5 Nov 2008 14:26:16 -0800 From: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [chimera-dev] atom spec. in BNF To: "David A. C. Beck" <dacb@u.washington.edu> Cc: chimera-dev@cgl.ucsf.edu Message-ID: <88F81EBE-CCD4-495F-9316-FEA5D095965D@cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii" On Nov 5, 2008, at 2:03 PM, David A. C. Beck wrote:
Does anyone have BNF notation for the atom specification 'language' used by Chimera?
I don't think so. What's the use case here? If you're in the context of Chimera, you should be able to use Chimera's own atom-spec parsing facilities, e.g. chimera.specifier.evalSpec(). Outside of Chimera, I'm aware of a pretty extensive but not totally complete parser in perl: Chemistry::MidasPattern - Select atoms in macromolecules - search.cpan.org --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu