Article View: sci.polymers
Article #76Re: How to visualize a pdb-like file
From: George Elkins
Date: Wed, 21 Jan 2004 00:45
Date: Wed, 21 Jan 2004 00:45
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2607 bytes
"D.K." <no.email@thanks.to.spam.net> wrote in message
news:bouk1j$arl$1@news.doit.wisc.edu...
> In article <6e6c00d7.0311110221.606cc1ee@posting.google.com>,
> horacio@um.es (Horacio horacio@um.es) wrote:
> >I have a pdb-like file which represents the model of a molecule.
> >
> >The exact format is the following:
> >
> >x1, y1, z1, r1
> >..
> >xn, yn, zn, rn
>
> Why not make a real PDB file out of it? Here is the format:
>
> http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
>
> For example:
>
> ATOM 7 CG2 THR A 15 20.613 65.449 44.328 1.00 55.84
>
> In your case you can all atoms UNK (it is "CG2" above), number
> atoms sequentially ("7"), give them all any 3 letter residue name
> ("THR"), use any chain ID and number ("A" and "15"), keep occupancy
> as 1.00 and set temperature factors ("55.84") as anything (20.00 is
> common for no real value). "20.613 65.449 44.328" are cartesian
> coordinates.
>
> Rasmol will be happy, as will be 90% of all other programs. All in
> all, it's a copy and paste job that can be done in Word using
> vertical copy selection.
>
> DK
And you can write a Perl script in 10 minutes which will automate this
conversion.
George Elkins
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X-Google-Language: ENGLISH,ASCII-7-bit X-Google-Thread: fd9c4,3f5e68e288426555 X-Google-Attributes: gidfd9c4,public X-Google-Thread: f4886,3f5e68e288426555 X-Google-Attributes: gidf4886,public X-Google-Thread: f7944,3f5e68e288426555 X-Google-Attributes: gidf7944,public X-Google-Thread: 10b271,48ffa0a9411943ca,start X-Google-Attributes: gid10b271,public X-Google-ArrivalTime: 2004-01-20 16:45:45 PST Path: arc1-ca.pugleaf.net!archiver1.google.com!news2.google.com!news.maxwell.syr.edu!wn11feed!worldnet.att.net!199.45.49.37!cyclone1.gnilink.net!spamkiller2.gnilink.net!nwrdny03.gnilink.net.POSTED!4efb0a2c!not-for-mail From: "George Elkins" <netnews.20.elkins@spamgourmet.com> Newsgroups: sci.polymers,bionet.molbio.proteins,sci.chem,sci.physics References: <6e6c00d7.0311110221.606cc1ee@posting.google.com> <bouk1j$arl$1@news.doit.wisc.edu> Subject: Re: How to visualize a pdb-like file Lines: 40 X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Message-ID: <ZYjPb.4846$LM4.4591@nwrdny03.gnilink.net> Date: Wed, 21 Jan 2004 00:45:45 GMT NNTP-Posting-Host: 141.153.146.208 X-Complaints-To: abuse@verizon.net X-Trace: nwrdny03.gnilink.net 1074645945 141.153.146.208 (Tue, 20 Jan 2004 19:45:45 EST) NNTP-Posting-Date: Tue, 20 Jan 2004 19:45:45 EST