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<P><FONT SIZE=2>Great suggestion, I'll just use cat and strip the END lines. Since I want to then use these with morph conformations will I also have to resequence the atom id's?<BR>
<BR>
Ed<BR>
<BR>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>
Edward Brignole<BR>
NIH Kirschstein Postdoctoral Fellow<BR>
Francisco Asturias Lab, CB227<BR>
Center for Integrative Molecular Biosciences<BR>
The Scripps Research Institute<BR>
www.scripps.edu/~brignole<BR>
<BR>
brignole@scripps.edu<BR>
443-653-2070 (cell)<BR>
858-784-8598 (lab)<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: Eric Pettersen [<A HREF="mailto:pett@cgl.ucsf.edu">mailto:pett@cgl.ucsf.edu</A>]<BR>
Sent: Wed 4/1/2009 1:26 PM<BR>
To: Edward Brignole<BR>
Cc: chimera-users@cgl.ucsf.edu BB<BR>
Subject: Re: [Chimera-users] write selected command<BR>
<BR>
Other possibilities include using the "combine" command to combine <BR>
models 6, 8, and 9 into a single model (with model 0 as the 'refMol') <BR>
and then use the write command on that (omitting 'relative 0'), or <BR>
writing the models to separate files and using 'system cat file1 file2 <BR>
file3 > file4' to combine them (though there would be END records <BR>
between the models that way).<BR>
<BR>
--Eric<BR>
<BR>
Eric Pettersen<BR>
UCSF Computer Graphics Lab<BR>
<A HREF="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A><BR>
<BR>
<BR>
On Apr 1, 2009, at 1:11 PM, Elaine Meng wrote:<BR>
<BR>
> Hi Ed,<BR>
> The "write" command only allows you to save one model at a time.<BR>
> <<A HREF="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html</A>><BR>
><BR>
> To save multiple models to one PDB file you have to use the GUI<BR>
> ("File... Save PDB" or "Actions... Write PDB").<BR>
> <<A HREF="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb</A>><BR>
><BR>
> Sorry about that,<BR>
> Elaine<BR>
> -----<BR>
> Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu<BR>
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<BR>
> Department of Pharmaceutical Chemistry<BR>
> University of California, San Francisco<BR>
> <A HREF="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</A><BR>
><BR>
> On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote:<BR>
><BR>
>> Elaine and co,<BR>
>><BR>
>> I have a mess of models that I'm opening, repositioning a ligand<BR>
>> using match to various positions in each model. No problem there.<BR>
>> For each model and ligand position I select the correct chains from<BR>
>> that model with the repositioned ligand models but can't manage to<BR>
>> save coordinates. Obviously there's the save pdb dialog but for all<BR>
>> these models and ligands this will be more convenient scripted into<BR>
>> chimera commands. I've got it all working except this:<BR>
>><BR>
>> select #6:.a-p #8 #9<BR>
>> write selected relative 0 #6,8,9 /path/to/file.pdb<BR>
>> ~select<BR>
>><BR>
>> The part it doesn't like is the model_numbers and I've tried<BR>
>> various permutations without success. The only way I can get it to<BR>
>> work is if I only specify one model number.<BR>
>><BR>
>> Can you please help me figure out how to phrase this command<BR>
>> correctly? An example or two on that commands page might make the<BR>
>> syntax easier to decipher.<BR>
>><BR>
>> Thank you for your excellent program and support.<BR>
>><BR>
>> Ed<BR>
>><BR>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>
>> Edward Brignole<BR>
>> NIH Kirschstein Postdoctoral Fellow<BR>
>> Francisco Asturias Lab, CB227<BR>
>> Center for Integrative Molecular Biosciences<BR>
>> The Scripps Research Institute<BR>
>> www.scripps.edu/~brignole<BR>
>><BR>
>> brignole@scripps.edu<BR>
>> 443-653-2070 (cell)<BR>
>> 858-784-8598 (lab)<BR>
>><BR>
>><BR>
>><BR>
>><BR>
>> _______________________________________________<BR>
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><BR>
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