[Chimera-users] write selected command

[Edward Brignole]

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?

Ed

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Edward Brignole
NIH Kirschstein Postdoctoral Fellow
Francisco Asturias Lab, CB227
Center for Integrative Molecular Biosciences
The Scripps Research Institute
www.scripps.edu/~brignole

brignole at scripps.edu
443-653-2070 (cell)
858-784-8598 (lab)



-----Original Message-----
From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
Sent: Wed 4/1/2009 1:26 PM
To: Edward Brignole
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] write selected command
 
Other possibilities include using the "combine" command to combine  
models 6, 8, and 9 into a single model (with model 0 as the 'refMol')  
and then use the write command on that (omitting 'relative 0'), or  
writing the models to separate files and using 'system cat file1 file2  
file3 > file4' to combine them (though there would be END records  
between the models that way).

--Eric

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


On Apr 1, 2009, at 1:11 PM, Elaine Meng wrote:

> Hi Ed,
> The "write" command only allows you to save one model at a time.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
>
> To save multiple models to one PDB file you have to use the GUI
> ("File... Save PDB" or "Actions... Write PDB").
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
>
> Sorry about that,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
>
> On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote:
>
>> Elaine and co,
>>
>> I have a mess of models that I'm opening, repositioning a ligand
>> using match to various positions in each model. No problem there.
>> For each model and ligand position I select the correct chains from
>> that model with the repositioned ligand models but can't manage to
>> save coordinates. Obviously there's the save pdb dialog but for all
>> these models and ligands this will be more convenient scripted into
>> chimera commands. I've got it all working except this:
>>
>> select #6:.a-p #8 #9
>> write selected relative 0 #6,8,9 /path/to/file.pdb
>> ~select
>>
>> The part it doesn't like is the model_numbers and I've tried
>> various permutations without success. The only way I can get it to
>> work is if I only specify one model number.
>>
>> Can you please help me figure out how to phrase this command
>> correctly? An example or two on that commands page might make the
>> syntax easier to decipher.
>>
>> Thank you for your excellent program and support.
>>
>> Ed
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Edward Brignole
>> NIH Kirschstein Postdoctoral Fellow
>> Francisco Asturias Lab, CB227
>> Center for Integrative Molecular Biosciences
>> The Scripps Research Institute
>> www.scripps.edu/~brignole
>>
>> brignole at scripps.edu
>> 443-653-2070 (cell)
>> 858-784-8598 (lab)
>>
>>
>>
>>
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