[Chimera-users] write selected command

[Eric Pettersen]

Hi Ed,
	If the purpose of the combination is to use Morph Conformations, then  
I think you're in for a world of hurt unless you use the 'combine'  
method.  One problem with the 'cat' method is the serial numbers as  
you surmised.  If you have any non-standard residues that require  
CONECT records then the serial numbers will be a real issue.  Another  
problem is that if you have any chains in models 8 and 9 that  
duplicate the ones you're using from #6 (a-p) or duplicate each other  
then Morph Conformations will probably fall over.  'combine' will  
rename chains that are in conflict and renumber problem residues.   
'write' with the combined model will produce unique serial numbers.
	So your previous commands:

select #6:.a-p #8 #9
write selected relative 0 #6,8,9 /path/to/file.pdb
  ~select

could instead be:

sel #6:.a-p
sel invert sel
del sel
combine #6,8,9 refMol 0 modelId 7
write #7 /path/to/file.pdb

BTW, you have to use a daily build to get the 'modelId' part of the  
'combine' command.
	If your models #8 and 9 are just small molecules then you may be able  
to get away with the 'cat' method by stripping CONECT records in  
addition to END records -- making Chimera come up with the  
connectivity itself (though if the residues had the same number and  
chain ID as other residues...).

--Eric
	
On Apr 1, 2009, at 1:32 PM, Edward Brignole wrote:

> 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)
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> Chimera-users mailing list
> >> Chimera-users at cgl.ucsf.edu
> >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>

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