[Chimera-users] adding CONECT records with nogui option

[Eric Pettersen]

Hi Shyamala,
	If you know how to do something using the Chimera command line, you  
can do the exact same thing in Python by using Chimera's runCommand()  
function, e.g.:

from chimera import runCommand
runCommand("pdbrun conect cat > " + fname + ".pdb")

	You only need to use the pdbrun command above if you need to write  
out CONECT records for both standard and non-standard residues for  
some reason.  The normal command for saving PDBs ("write") will output  
CONECT records for non-standard residues.
	As for programming resources, there are some but not as many/much as  
we would like.  First there is the Chimera Programmer's Guide which  
has examples and an FAQ.  Second is to look at modules in <your  
chimera>/share that perform functions similar to what you want to do.   
Third is to search chimera-users for scripts that have been posted to  
see how they work.  We want to put up a wiki page of scripts but  
haven't gotten to that yet.  Last but not least is if you get stuck,  
post questions on the chimera-dev mailing list -- they should be  
answered quickly.

--Eric

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


On Mar 13, 2009, at 3:08 PM, shyamala wrote:

> Hi Chimera users,
>
> I am sure there is a simple way to do this, but I need some help.
> I want to add CONECT records to a pdb file, given that the input file
> contains all necessary atom coordinate information.
> I need to do this within my shell script and I want to start chimera  
> using
> the nongui option.
> Now, doing some google seach brought up this solution to add CONECT
> records (in the command line within CHIMERA gui)
> pdbrun nouser conect cat > filename.pdb
>
> where filename.pdb is the name of the output file with CONECT records
> added.
>
> the above mentioned command works when I pull up the file on GUI  
> CHIMERA
>
> My question is then how would I use such a command when I want to  
> use it
> in the nogui option. I have multiple files (>100) for which I need to
> add CONECT records and I want to do it with a script.
>
> Also, if someone could point me to a good resource for writing python
> scripts that can be then passed on to chimera, I would be grateful.
>
> Thanks,
>
> Shyamala
>
> Shyamala Iyer
> Graduate Student
> Department of Microbiology
> PO BOX 357242
> University of Washington
> Seattle, WA, 98195
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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