[Chimera-users] adding CONECT records with nogui option

Eric Pettersen pett at cgl.ucsf.edu
Mon Mar 16 11:53:37 PDT 2009

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 Pettersen
                         UCSF Computer Graphics Lab

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  
> 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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