[Chimera-users] adding CONECT records with nogui option

shyamala shyamala at u.washington.edu
Fri Mar 13 15:08:27 PDT 2009

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 

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.



Shyamala Iyer
Graduate Student
Department of Microbiology
PO BOX 357242
University of Washington
Seattle, WA, 98195

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