[Chimera-users] Pyrazine problem

[Elaine Meng]

Hi Francesco,
Chimera tries to figure out atom types, but in this case they need to  
be adjusted before you further process the molecule (addh,  
addcharge, ...).

Open your file pyrazine.pdb and label with Chimera atom types, for  
example with the commands:

labelopt info idatmType
label

Then you can see the carbons are C2 and the nitrogens Npl.  Instead  
you want Car and N2.  The atom types are described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

I would use the comand "setattr" to change the atom types,
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
for example:

sel @/idatmType=C2
setattr a idatmType Car sel
sel @/idatmType=Npl
setattr a idatmType N2 sel
label

( ** The labels don't change automatically, you have to "label" again  
to see the changes. **)
Now the molecule should behave as expected.

Actually instead of using a separate program to build the molecule or  
building it up step by step in Chimera, it is much easier to look up a  
CID in PubChem and fetch from Pub3D, for example for pyrazine:

open pubchem:9261

...or specify with a SMILES string and use the smi23d web server, for  
example:

open smiles:n1ccncc1

However, these both currently have the same atom type problem.  We  
will try to improve the automatic atom type assignment - sorry about  
that.
Best,
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