[Chimera-users] Command line syntax questions

[Elaine Meng]

Hi Divita,
Answers interleaved below...

> On May 30, 2018, at 10:53 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
> 
> Hi 
> I am trying to write an alias and am curious if I can do the following using command line (in order to include them in the alias): 
> 	• Separate chains that belong to the same model – can I change the model # on a single chain from an existing model? For example, I built a DNA duplex, selected one chain (sel :.A) and tried to change the model # (combine sel model 8 close true) but the new model also includes chain B.

Yes, as mentioned in the “combine” documentation,
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
“Although a narrower atom-spec may be supplied, the entire model(s) containing the specified atoms will be included in a new model”

Ways to do it:
(A) if you want multiple models with different parts of the same initial model, use “split”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>

 It will make model #0 into model #0.1, #0.2, etc.  Even though they have the same main number, you can specify or otherwise deal with them independently like other models.  Then if you want to renumber and/or change chain ID, you can use commands “resrenumber” and “changechains”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html>

(B) simply delete the rest of the structure, e.g. command “delete ~sel” (delete NOT selected) or “delete ~:.a” (delete NOT chain A), command “delete solvent” etc. to get rid of what you don’t want.  Then you can change chain ID and residue numbering as above.

> 	• Change residue number of a residue in a chain. I combined a small molecule to a DNA chain between residues 18 and 19, but after combining, the molecule’s residue number remains 1. I would like to change it to 19 or 18.

> 	• Following point #2, I also want to assign the new molecule the same chain ID – A. In the pdb file, the chain ID is blank for the newly inserted molecule.

Sorry, you can’t use “resrenumber” and “changechains” to assign some atoms the same residue number and chain ID as another residue that is already in the model. The easiest way by far is to text-edit the PDB file (using your favorite text-editor outside of Chimera), but of course that can’t be done in your alias.

It sounds like you wanted that molecule to be bonded to something in the DNA.  There is a “bond” command, but you would need to specify the two atoms to bond.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>
>  
> Thank you for your help. I also want to mention that the Chimera user discussion portal has been very helpful otherwise!

You’re welcome,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco