[Chimera-users] Command line syntax questions

[Divita Mathur, Contractor Code 6910, FN]

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):


  1.  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.
  2.  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.
  3.  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.

Thank you for your help. I also want to mention that the Chimera user discussion portal has been very helpful otherwise!

Best,

--
Divita Mathur
Postdoctoral Research Fellow
Center for Bio/Molecular Science and Engineering
Naval Research Laboratory
Washington DC 20375
(202) 767-0687 (Office)
divita.mathur.ctr.in at nrl.navy.mil
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