[Chimera-users] Getting names of selected atoms and renaming

Vladyslav Dziuba xenonbat at ya.ru
Thu Mar 16 18:03:10 PDT 2017


Dear Sir or Madam,
I have some difficulties with using ORCA and UCSF Chimera together. Let me describe my problem first. I need to freeze some atoms (actually, a lot of atoms) in my calculations (geometry optimization), e.g. make their coordinates constant. To do that I need to specify numbers of atoms from xyz file, which is obtained from pdb-file. The problem is that for every atom in pdb-file OpenBabel generates a new number (for example H27 may become 100th atom in xyz file), so that specifying atoms that must be frozen becomes much more complicated. Given that, I'd like to ask to help me find answer on some questions:
1. How can I rename atoms? It would greatly help me identificate atoms that must be frozen. Can I rename only all selected atoms?
2.Can I modify names of selected atoms?
3. How can I get list of numbers of selected atoms? For instance I've chosen some aminoacids residues and I want to get names or numbers of all atoms chosen.
Because if I one wants to get a list of atoms in xyz file, he needs names or numbers of atoms in pdb file, but the last ones are disordered. Manual atom picking and comparison in pdb- and xyz-files is very time-consuming. UCSF Chimera is a truly powerful program so I believe there must exist an elegant solution to my problem.
Hope to receive a letter from you soon.
Thanks in advance!
Best regards,
Vladislav Dziuba


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