Hi Neena, Is the split_states necessary? You can query the distance between atoms on the state-level as well without having to break up your structure. Here's two approaches that show either way; I recommend the second if possible. You'll of course have to switch out the selection string to fit your own atom pairs.
from pymol import cmd # Approach 1: With splitting states cmd.fetch('1L2Y') cmd.split_states('1L2Y') for i in range(cmd.count_states('1L2Y')): nmr_frame = f"1L2Y_{i + 1:04d}" sele1 = f"/{nmr_frame}/A/A/ILE`4/O" sele2 = f"/{nmr_frame}/A/A/ASP`9/CA" dist = cmd.dist(f"dist_{nmr_frame}", sele1, sele2) print(dist) print("--------------------") # Approach 2: Without splitting states for i in range(cmd.count_states('1L2Y')): sele1 = "/1L2Y/A/A/ILE`4/O" sele2 = "/1L2Y/A/A/ASP`9/CA" dist = cmd.get_distance(sele1, sele2, state=-1) print(dist) Hope that helps, Jarrett J On Wed, Jul 19, 2023 at 9:48 PM Neena Susan Eappen <neenasusan...@gmail.com> wrote: > Hello PyMOL users, > > Can I get some insight on how to approach this analysis? > > Many thanks, > Neena > > On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen <neenasusan...@gmail.com> > wrote: > >> Hello PyMOL Team, >> >> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38 >> NMR structures deposited in it. >> Using split_states command, I can see all 38 structures. >> I want to find polar contacts between same 3 residues in all these 38 >> structures and extract corresponding distance values for polar contacts. >> >> Question: Is there a single command to select 3 residues in all these 38 >> structures and find polar contacts within this selection? >> >> Many thanks, >> Neena >> > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Senior Developer, PyMOL
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