Re: [PyMOL] Question on residue selection in multiple PDB

[Jarrett J. <jar...@sc...>]

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 <nee...@gm...>
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 <nee...@gm...>
> 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
>>
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-- 

*Jarrett Johnson* | Senior Developer, PyMOL