Thank you so much Jarrett, yes it works very well!
On Thu, 20 Jul 2023 at 08:51, Jarrett Johnson <
jarrett.john...@schrodinger.com> wrote:
> Sorry, typo. For the second approach, state should be `i + 1` and not `-1`"
>
> Jarrett J.
>
> On Thu, Jul 20, 2023 at 8:49 AM Jarrett Johnson <
> jarrett.john...@schrodinger.com> wrote:
>
>> 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
>>>>
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>>
>>
>>
>> --
>>
>> *Jarrett Johnson* | Senior Developer, PyMOL
>>
>>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>
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