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Hi, Jarrett

This is more than helpful! I just need to fix my own mistake in the selection

cmd.select(base_interface, "byres((not (/base//H+L) & base) within 10 of /base//H+L)")

Maybe one more question:

Selection: “not (/base//H+L)” returns all residues in pred, as well as the P chain of base. I understand this.
However, why “not /base//H+L” returns an empty selection?

Thanks!

From: Jarrett Johnson <jar...@sc...>
Sent: Thursday, June 29, 2023 6:31 AM
To: Zhou, Yingyao <yin...@no...>
Cc: pym...@li...
Subject: Re: [PyMOL] Help with selecting interface residues between two structures


This Message is from an External Sender. Do not click links or open attachments unless you trust the sender.
Hi,

There might be a cleaner way to do this, but I propose creating a mapping of your chains from base to pred and use the `iterate` command to get the relevant identifiers and map them back to the prediction. Here is a full script that pulls from the PDB that attempts this idea.

from pymol
import cmd



# our reference

cmd.fetch('3hfm',
'base')

# dummy prediction

cmd.copy('pred',
'base')



# Heavy & Light chains in 3hfm are named L and H

# Antigen is Y so lets rename to A to simulate your case

cmd.alter('base & chain Y',
'chain="A"')



# change chain to emulate same residues different chain names

cmd.alter('pred & chain L',
'chain="A"')

cmd.alter('pred & chain H',
'chain="B"')

cmd.alter('pred & chain Y',
'chain="C"')



base_interface
= 'int_base'

cmd.select(base_interface,
'byres(base & (/base//H+L around 5))')



# After preparation:

# create a mapping of chains from base to pred

base_to_pred_chains
= {'L':
'A', 'H':
'B', 'A':
'C'}



# Create a list of identifiers in the interface from the selection

myspace
= {'int_set':
set()}

cmd.iterate(base_interface,
'int_set.add((chain, resi, resn))', space=myspace)



# Map them to a new selection onto the prediction

pred_interface
= 'int_pred'

cmd.select(pred_interface,
'none')

for
chain, resi,
resn in
myspace['int_set']:

    new_chain
= base_to_pred_chains[chain]

    # Add each pred residue to the selection

    cmd.select(pred_interface,

               f'pred & chain
{new_chain} & resi
{resi} & resn
{resn}',

               merge=1)


Hope that helps,
Jarrett J

On Thu, Jun 29, 2023 at 12:59 AM Zhou, Yingyao via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:
I am a relatively new PyMOL user and would like to get some helps from the community.

I have two structures for the same antibody-antigen complex (with three chains: light chain L, heavy chain H, and an antigen chain A) .
Structure “base” is the experimental true structure, structure “pred” is the predicted structure. My goal is to determine how close the predicted interface is w.r.t. the experimental truth.

I first select the interface residues as defined by “base”

load base.pdb
load pred.pdb
select int_base, byres(base & (/base//H+L around 5))

How do I select the same corresponding residues in object “pred”?

In addition, what if in the pred structure, chains are named A, B, and C, corresponding to base structure L, H, A, respectively, how will I handle that?
(I was planning to rename the chains, if there is no nice trick to transfer the selections from base to pred)

Thanks!


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--

Jarrett Johnson | Senior Developer, PyMOL
[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

Hi,

There might be a cleaner way to do this, but I propose creating a mapping
of your chains from base to pred and use the `iterate` command to get the
relevant identifiers and map them back to the prediction. Here is a full
script that pulls from the PDB that attempts this idea.

from pymol import cmd

# our reference
cmd.fetch('3hfm', 'base')
# dummy prediction
cmd.copy('pred', 'base')

# Heavy & Light chains in 3hfm are named L and H
# Antigen is Y so lets rename to A to simulate your case
cmd.alter('base & chain Y', 'chain="A"')

# change chain to emulate same residues different chain names
cmd.alter('pred & chain L', 'chain="A"')
cmd.alter('pred & chain H', 'chain="B"')
cmd.alter('pred & chain Y', 'chain="C"')

base_interface = 'int_base'
cmd.select(base_interface, 'byres(base & (/base//H+L around 5))')

# After preparation:
# create a mapping of chains from base to pred
base_to_pred_chains = {'L': 'A', 'H': 'B', 'A': 'C'}

# Create a list of identifiers in the interface from the selection
myspace = {'int_set': set()}
cmd.iterate(base_interface, 'int_set.add((chain, resi, resn))', space=
myspace)

# Map them to a new selection onto the prediction
pred_interface = 'int_pred'
cmd.select(pred_interface, 'none')
for chain, resi, resn in myspace['int_set']:
    new_chain = base_to_pred_chains[chain]
    # Add each pred residue to the selection
    cmd.select(pred_interface,
               f'pred & chain {new_chain} & resi {resi} & resn {resn}',
               merge=1)

Hope that helps,
Jarrett J

On Thu, Jun 29, 2023 at 12:59 AM Zhou, Yingyao via PyMOL-users <
pym...@li...> wrote:

> I am a relatively new PyMOL user and would like to get some helps from the
> community.
>
>
>
> I have two structures for the same antibody-antigen complex (with three
> chains: light chain L, heavy chain H, and an antigen chain A) .
>
> Structure “base” is the experimental true structure, structure “pred” is
> the predicted structure. My goal is to determine how close the predicted
> interface is w.r.t. the experimental truth.
>
>
>
> I first select the interface residues as defined by “base”
>
>
>
> load base.pdb
>
> load pred.pdb
>
> select int_base, byres(base & (/base//H+L around 5))
>
>
>
> How do I select the same corresponding residues in object “pred”?
>
>
>
> In addition, what if in the pred structure, chains are named A, B, and C,
> corresponding to base structure L, H, A, respectively, how will I handle
> that?
>
> (I was planning to rename the chains, if there is no nice trick to
> transfer the selections from base to pred)
>
>
>
> Thanks!
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Senior Developer, PyMOL

I am a relatively new PyMOL user and would like to get some helps from the community.

I have two structures for the same antibody-antigen complex (with three chains: light chain L, heavy chain H, and an antigen chain A) .
Structure "base" is the experimental true structure, structure "pred" is the predicted structure. My goal is to determine how close the predicted interface is w.r.t. the experimental truth.

I first select the interface residues as defined by "base"

load base.pdb
load pred.pdb
select int_base, byres(base & (/base//H+L around 5))

How do I select the same corresponding residues in object "pred"?

In addition, what if in the pred structure, chains are named A, B, and C, corresponding to base structure L, H, A, respectively, how will I handle that?
(I was planning to rename the chains, if there is no nice trick to transfer the selections from base to pred)

Thanks!

Dear PyMOL users and experts,

I wonder if anybody has insight into the following problem concerning 
the determination of hydrogen bonding interactions in PyMOL via the dist 
command with the mode=2 option. For an upcoming local PyMOL workshop, 
which I organize for PhD students, I tried to find a way to detect 
hydrogen bonding interactions of a ligand with its receptor within PyMOL.

This is described to some extent in
https://pymol.org/dokuwiki/doku.php?id=setting:h_bond
or
https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts

The documentation suggests that if resonable positions of the polar 
hydrogens are available, one can detect hydrogen bonds using distance 
and donor angle criteria. I added hydrogen bonds using Protoss of the 
ProteinPlus webserver to the structure 4eiy. However, when analyzing the 
environment of the ligand, I notice that many hydrogen bonds are 
detected quite fine, but there are many others, which are not displayed, 
although they have quite perfect geometry. Furthermore, for some 
hydrogen bonds, the heavy atoms are connected, in contrast to the 
settings (and the correct display of many other interactions).

If somebody wants to test, the pdb file is available here: 
https://research.uni-leipzig.de/straeter/pymol/data/4eiy_protoss.pdb

and these are the commands:

load 4eiy_protoss.pdb
hide all
zoom resn ZMA
clip slab, 8
show sticks
dist hbonds, all, all, mode=2

For example, for water molecules 2522 or 2527 in the vicinity of the 
ligand, the non-hydrogen atoms are connected by the H-bond. Waters 2584, 
2514 and Tyr-9 OH are well set for a hydrogen bonding interaction, but 
this is not detected.

I wonder, what the cause of these apparent inconsistencies might be. Is 
it the algorithm or the detection of the donor/acceptor functionalities?

If the hydrogens are deleted before the running the dist command, these 
hydrogen bonds are shown, but also others which are only very weak based 
on the deviations from donor angle linearity.

Best regards,

Norbert

Hello,

Using PyMOL's figures for the purpose of fulfilling academic requirements
such as a thesis or a dissertation is permissible.

Best,
Jarrett J.

On Wed, Jun 14, 2023 at 10:59 AM deniz tunalıer <den...@gm...>
wrote:

> Hi PyMOL users,
>
> I'm using Edu-PyMOL and I'm wondering if I can use figures that I created
> with it in my master's thesis? Or do I need to buy a license? Thanks in
> advance. Looking forward to your response.
>
> Best wishes,
> Deniz
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Hi PyMOL Support Team

I'm having trouble getting the download credentials for the PyMOL educational version. I completed the registration process on 20/06/23 and verified my educational status, but haven't received any email with the credentials or instructions. Can you please assist me with this issue?

Thanks, Parinya

I am currently working on a plugin for PyMol that should continuously add
new structures to the PyMol view while the function is running.

This is some demo code:
import time
from pymol import cmd

@cmd.extend
def custom_function(inp):
    for i in range(len(inp)):
        time.sleep(2)
        print(i) # here we would load the structures

However, this doesn't work. It prints in the system console just in time
but not in the Pymol console (and if I call e.g cmd.load("somepdb") also
the structure doesn't get added to the view) until the function has
completed running.

Is there a way around this ?

Thanks,
Simon

*Simon Dürr*
in...@si...
https://simonduerr.eu

Hi,

The Schrödinger Education team is hosting a free event from June 13-16th
called Educator's Week 2023 <," rel="nofollow">https://events.bizzabo.com/467368>, connecting
educators from all over the world to discuss the growing role of
educational technology in the classroom and integrating computational
molecular modeling into modern science curricula.

*June 13-15, 2023*
11:00 AM to 2:00 PM ET
Virtual conference with live presentations

*Register for the free event. <*" rel="nofollow">https://events.bizzabo.com/467368>*

We're very excited that* Noeris Salam from Schrödinger *will be giving a
virtual talk today, June 14th, on *PyMOL 3.0 Beta* and will discuss the new
movie-making features. We'll also be hosting several teachers and
professors who will highlight how PyMOL and molecular modeling are
revolutionizing elementary school science, among other chemistry and
biology teachers and college-level professors.

Hope to see you there!

Best,

Schrödinger Education Team | Teaching

Hi PyMOL users,

I'm using Edu-PyMOL and I'm wondering if I can use figures that I created
with it in my master's thesis? Or do I need to buy a license? Thanks in
advance. Looking forward to your response.

Best wishes,
Deniz

Hi Jarrett,
That command seems to just move the object back to its original position
instead of resetting the matrix values with the object kept in its new
position.
Regards,
Philip

On Fri, Jun 2, 2023 at 12:56 PM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Philip,
>
> Have you tried the `matrix_reset` command instead?
>
> Best
> Jarrett J.
>
> On Fri, Jun 2, 2023 at 3:46 PM Philip Kiser <pk...@uc...> wrote:
>
>> Hi Everyone,
>> Is there a way to set an object TTT matrix to the identity after
>> performing a transformation (e.g. superposition)? I want to leave the
>> object in its new position and just reset the matrix so the new position
>> has an identity TTT matrix. From the PyMOL wiki, it seems "reset" should be
>> the right command, but it is not working in my hands. Thank you for any
>> tips you can provide.
>> Regards,
>> Philip
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> <" rel="nofollow">https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li....net__;!!CzAuKJ42GuquVTTmVmPViYEvSg!I8vAXv2W562ZF7bJqLlWlKsmMv-JVak8dAiGK6zvjBHEdcQgqh4ZWi1vaB-cp_AfzNAfc5X4d6JXJOu_JxTn9K-DbDD8$>
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>> <" rel="nofollow">https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!CzAuKJ42GuquVTTmVmPViYEvSg!I8vAXv2W562ZF7bJqLlWlKsmMv-JVak8dAiGK6zvjBHEdcQgqh4ZWi1vaB-cp_AfzNAfc5X4d6JXJOu_JxTn9Mz1uKrY$>
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

Ah apologies,

I am not sure of the most efficient way to do it, but one could store the
TTT matrix, reset the matrix, and transform the object as a selection so
that the positions themselves are changed and not the object transform.

Something like
PyMOL>mat = cmd.get_object_matrix('1obyA')
PyMOL>cmd.matrix_reset('1obyA')
PyMOL>cmd.transform_selection('1obyA', mat)


comes to mind.

On Fri, Jun 2, 2023 at 4:04 PM Philip Kiser <pk...@uc...> wrote:

> Hi Jarrett,
> That command seems to just move the object back to its original position
> instead of resetting the matrix values with the object kept in its new
> position.
> Regards,
> Philip
>
> On Fri, Jun 2, 2023 at 12:56 PM Jarrett Johnson <
> jar...@sc...> wrote:
>
>> Hi Philip,
>>
>> Have you tried the `matrix_reset` command instead?
>>
>> Best
>> Jarrett J.
>>
>> On Fri, Jun 2, 2023 at 3:46 PM Philip Kiser <pk...@uc...> wrote:
>>
>>> Hi Everyone,
>>> Is there a way to set an object TTT matrix to the identity after
>>> performing a transformation (e.g. superposition)? I want to leave the
>>> object in its new position and just reset the matrix so the new position
>>> has an identity TTT matrix. From the PyMOL wiki, it seems "reset" should be
>>> the right command, but it is not working in my hands. Thank you for any
>>> tips you can provide.
>>> Regards,
>>> Philip
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> <" rel="nofollow">https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li....net__;!!CzAuKJ42GuquVTTmVmPViYEvSg!I8vAXv2W562ZF7bJqLlWlKsmMv-JVak8dAiGK6zvjBHEdcQgqh4ZWi1vaB-cp_AfzNAfc5X4d6JXJOu_JxTn9K-DbDD8$>
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>> <" rel="nofollow">https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!CzAuKJ42GuquVTTmVmPViYEvSg!I8vAXv2W562ZF7bJqLlWlKsmMv-JVak8dAiGK6zvjBHEdcQgqh4ZWi1vaB-cp_AfzNAfc5X4d6JXJOu_JxTn9Mz1uKrY$>
>>
>>
>>
>> --
>>
>> *Jarrett Johnson* | Senior Developer, PyMOL
>>
>>

-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Hi Philip,

Have you tried the `matrix_reset` command instead?

Best
Jarrett J.

On Fri, Jun 2, 2023 at 3:46 PM Philip Kiser <pk...@uc...> wrote:

> Hi Everyone,
> Is there a way to set an object TTT matrix to the identity after
> performing a transformation (e.g. superposition)? I want to leave the
> object in its new position and just reset the matrix so the new position
> has an identity TTT matrix. From the PyMOL wiki, it seems "reset" should be
> the right command, but it is not working in my hands. Thank you for any
> tips you can provide.
> Regards,
> Philip
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Hi Everyone,
Is there a way to set an object TTT matrix to the identity after performing
a transformation (e.g. superposition)? I want to leave the object in its
new position and just reset the matrix so the new position has an identity
TTT matrix. From the PyMOL wiki, it seems "reset" should be the right
command, but it is not working in my hands. Thank you for any tips you can
provide.
Regards,
Philip