pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Help with selecting interface residues between two structures

[Zhou, Y. <yin...@no...>]

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] hydrogen bond detection via the dist command and mode=2 option

[Norbert S. <st...@bb...>]

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

Re: [PyMOL] Edu-PyMOL for master thesis

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

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

[PyMOL] Need Download Credentials for Educational PyMOL

[Mr. P. T. <par...@cg...>]

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

[PyMOL] Custom Functions are blocking

[Simon D. <ha...@si...>]

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

[PyMOL] You're invited to Educator's Week 2023

[Teaching w. S. <tea...@sc...>]

Hi,

The Schrödinger Education team is hosting a free event from June 13-16th
called Educator's Week 2023 <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. <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

[PyMOL] Edu-PyMOL for master thesis

[deniz t. <den...@gm...>]

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

Re: [PyMOL] reset TTT matrix to identity

[Philip K. <pk...@uc...>]

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...
>> <https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li....net__;!!CzAuKJ42GuquVTTmVmPViYEvSg!I8vAXv2W562ZF7bJqLlWlKsmMv-JVak8dAiGK6zvjBHEdcQgqh4ZWi1vaB-cp_AfzNAfc5X4d6JXJOu_JxTn9K-DbDD8$>
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>> <https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!CzAuKJ42GuquVTTmVmPViYEvSg!I8vAXv2W562ZF7bJqLlWlKsmMv-JVak8dAiGK6zvjBHEdcQgqh4ZWi1vaB-cp_AfzNAfc5X4d6JXJOu_JxTn9Mz1uKrY$>
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

Re: [PyMOL] reset TTT matrix to identity

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

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...
>>> <https://urldefense.com/v3/__http://www.mail-archive.com/pym...@li....net__;!!CzAuKJ42GuquVTTmVmPViYEvSg!I8vAXv2W562ZF7bJqLlWlKsmMv-JVak8dAiGK6zvjBHEdcQgqh4ZWi1vaB-cp_AfzNAfc5X4d6JXJOu_JxTn9K-DbDD8$>
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>> <https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!CzAuKJ42GuquVTTmVmPViYEvSg!I8vAXv2W562ZF7bJqLlWlKsmMv-JVak8dAiGK6zvjBHEdcQgqh4ZWi1vaB-cp_AfzNAfc5X4d6JXJOu_JxTn9Mz1uKrY$>
>>
>>
>>
>> --
>>
>> *Jarrett Johnson* | Senior Developer, PyMOL
>>
>>

-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] reset TTT matrix to identity

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

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

[PyMOL] reset TTT matrix to identity

[Philip K. <pk...@uc...>]

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] add hydrogens to .mol2 files

[Joel T. <joe...@ot...>]

Hi all,

I have just noticed that when you add hydrogens to a protein file that is a .mol2, hydrogens are added to carboxylates to make them the acid (unionised). This does not occur for a pdb file (they are ionised).

Can this be fixed in a future version? I would have thought that the atom typing would be such that it recognises the appropriate ionised state (along with the residue)

Joel

Joel Tyndall | BSc(Hons) PhD

Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Ph: 64 3 479 7293
Website | pharmacy.otago.ac.nz

[PyMOL] Pymol education uses for thesis

[Lauren D. <lau...@hd...>]

Hi,
I am currently a master of philosophy student and am using Pymol education. I will need to write a thesis and was wondering if I can use this within my thesis or not.
Thanks
Lauren

Re: [PyMOL] centerofmass command gives error

[Petro <sub...@kh...>]

Thanks.
Yes it helps.


On Tue, 23 May 2023 at 15:21, Jared Sampson <jar...@co...>
wrote:

> Hi Petro - It looks like that structure has a deuterium atom.  Assuming
> you're interested in the non-deuterated molecule, you can convert it to a
> hydrogen and the command will work.
>
> ```
> alter elem D, elem="H"
> rebuild
> print(cmd.centerofmass("polymer"))
> ```
>
> Or if you want to stick with Python API syntax, the first two commands
> would be:
>
> ```
> cmd.alter('elem D', 'elem="H"')  # note the second argument is a string
> for the `expression` keyword arg, thus double quotes inside single quotes
> cmd.rebuild()
> ```
>
> Hope that helps.
>
> Cheers,
> Jared
>
> On Tue, May 23, 2023 at 6:44 AM Petro <sub...@kh...> wrote:
>
>>
>> Hi everybody
>> I get the following error when I try to use center of mass commanand.
>> Any Idea what is wrong?
>> Thanks.
>> Petro.
>>
>> --------------------------------------------------------------------------KeyError                                  Traceback (most recent call last)
>> Cell In[4], line 4      2 cmd.reinitialize()      3 cmd.fetch('1AKK')----> 4 cmd.centerofmass('polymer')
>>
>> File ~\miniconda3\envs\pymol\lib\site-packages\pymol\querying.py:1565, in centerofmass(selection, state, quiet, _self)   1563 model = _self.get_model(selection, state)   1564 for a in model.atom:-> 1565     m = a.get_mass() * (a.q or 1.0)   1566     com = cpv.add(com, cpv.scale(a.coord, m))   1567     totmass += m
>>
>> File ~\miniconda3\envs\pymol\lib\site-packages\chempy\__init__.py:82, in Atom.get_mass(self)     80 def get_mass(self):     81     '''Given the chemical symbol the atomic mass is returned'''---> 82     return atomic_mass[self.symbol]
>> KeyError: 'D'
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] centerofmass command gives error

[Jared S. <jar...@co...>]

Hi Petro - It looks like that structure has a deuterium atom.  Assuming
you're interested in the non-deuterated molecule, you can convert it to a
hydrogen and the command will work.

```
alter elem D, elem="H"
rebuild
print(cmd.centerofmass("polymer"))
```

Or if you want to stick with Python API syntax, the first two commands
would be:

```
cmd.alter('elem D', 'elem="H"')  # note the second argument is a string for
the `expression` keyword arg, thus double quotes inside single quotes
cmd.rebuild()
```

Hope that helps.

Cheers,
Jared

On Tue, May 23, 2023 at 6:44 AM Petro <sub...@kh...> wrote:

>
> Hi everybody
> I get the following error when I try to use center of mass commanand.
> Any Idea what is wrong?
> Thanks.
> Petro.
>
> --------------------------------------------------------------------------KeyError                                  Traceback (most recent call last)
> Cell In[4], line 4      2 cmd.reinitialize()      3 cmd.fetch('1AKK')----> 4 cmd.centerofmass('polymer')
>
> File ~\miniconda3\envs\pymol\lib\site-packages\pymol\querying.py:1565, in centerofmass(selection, state, quiet, _self)   1563 model = _self.get_model(selection, state)   1564 for a in model.atom:-> 1565     m = a.get_mass() * (a.q or 1.0)   1566     com = cpv.add(com, cpv.scale(a.coord, m))   1567     totmass += m
>
> File ~\miniconda3\envs\pymol\lib\site-packages\chempy\__init__.py:82, in Atom.get_mass(self)     80 def get_mass(self):     81     '''Given the chemical symbol the atomic mass is returned'''---> 82     return atomic_mass[self.symbol]
> KeyError: 'D'
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] centerofmass command gives error

[Petro <sub...@kh...>]

Hi everybody
I get the following error when I try to use center of mass commanand.
Any Idea what is wrong?
Thanks.
Petro.

--------------------------------------------------------------------------KeyError
                                 Traceback (most recent call last)
Cell In[4], line 4      2 cmd.reinitialize()      3
cmd.fetch('1AKK')----> 4 cmd.centerofmass('polymer')

File ~\miniconda3\envs\pymol\lib\site-packages\pymol\querying.py:1565,
in centerofmass(selection, state, quiet, _self)   1563 model =
_self.get_model(selection, state)   1564 for a in model.atom:-> 1565
  m = a.get_mass() * (a.q or 1.0)   1566     com = cpv.add(com,
cpv.scale(a.coord, m))   1567     totmass += m

File ~\miniconda3\envs\pymol\lib\site-packages\chempy\__init__.py:82,
in Atom.get_mass(self)     80 def get_mass(self):     81     '''Given
the chemical symbol the atomic mass is returned'''---> 82     return
atomic_mass[self.symbol]
KeyError: 'D'

Re: [PyMOL] save format for molecule files

[Xavier F. <xav...@gm...>]

Thomas, Joel,

yes, writing to mol2 works. Thanks for the suggestion!

Xavier

Missatge de Thomas Holder <th...@th...> del dia dj., 18 de maig
2023 a les 5:38:

> Hi Xavier,
>
> The best option to transfer bond orders from PyMOL to Maestro might be
> with .mol2 (or .sdf) format. These formats can store aromatic bond
> orders and Maestro will convert that to meaningful double/single bonds
> when loading the file.
>
> - .pdb format can't store aromatic bonds (and double bonds only with
> an unofficial trick)
> - .mae format can't store aromatic bonds
> - Maestro doesn't have aromatic bond orders
> - PyMOL has limited capabilities for detecting bond orders and can't
> convert aromatic bonds to single/double bonds (kekulization)
> - .sdf format doesn't have protein and residue level information, but
> .mol2 does
>
> Cheers,
>   Thomas
>
> On Wed, May 17, 2023 at 4:51 PM Xavier Fradera <xav...@gm...>
> wrote:
> >
> > Hi,
> >
> > I'm trying to save some molecule files (protein+ligand complex) from
> pymol to a format that is readable by maestro. I've tried saving in .mae or
> .pdb format, but bond orders in ligands are lost (all bonds are single).
> I've played with the "PDB options" in the save command and managed to get
> double bonds right, but the aromatic ones are ignored.
> >
> > Does anyone know how to write files that can be read properly by maestro?
> >
> > Alternatively, is there a way to convert aromatic bonds into alternating
> single/double bonds, as I think this would be easier to output based on my
> tests?
> >
> > thanks,
> > Xavier
> >
> > --
> > Xavier Fradera
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 
Xavier Fradera

Re: [PyMOL] Generating of Rg for every state in PyMOL

[#JESSICA L. J. <JESSICAJ002@e.ntu.edu.sg>]

Hi Jarrett,

Thank you very much for your kind and comprehensive advice, really appreciate it!
I will try it out.

Kind regards,
Jessica Lim
________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: Thursday, May 18, 2023 8:32 PM
To: #JESSICA LIM JIAYING# <JESSICAJ002@e.ntu.edu.sg>
Cc: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] Generating of Rg for every state in PyMOL

Hi Jessica,

It seems in the gyradius psico script, by default it will calculate the radius of gyration for the current state. You can provide a specific state to this argument and generate the list yourself in a script.

```
from psico.querying import gyradius

from pymol import cmd

obj = "1nmr"
cmd.fetch(obj)

# for loop
for i in range(cmd.count_states(obj)):
    print(f"State {i+1}: {gyradius(obj, state=i+1)}")

# list comprehension
gy_list = [gyradius(obj, state=i+1) for i in range(cmd.count_states(obj))]
print(gy_list)
```

Hope that helps,
Jarrett J


On Thu, May 18, 2023 at 8:05 AM #JESSICA LIM JIAYING# via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:
Hi all,

I am having difficulty in trying to print out a list of the radius of gyration for all states in my PDB file. I have several files of 100 states each and would like to generate a list of the radius of gyration for every individual state. However, I have only been successful at using the command gyradius as part of the psico package in PyMOL but it only outputs a single value, and I would have to click manually to the next state and re-enter the command to get the next value. Hence, I would like to be able to obtain a list of values without having to click through 100 different states.

Any advice or suggestions on how this can be done will be greatly appreciated, thank you!

Kind regards,
Jessica Lim
_______________________________________________
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Archives: http://www.mail-archive.com/pym...@li...
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--

Jarrett Johnson | Senior Developer, PyMOL

[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

Re: [PyMOL] Generating of Rg for every state in PyMOL

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

Hi Jessica,

It seems in the gyradius psico script, by default it will calculate the
radius of gyration for the current state. You can provide a specific state
to this argument and generate the list yourself in a script.

```
from psico.querying import gyradius

from pymol import cmd

obj = "1nmr"
cmd.fetch(obj)

# for loop
for i in range(cmd.count_states(obj)):
    print(f"State {i+1}: {gyradius(obj, state=i+1)}")

# list comprehension
gy_list = [gyradius(obj, state=i+1) for i in range(cmd.count_states(obj))]
print(gy_list)
```

Hope that helps,
Jarrett J


On Thu, May 18, 2023 at 8:05 AM #JESSICA LIM JIAYING# via PyMOL-users <
pym...@li...> wrote:

> Hi all,
>
> I am having difficulty in trying to print out a list of the radius of
> gyration for all states in my PDB file. I have several files of 100 states
> each and would like to generate a list of the radius of gyration for every
> individual state. However, I have only been successful at using the command *gyradius
> *as part of the psico package in PyMOL but it only outputs a single
> value, and I would have to click manually to the next state and re-enter
> the command to get the next value. Hence, I would like to be able to obtain
> a list of values without having to click through 100 different states.
>
> Any advice or suggestions on how this can be done will be greatly
> appreciated, thank you!
>
> Kind regards,
> Jessica Lim
> _______________________________________________
> 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

[PyMOL] Generating of Rg for every state in PyMOL

[#JESSICA L. J. <JESSICAJ002@e.ntu.edu.sg>]

Hi all,

I am having difficulty in trying to print out a list of the radius of gyration for all states in my PDB file. I have several files of 100 states each and would like to generate a list of the radius of gyration for every individual state. However, I have only been successful at using the command gyradius as part of the psico package in PyMOL but it only outputs a single value, and I would have to click manually to the next state and re-enter the command to get the next value. Hence, I would like to be able to obtain a list of values without having to click through 100 different states.

Any advice or suggestions on how this can be done will be greatly appreciated, thank you!

Kind regards,
Jessica Lim

Re: [PyMOL] save format for molecule files

[Thomas H. <th...@th...>]

Hi Xavier,

The best option to transfer bond orders from PyMOL to Maestro might be
with .mol2 (or .sdf) format. These formats can store aromatic bond
orders and Maestro will convert that to meaningful double/single bonds
when loading the file.

- .pdb format can't store aromatic bonds (and double bonds only with
an unofficial trick)
- .mae format can't store aromatic bonds
- Maestro doesn't have aromatic bond orders
- PyMOL has limited capabilities for detecting bond orders and can't
convert aromatic bonds to single/double bonds (kekulization)
- .sdf format doesn't have protein and residue level information, but .mol2 does

Cheers,
  Thomas

On Wed, May 17, 2023 at 4:51 PM Xavier Fradera <xav...@gm...> wrote:
>
> Hi,
>
> I'm trying to save some molecule files (protein+ligand complex) from pymol to a format that is readable by maestro. I've tried saving in .mae or .pdb format, but bond orders in ligands are lost (all bonds are single). I've played with the "PDB options" in the save command and managed to get double bonds right, but the aromatic ones are ignored.
>
> Does anyone know how to write files that can be read properly by maestro?
>
> Alternatively, is there a way to convert aromatic bonds into alternating single/double bonds, as I think this would be easier to output based on my tests?
>
> thanks,
> Xavier
>
> --
> Xavier Fradera
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Generate electrostatics by Python command

[Thomas H. <th...@th...>]

Hi Petro,

This should work (example with PDB 1ubq):

from pmg_tk.startup.apbs_gui.creating import pdb2pqr_cli
from pmg_tk.startup.apbs_gui.electrostatics import map_new_apbs
cmd.fetch("1ubq")
pdb2pqr_cli("prepared01", "1ubq", options=["--ff", "amber"])
map_new_apbs("apbs_map01", "prepared01")
cmd.ramp_new("apbs_ramp01", "apbs_map01", [-5, 0, 5])
cmd.set("surface_ramp_above_mode", 1, "prepared01")
cmd.set("surface_color", "apbs_ramp01", "prepared01")
cmd.show("surface", "prepared01")

Tested with Incentive PyMOL 2.5.2 on Linux.

Cheers,
  Thomas

On Wed, May 17, 2023 at 4:51 PM Petro <sub...@kh...> wrote:
>
> Hi.
> How can I generate electrostatics using Python API?
> Thanks.
> Petro.
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Disable cartoon representation on load

[Thomas H. <th...@th...>]

Hi Petro,

Put this line in your pymolrc file (File > Edit pymolrc):

set auto_show_classified, 0

See also:
https://pymolwiki.org/index.php/pymolrc
https://pymolwiki.org/index.php/auto_show_classified
https://sourceforge.net/p/pymol/mailman/message/36155392/

Cheers,
  Thomas

On Wed, May 17, 2023 at 4:51 PM Khoroshyy Petro <kho...@gm...> wrote:
>
> Hi.
> How can I force pymol to show things in lines, not in cartoons, by default?
> Thanks.
> Petro.
>
>
> --
> ______________________________
> Petro Khoroshyy
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> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Surface and cartoon transparency together?

[Thomas H. <th...@th...>]

Hi Petro,

Try "Setting > Transparency > Multi-Layer" or "Multi-Layer (Real-time OIT)"

See also:
https://pymolwiki.org/index.php/transparency_mode

Cheers,
  Thomas

On Wed, May 17, 2023 at 4:51 PM Petro <sub...@kh...> wrote:
>
> HI., I have tried to use surface and cartoon transparency together but then I can see only the surface. Cartoon disappears completely. Any trick to get it working? Thanks,
> Petro
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
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Re: [PyMOL] save format for molecule files

[Joel T. <joe...@ot...>]

Have you tried .mol2 files. I would expect Maestro to recognise that and it should include bond order etc

J

________________________________
Joel Tyndall, PhD
Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea               +64 3 4797293
Fax / Waeawhakaahua     +64 3 4797034
From: Xavier Fradera <xav...@gm...>
Sent: Wednesday, May 17, 2023 11:54 PM
To: pym...@li...
Subject: [PyMOL] save format for molecule files

Hi,

I'm trying to save some molecule files (protein+ligand complex) from pymol to a format that is readable by maestro. I've tried saving in .mae or .pdb format, but bond orders in ligands are lost (all bonds are single). I've played with the "PDB options" in the save command and managed to get double bonds right, but the aromatic ones are ignored.

Does anyone know how to write files that can be read properly by maestro?

Alternatively, is there a way to convert aromatic bonds into alternating single/double bonds, as I think this would be easier to output based on my tests?

thanks,
Xavier

--
Xavier Fradera