pymol-users — Collaborative support and tips for PyMOL users

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...
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>> Unsubscribe:
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>
>
>
> --
>
> *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...__;!!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
_______________________________________________
PyMOL-users mailing list
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
> _______________________________________________
> 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...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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

Re: [PyMOL] Surface and cartoon transparency together?

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

Thanks.
I will try it.
Best regards.
Petro.


On Wed, 17 May 2023 at 19:49, Jarrett Johnson <
jar...@sc...> wrote:

> Hi Petro,
>
> You might have luck using Order Independent Transparency:
>
> `set transparency_mode, 3`
>
> Hope that helps,
> Jarrett J
>
> On Wed, May 17, 2023 at 10:50 AM 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...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

Re: [PyMOL] Surface and cartoon transparency together?

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

Hi Petro,

You might have luck using Order Independent Transparency:

`set transparency_mode, 3`

Hope that helps,
Jarrett J

On Wed, May 17, 2023 at 10:50 AM 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...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] [EXTERNAL] Generate electrostatics by Python command

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

Hi Blaine.
Thank you for your reply.
I was not clear. I meant the surface which can be generated via action ->
generate -> vacuum electrostatic -> protein contact potential (local)
Is there a way to access it via Python?

Thank you and best regards.
Petro.


On Wed, 17 May 2023 at 17:32, Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Petro,
>
> APBS is a plugin and not directly part of PyMOL.
>
> You can run apbs from the command line via subprocess in Python.
>
> https://apbs.readthedocs.io/en/latest/using/index.html
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ------------------------------
> *From:* Petro <sub...@kh...>
> *Sent:* Tuesday, May 16, 2023 2:19 PM
> *To:* pym...@li... <pym...@li...
> >
> *Subject:* [EXTERNAL] [PyMOL] Generate electrostatics by Python command
>
> Hi.
> How can I generate electrostatics using Python API?
> Thanks.
> Petro.
>

Re: [PyMOL] [EXTERNAL] Disable cartoon representation on load

[Khoroshyy P. <kho...@gm...>]

Thank you.
I will try that.
Best regards.
Petro.


On Wed, 17 May 2023 at 17:17, Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Petro,
>
> Add the following to your .pymolrc file (pymolrc.pml on Windows)
>
> cmd.do("hide cartoon")
> cmd.do("show sticks")
>
> # I also add these lines to my pymolrc
> set bg_rgb, white
> set stick_radius, 0.125
> set valence, off
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ------------------------------
> *From:* Khoroshyy Petro <kho...@gm...>
> *Sent:* Tuesday, May 16, 2023 8:00 AM
> *To:* pym...@li... <pym...@li...
> >
> *Subject:* [EXTERNAL] [PyMOL] Disable cartoon representation on load
>
> Hi.
> How can I force pymol to show things in lines, not in cartoons, by default?
> Thanks.
> Petro.
>
>
> --
> ______________________________
> Petro Khoroshyy
>

Re: [PyMOL] [EXTERNAL] Disable cartoon representation on load

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Petro,

Add the following to your .pymolrc file (pymolrc.pml on Windows)

cmd.do("hide cartoon")
cmd.do("show sticks")

# I also add these lines to my pymolrc
set bg_rgb, white
set stick_radius, 0.125
set valence, off

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________
From: Khoroshyy Petro <kho...@gm...>
Sent: Tuesday, May 16, 2023 8:00 AM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] Disable cartoon representation on load

Hi.
How can I force pymol to show things in lines, not in cartoons, by default?
Thanks.
Petro.


--
______________________________
Petro Khoroshyy

Re: [PyMOL] [EXTERNAL] Generate electrostatics by Python command

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Petro,

APBS is a plugin and not directly part of PyMOL.

You can run apbs from the command line via subprocess in Python.

https://apbs.readthedocs.io/en/latest/using/index.html

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________
From: Petro <sub...@kh...>
Sent: Tuesday, May 16, 2023 2:19 PM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] Generate electrostatics by Python command

Hi.
How can I generate electrostatics using Python API?
Thanks.
Petro.

[PyMOL] save format for molecule files

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

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