pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] intermezzo plugin for analysis of protein-ligand interactions

[Enrico M. <jms...@gm...>]

Dear Pymol Users!
I am looking for some pymol plugin for the detailed analysis of
protein-ligand interactions. I have already seen:
http://mordred.bioc.cam.ac.uk/intermezzo/
but I could not understand how I could install it ( I am using pymol
2.4 pro installed on my MACBOOK and it seems to me that the package
had been developed for the previous release).

On the site I found:

"Additionally, it will soon also be possible to install the plugin
using the "Install from PyMOLWiki" and "Install from Repository"
sections."

but eventually I could not find it in pymolWIKI.

May you suggest some other solutions which would work with my pymol version ?

Many thanks in advance
Enrico

Re: [PyMOL] pair_fit crashes Pymol 2.5.2 (incentive, OSX) ?

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

Hi James,

This is a known issue. Try disabling undo before using the command.

Best,

Jarrett Johnson

On Mon, Feb 14, 2022 at 10:37 AM James Procter (Staff) <
J.P...@du...> wrote:

> Dear pymol-users
>
> Could anyone confirm that the following test of the pair_fit command
> causes a crash in the latest Pymol incentive release (2.5.2, 21st August
> 2021) ?
>
> fetch 1uwh 1z5m
> pair_fit 1uwh//A/563-582/CA, 1z5m///193-212/CA
>
> I've found this crashes 2.5.2-incentive on OSX but works fine on 2.5.0-ce
> (via homebrew).
>
>
> Thanks in advance !
> Jim Procter.
>
> Jalview Coordinator | Barton Group | University of Dundee
> www.jalview.org | www.compbio.dundee.ac.uk
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> 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] pair_fit crashes Pymol 2.5.2 (incentive, OSX) ?

[James P. (Staff) <J.P...@du...>]

Thanks Jarret - works perfectly.
________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: 16 February 2022 18:10
To: James Procter (Staff) <J.P...@du...>
Cc: pym...@li... <pym...@li...>
Subject: Re: [PyMOL] pair_fit crashes Pymol 2.5.2 (incentive, OSX) ?




CAUTION: This email originated from outside the University of Dundee. Do not click links or open attachments unless you recognise the sender's email address and know the content is safe.

Hi James,

This is a known issue. Try disabling undo before using the command.

Best,

Jarrett Johnson

On Mon, Feb 14, 2022 at 10:37 AM James Procter (Staff) <J.P...@du...<mailto:J.P...@du...>> wrote:
Dear pymol-users

Could anyone confirm that the following test of the pair_fit command causes a crash in the latest Pymol incentive release (2.5.2, 21st August 2021) ?

fetch 1uwh 1z5m
pair_fit 1uwh//A/563-582/CA, 1z5m///193-212/CA

I've found this crashes 2.5.2-incentive on OSX but works fine on 2.5.0-ce (via homebrew).


Thanks in advance !
Jim Procter.

Jalview Coordinator | Barton Group | University of Dundee
www.jalview.org<http://www.jalview.org> | www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>

The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
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Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


--

Jarrett Johnson | Senior Developer, PyMOL

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

The University of Dundee is a registered Scottish Charity, No: SC015096

Re: [PyMOL] CGO object code structure

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

Quick follow-up: I just learned from Jarrett Johnson that it is possible to
add alpha to CGO objects on a per-shape basis.  Just prepend `[cgo.ALPHA,
0.5]` (substituting your desired alpha value, of course) before the CONE
(or other) shape.  This alpha value will be used for all subsequent shapes
until you set another `cgo.ALPHA` value by the same method.

Hope that helps.

Cheers,
Jared

On Mon, Feb 14, 2022 at 10:04 AM Jared Sampson <jar...@co...>
wrote:

> Hi Marcelo -
>
> No I don't believe so.  In PyMOL, a CGO `CONE` is a fixed-length list of
> floats.  You can see in the cgo.py source
> <https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/cgo.py#L65> that
> `cgo.CONE` itself is actually a float, too (specifically, 27.0).  My
> understanding is that under-the-hood the parser is doing something like:
>
> 1. Look at the list of floats passed to `cmd.load_cgo()` and read the
> first one as an instruction;
> 2. Determine how many more values to expect from that instruction (e.g.
> for `CONE` it would expect 16 additional floats);
> 3. Read those values and use them to create the geometry;
> 4. If there are any values left in the list, treat the next float as a
> completely separate instruction, and repeat this process until there are no
> values left.
>
> In order to add alpha to a color channel (which I'm not even sure is
> compatible with the way PyMOL handles colors—though I'd leave that question
> to one of the developers), one would have to add an additional instruction
> keyword in cgo.py with a different expected set length of float arguments,
> then implement how to translate that instruction into geometry in the
> underlying C++.
>
> Of course if that's something you're really interested in doing, you could
> certainly take a crack at implementing it in Open Source PyMOL and submit a
> pull request.  :)
>
> Hope that helps.
>
> Cheers,
> Jared
>
> On Sun, Feb 13, 2022 at 9:49 PM Marcelo Depólo Polêto <
> mar...@gm...> wrote:
>
>> Thank you Jared,
>>
>> Yes, I have been using *set cgo_transparency*, but is there a way of
>> embedding alpha in the CONE object definition? Since I have been using
>> color1='blue' and color2='red', can I just append an alpha float to the
>> color lists?
>>
>> Best regards,
>> --
>> Marcelo
>>
>> Em dom., 13 de fev. de 2022 às 21:42, Jared Sampson <
>> jar...@co...> escreveu:
>>
>>> I forgot to add that the transparency can be handled by e.g.
>>>
>>>     set cgo_transparency, 0.5, my_cgo_object
>>>
>>> Cheers,
>>> Jared
>>>
>>> On Sun, Feb 13, 2022 at 9:38 PM Jared Sampson <
>>> jar...@co...> wrote:
>>>
>>>> Hi Marcelo -
>>>>
>>>> Looks like you have the right format for `CONE`.  This should really be
>>>> in the Wiki...and apparently is not.  I've just made a couple of pages,
>>>> others can of course feel free to elaborate:
>>>>
>>>> https://pymolwiki.org/index.php/CGO_Shapes
>>>> https://pymolwiki.org/index.php/Load_CGO
>>>>
>>>> You may also find it useful to look at the Open Source PyMOL source
>>>> code, perhaps starting with:
>>>>
>>>> https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/cgo.py
>>>>
>>>> Hope that helps.
>>>>
>>>> Cheers,
>>>> Jared
>>>>
>>>>
>>>> On Sat, Feb 12, 2022 at 10:51 PM Marcelo Depólo Polêto <
>>>> mar...@gm...> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I am building a CGO object of a cone and I want to embed a
>>>>> transparency value to it. So far I managed to create the cone with the line
>>>>> below:
>>>>>
>>>>> *obj = [cgo.CONE] + begin + end + [radius_begin, radius_end] + color1
>>>>> + color2 + [1.0, 1.0]*
>>>>>
>>>>> Could someone provide more information on how the CGO objects are
>>>>> structured (which values are expected and their formats)?
>>>>>
>>>>> Best regards,
>>>>> --
>>>>> *Marcelo Depólo Polêto, Ph.D.*
>>>>> Postdoctoral Associate
>>>>> Office: 106B Engel Hall
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> 340 West Campus Dr.
>>>>> Blacksburg, VA 24061
>>>>> gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>:
>>>>> he/him/his
>>>>> _______________________________________________
>>>>> PyMOL-users mailing list
>>>>> Archives:
>>>>> http://www.mail-archive.com/pym...@li...
>>>>> Unsubscribe:
>>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>>
>>>>
>>
>> --
>> --
>> *Marcelo Depólo Polêto, Ph.D.*
>> Postdoctoral Associate
>> Office: 106B Engel Hall
>> Department of Biochemistry
>> Virginia Tech
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>:
>> he/him/his
>>
>

Re: [PyMOL] Installing in Linux

[Robert C. <rob...@qu...>]

Hello Peter,

Which Linux distribution are you using?  If you are using one of the Debian-based versions like Ubuntu, then PyMOL is likely available in the distribution's repository.  Then you could use the package management system to install it or simply type in a terminal window:

  sudo apt-get install pymol

Depending on which distribution you are using there may be other steps involved to allow it to find PyMOL.

Cheers,
Rob

On Mon, 2022-02-14 13:05  -0500,  Peter Kahn <pk...@se...> wrote:

> Greetings,
> 
> I've downloaded the Pymol package of executable files and had no
> trouble installing in Windows but don't know how to proceed in Linux?
>  Can anyone point me in the right direction?
> 
> Thanks,
> Peter



-- 
Robert L. Campbell, Ph.D.
Undergraduate Chair (Acting), Biochemistry Program
Academic Advisor, BHSc Program
Assistant Professor, Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
tel: 613-533-6821   http://pldserver1.biochem.queensu.ca/~rlc

[PyMOL] Align with Axis and Rewrite Coordinates

[Reed, C. (creed) <cr...@br...>]

Is there a way to open a crystal structure and realign the structure with an axis, then save the transformed coordinates?  I want all atoms to remain in the same position with respect to each other...just not with respect to the crystallographically defined x, y, z.  I have tried alter_state command with rebuild....but I only seem to be able to find commands that translate along the x, y, z.

Thanks,

Carly R. Reed
Associate Professor and Advisement Coordinator
SUNY Brockport
Department of Chemistry and Biochemistry
(585)395-5588 (office)
(330)575-6754 (cell)

[PyMOL] Installing in Linux

[Peter K. <pk...@se...>]

Greetings,

I've downloaded the Pymol package of executable files and had no trouble 
installing in Windows but don't know how to proceed in Linux?  Can 
anyone point me in the right direction?

Thanks,
Peter
-- 
Peter C. Kahn, Ph.D.
Professor of Biochemistry
Department of Biochemistry & Microbiology
Rutgers University
76 Lipman Drive
New Brunswick, NJ 08901

Telephone: 848-932-5618
Telefax:   732-932-8965
Email: pet...@ru...

[PyMOL] pair_fit crashes Pymol 2.5.2 (incentive, OSX) ?

[James P. (Staff) <J.P...@du...>]

Dear pymol-users

Could anyone confirm that the following test of the pair_fit command causes a crash in the latest Pymol incentive release (2.5.2, 21st August 2021) ?

fetch 1uwh 1z5m
pair_fit 1uwh//A/563-582/CA, 1z5m///193-212/CA

I've found this crashes 2.5.2-incentive on OSX but works fine on 2.5.0-ce (via homebrew).


Thanks in advance !
Jim Procter.

Jalview Coordinator | Barton Group | University of Dundee
www.jalview.org<http://www.jalview.org> | www.compbio.dundee.ac.uk

The University of Dundee is a registered Scottish Charity, No: SC015096

Re: [PyMOL] CGO object code structure

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

Hi Marcelo -

No I don't believe so.  In PyMOL, a CGO `CONE` is a fixed-length list of
floats.  You can see in the cgo.py source
<https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/cgo.py#L65>
that
`cgo.CONE` itself is actually a float, too (specifically, 27.0).  My
understanding is that under-the-hood the parser is doing something like:

1. Look at the list of floats passed to `cmd.load_cgo()` and read the first
one as an instruction;
2. Determine how many more values to expect from that instruction (e.g. for
`CONE` it would expect 16 additional floats);
3. Read those values and use them to create the geometry;
4. If there are any values left in the list, treat the next float as a
completely separate instruction, and repeat this process until there are no
values left.

In order to add alpha to a color channel (which I'm not even sure is
compatible with the way PyMOL handles colors—though I'd leave that question
to one of the developers), one would have to add an additional instruction
keyword in cgo.py with a different expected set length of float arguments,
then implement how to translate that instruction into geometry in the
underlying C++.

Of course if that's something you're really interested in doing, you could
certainly take a crack at implementing it in Open Source PyMOL and submit a
pull request.  :)

Hope that helps.

Cheers,
Jared

On Sun, Feb 13, 2022 at 9:49 PM Marcelo Depólo Polêto <
mar...@gm...> wrote:

> Thank you Jared,
>
> Yes, I have been using *set cgo_transparency*, but is there a way of
> embedding alpha in the CONE object definition? Since I have been using
> color1='blue' and color2='red', can I just append an alpha float to the
> color lists?
>
> Best regards,
> --
> Marcelo
>
> Em dom., 13 de fev. de 2022 às 21:42, Jared Sampson <
> jar...@co...> escreveu:
>
>> I forgot to add that the transparency can be handled by e.g.
>>
>>     set cgo_transparency, 0.5, my_cgo_object
>>
>> Cheers,
>> Jared
>>
>> On Sun, Feb 13, 2022 at 9:38 PM Jared Sampson <jar...@co...>
>> wrote:
>>
>>> Hi Marcelo -
>>>
>>> Looks like you have the right format for `CONE`.  This should really be
>>> in the Wiki...and apparently is not.  I've just made a couple of pages,
>>> others can of course feel free to elaborate:
>>>
>>> https://pymolwiki.org/index.php/CGO_Shapes
>>> https://pymolwiki.org/index.php/Load_CGO
>>>
>>> You may also find it useful to look at the Open Source PyMOL source
>>> code, perhaps starting with:
>>>
>>> https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/cgo.py
>>>
>>> Hope that helps.
>>>
>>> Cheers,
>>> Jared
>>>
>>>
>>> On Sat, Feb 12, 2022 at 10:51 PM Marcelo Depólo Polêto <
>>> mar...@gm...> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I am building a CGO object of a cone and I want to embed a transparency
>>>> value to it. So far I managed to create the cone with the line below:
>>>>
>>>> *obj = [cgo.CONE] + begin + end + [radius_begin, radius_end] + color1 +
>>>> color2 + [1.0, 1.0]*
>>>>
>>>> Could someone provide more information on how the CGO objects are
>>>> structured (which values are expected and their formats)?
>>>>
>>>> Best regards,
>>>> --
>>>> *Marcelo Depólo Polêto, Ph.D.*
>>>> Postdoctoral Associate
>>>> Office: 106B Engel Hall
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>> gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>:
>>>> he/him/his
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>> Unsubscribe:
>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>
>>>
>
> --
> --
> *Marcelo Depólo Polêto, Ph.D.*
> Postdoctoral Associate
> Office: 106B Engel Hall
> Department of Biochemistry
> Virginia Tech
> 340 West Campus Dr.
> Blacksburg, VA 24061
> gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>:
> he/him/his
>

Re: [PyMOL] CGO object code structure

[Marcelo D. P. <mar...@gm...>]

Thank you Jared,

Yes, I have been using *set cgo_transparency*, but is there a way of
embedding alpha in the CONE object definition? Since I have been using
color1='blue' and color2='red', can I just append an alpha float to the
color lists?

Best regards,
--
Marcelo

Em dom., 13 de fev. de 2022 às 21:42, Jared Sampson <
jar...@co...> escreveu:

> I forgot to add that the transparency can be handled by e.g.
>
>     set cgo_transparency, 0.5, my_cgo_object
>
> Cheers,
> Jared
>
> On Sun, Feb 13, 2022 at 9:38 PM Jared Sampson <jar...@co...>
> wrote:
>
>> Hi Marcelo -
>>
>> Looks like you have the right format for `CONE`.  This should really be
>> in the Wiki...and apparently is not.  I've just made a couple of pages,
>> others can of course feel free to elaborate:
>>
>> https://pymolwiki.org/index.php/CGO_Shapes
>> https://pymolwiki.org/index.php/Load_CGO
>>
>> You may also find it useful to look at the Open Source PyMOL source code,
>> perhaps starting with:
>>
>> https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/cgo.py
>>
>> Hope that helps.
>>
>> Cheers,
>> Jared
>>
>>
>> On Sat, Feb 12, 2022 at 10:51 PM Marcelo Depólo Polêto <
>> mar...@gm...> wrote:
>>
>>> Hi all,
>>>
>>> I am building a CGO object of a cone and I want to embed a transparency
>>> value to it. So far I managed to create the cone with the line below:
>>>
>>> *obj = [cgo.CONE] + begin + end + [radius_begin, radius_end] + color1 +
>>> color2 + [1.0, 1.0]*
>>>
>>> Could someone provide more information on how the CGO objects are
>>> structured (which values are expected and their formats)?
>>>
>>> Best regards,
>>> --
>>> *Marcelo Depólo Polêto, Ph.D.*
>>> Postdoctoral Associate
>>> Office: 106B Engel Hall
>>> Department of Biochemistry
>>> Virginia Tech
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>> gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>:
>>> he/him/his
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>

-- 
--
*Marcelo Depólo Polêto, Ph.D.*
Postdoctoral Associate
Office: 106B Engel Hall
Department of Biochemistry
Virginia Tech
340 West Campus Dr.
Blacksburg, VA 24061
gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>:
he/him/his

Re: [PyMOL] CGO object code structure

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

I forgot to add that the transparency can be handled by e.g.

    set cgo_transparency, 0.5, my_cgo_object

Cheers,
Jared

On Sun, Feb 13, 2022 at 9:38 PM Jared Sampson <jar...@co...>
wrote:

> Hi Marcelo -
>
> Looks like you have the right format for `CONE`.  This should really be in
> the Wiki...and apparently is not.  I've just made a couple of pages, others
> can of course feel free to elaborate:
>
> https://pymolwiki.org/index.php/CGO_Shapes
> https://pymolwiki.org/index.php/Load_CGO
>
> You may also find it useful to look at the Open Source PyMOL source code,
> perhaps starting with:
>
> https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/cgo.py
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Sat, Feb 12, 2022 at 10:51 PM Marcelo Depólo Polêto <
> mar...@gm...> wrote:
>
>> Hi all,
>>
>> I am building a CGO object of a cone and I want to embed a transparency
>> value to it. So far I managed to create the cone with the line below:
>>
>> *obj = [cgo.CONE] + begin + end + [radius_begin, radius_end] + color1 +
>> color2 + [1.0, 1.0]*
>>
>> Could someone provide more information on how the CGO objects are
>> structured (which values are expected and their formats)?
>>
>> Best regards,
>> --
>> *Marcelo Depólo Polêto, Ph.D.*
>> Postdoctoral Associate
>> Office: 106B Engel Hall
>> Department of Biochemistry
>> Virginia Tech
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>:
>> he/him/his
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] CGO object code structure

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

Hi Marcelo -

Looks like you have the right format for `CONE`.  This should really be in
the Wiki...and apparently is not.  I've just made a couple of pages, others
can of course feel free to elaborate:

https://pymolwiki.org/index.php/CGO_Shapes
https://pymolwiki.org/index.php/Load_CGO

You may also find it useful to look at the Open Source PyMOL source code,
perhaps starting with:
https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/cgo.py

Hope that helps.

Cheers,
Jared


On Sat, Feb 12, 2022 at 10:51 PM Marcelo Depólo Polêto <
mar...@gm...> wrote:

> Hi all,
>
> I am building a CGO object of a cone and I want to embed a transparency
> value to it. So far I managed to create the cone with the line below:
>
> *obj = [cgo.CONE] + begin + end + [radius_begin, radius_end] + color1 +
> color2 + [1.0, 1.0]*
>
> Could someone provide more information on how the CGO objects are
> structured (which values are expected and their formats)?
>
> Best regards,
> --
> *Marcelo Depólo Polêto, Ph.D.*
> Postdoctoral Associate
> Office: 106B Engel Hall
> Department of Biochemistry
> Virginia Tech
> 340 West Campus Dr.
> Blacksburg, VA 24061
> gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>:
> he/him/his
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] CGO object code structure

[Marcelo D. P. <mar...@gm...>]

Hi all,

I am building a CGO object of a cone and I want to embed a transparency
value to it. So far I managed to create the cone with the line below:

*obj = [cgo.CONE] + begin + end + [radius_begin, radius_end] + color1 +
color2 + [1.0, 1.0]*

Could someone provide more information on how the CGO objects are
structured (which values are expected and their formats)?

Best regards,
--
*Marcelo Depólo Polêto, Ph.D.*
Postdoctoral Associate
Office: 106B Engel Hall
Department of Biochemistry
Virginia Tech
340 West Campus Dr.
Blacksburg, VA 24061
gender pronouns <https://ccc.vt.edu/resources/Gender_Pronouns.html>:
he/him/his

Re: [PyMOL] Opening a .pse file causes GUI corruption.

[Mark S. <sa...@um...>]

Followup to previous posting:

Adding
	set use_shaders, 1
Fixed the problem.

Thanks,
Mark

         
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> On Feb 9, 2022, at 1:09 PM, Mark Saper <sa...@um...> wrote:
> 
> Followup to original posting.
> 
> The problem I described is when running on the MacBook Pro display.  If I connect an external monitor, and open the .pse file by double-clicking, the GUI is not affected.
> 
> Thanks,
> Mark
> 

[PyMOL] Opening a .pse file causes GUI corruption.

[Mark S. <sa...@um...>]

Dear Developers,

I am running Pymol 2.5.2 on MacOS X 12.2 and have noticed a problem that never existed with 10.14.  I save a .pse file from a recent session.  If I open the .pse by double-clicking it, then PyMOL opens, shows the model, but the GUI (right menu), and scene labels (bottom left) have small, and distorted text.  If I start an empty PyMOL session, and then open the .pse with the File>Open… command, the GUI is intact.  It would be very helpful, if this bug could be addressed and fixed in the next version.

I can screen-shots on request!

Many thanks,
Mark


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Re: [PyMOL] Opening a .pse file causes GUI corruption.

[Mark S. <sa...@um...>]

Followup to original posting.

The problem I described is when running on the MacBook Pro display.  If I connect an external monitor, and open the .pse file by double-clicking, the GUI is not affected.

Thanks,
Mark

[PyMOL] ccp4.tar.gz

[sunyeping <sun...@al...>]

[PyMOL] missing object control menu for new installation

[Yufeng T. <yuf...@gm...>]

HI there,

I am installing PyMOL on a virtual machine with Windows 10 Enterprise
and tried a few different versions of PyMOL, for all of them I have
the same problem of missing the "Object Control" menu in the GUI.
Attached is a screen copy of the display. I have tried the following:
1. PyMOL 2.5 for Windows Exe Installer from https://pymol.org/2/#download
2. Install Python 3.9 and install the Open Source PyMOL from Gohlke's whl file.
3. Installed Conda and install PyMOL from inside Conda following
pymol.org instruction.

In all three cases, the program can be installed and launched, but all
are missing the "Object Control" menu.

Any hint?

Yufeng

Re: [PyMOL] How to label atom at proper positions?

[sunyeping <sun...@al...>]

Hello professor,
Now I have a new question: how to label the selected CA atoms with strings representing mutations, like "T123D", "K339R", etc?
I tried to use these commands:
  select CAs, resi 123+339
  mut = ["T123D", "K139R", "G223S", "M321S"]
  label CAs, mut.pop
but I found that the labels are put in the wrong positions. So what is the correct way the show the labels for mutations?

Best regards 
------------------------------------------------------------------
From:Halil İbrahim Özdemir <ozd...@gm...>
Send Time:2022年1月19日(星期三) 14:05
To:孙业平 <sun...@al...>
Subject:Re: [PyMOL] How to label atom at proper positions?

You can modify the previous script like this,

# ONE LETTER CODES
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',    \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',    \
'GLY':'G', 'PRO':'P', 'CYS':'C'}

# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA

# Give Label Them as (Residue Name+Residue Number)
label CAs, "%s%s" % (one_letter[resn],resi)

# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs

Regards,

sunyeping <sun...@al...>, 19 Oca 2022 Çar, 06:43 tarihinde şunu yazdı:
Dear Professor Halil İbrahim Özdemir,

Thank you for your help. The labels shown now are fomatted as "(THR339)", "(SER308)", etc.
I wonder how to show them as single-letter codes plus the numbers without the parentheses, like "T339", "S308".
Thank you again.

Best,
------------------------------------------------------------------
From:Halil İbrahim Özdemir <ozd...@gm...>
Send Time:2022年1月18日(星期二) 18:50
To:孙业平 <sun...@al...>
Subject:Re: [PyMOL] How to label atom at proper positions?

Hi  Sunyeping,

You can easily apply the following script from PyMOL terminal. Have a nice days.

# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA

# Give Label Them as (Residue Name+Residue Number)
label CAs, "(%s%s)" % (resn, resi)

# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs

Regards,



sunyeping via PyMOL-users <pym...@li...>, 18 Oca 2022 Sal, 13:14 tarihinde şunu yazdı:
Dear pymol users,

I select a series of CA atoms in a structure in pymol and show them as sphere in pymol and want to label them. If using the label menu at the up-right conner of pymol, the labels shown overlaps with spheres and can not be seen. So I wish to show the labels at a bit distance from the seleccted atoms. Is there a method to do that? I will appreciate to any help! 

Best regards
 _______________________________________________
 PyMOL-users mailing list
 Archives: http://www.mail-archive.com/pym...@li...
 Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] visualisations of the hydrogen bonds using preset.ligand_cartoon

[Enrico M. <jms...@gm...>]

Dear Pymol Users!
I wonder to ask regarding the algorithm implemented in pymol for the
calculation of the hydrogen bonds between ligand and protein using
preset.ligand_cartoon demonstrating the interactions?
I've just compared predicted hydrogen bonds for the same complex that
I could observe with Chim*ra and found that there were differences:
pymol tends to predict more hydrogen bonds considering additional
interactions located on the longer distances. Are there some built-in
commands in pymol that would allow me to modulate geometrical criteria
(cut-offs?) for the hydrogen bonds search assuming that I am operating
with multi-model pdb (results of docking) using command:
preset.ligand_cartoon('my_pdb*',_self=cmd)
Many thanks in advance
Cheers
Enrico

Re: [PyMOL] distance-based selection of the side-chains

[Enrico M. <jms...@gm...>]

You are right, thank you!
Cheers,
Enrico

чт, 27 янв. 2022 г. в 13:32, Ali Saad Kusay <aku...@un...>:
>
> Hi Enrico,
>
> I think it's because you are selecting side chains, glycine has no sidechain and alanine has single carbon atom side chain so this representation won't work for it. You would need to remove the sidechains from the selection to make it apply to the backbone atoms, i.e. cmd.select('rep lines and poly)
>
> Cheers,
>
> Ali
>
> On 27/1/22, 11:22 pm, "Enrico Martinez" <jms...@gm...> wrote:
>
>     additional question in the same field:
>     as I've mentioned before, before applying distance-based filtering, I
>     would like to change the representation of the lines to ball-and-stick
>     for the residues involved in the interactions:
>     cmd.select('rep lines and sidechain')
>     cmd.show_as('sticks', 'sele')
>     cmd.set('stick_radius', '0.10')
>     cmd.set('stick_ball', 'on')
>     cmd.set('stick_ball_ratio', '2.2')
>
>     I've just noticed that some residues remain their "line"
>     representation, notably for hydrophobic (Gly, Ala) residues. How could
>     it be fixed ?
>
>     чт, 27 янв. 2022 г. в 12:38, Enrico Martinez <jms...@gm...>:
>     >
>     > Thank you very much, Ali!!
>     > Cheers,
>     > Enrico
>     >
>     > чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay <aku...@un...>:
>     > >
>     > > Hi Enrico,
>     > >
>     > > You need to use the byres or br. Selection (https://protect-au.mimecast.com/s/4MzUCROND2uvY6pqpi9A9Zw?domain=pymolwiki.org)
>     > >
>     > > I.e:
>     > > cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
>     > >
>     > > Also, consider hiding all protein residues and showing only the ones near the protein, i.e.:
>     > > cmd.show('sticks','br. poly within 4 of resn XXX')
>     > > ^ Where 4 is the distance and XXX should be substituted with the residue name of the ligand
>     > >
>     > > Cheers,
>     > >
>     > > Ali
>     > >
>     > > On 27/1/22, 10:12 pm, "Enrico Martinez" <jms...@gm...> wrote:
>     > >
>     > >     Dear Pymol Users!
>     > >     I am working on the visualization of the protein-ligand contacts
>     > >     identified using
>     > >     preset.ligand_cartoon('pdb',_self=cmd)
>     > >     Since the command also displays some residues, which are not involved
>     > >     in the interactions (with the radicals located too far away) with the
>     > >     ligand, I need to filter the displayed side-chains focusing only on
>     > >     the important interactions. I am using a distance-based criterion for
>     > >     the selection of the residues which I am going to hide.
>     > >
>     > >     this is what I've already tried:
>     > >
>     > >     # display visible side chains as the sticks
>     > >     cmd.select('rep lines and visible and sidechain')
>     > >     cmd.show('sticks', 'sele')
>     > >     # select all visible sticks of the sidechains far away from the ligand
>     > >     cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
>     > >     cmd.hide('everything', 'sele')
>     > >
>     > >     the problem is that the "select" command with such syntax, always
>     > >     selects the ATOMS, but not the whole side-chains. Is it possible to
>     > >     hide the whole side-chain using such syntax as well as it's displayed
>     > >     label?
>     > >     Many thanks in advance!
>     > >     Enrico
>     > >
>     > >
>     > >     _______________________________________________
>     > >     PyMOL-users mailing list
>     > >     Archives: https://protect-au.mimecast.com/s/_G8ICVARKgCxBJEoESz5b82?domain=mail-archive.com
>     > >     Unsubscribe: https://protect-au.mimecast.com/s/LPL4CWLVXkU53EQmQIKfUJc?domain=sourceforge.net
>     > >
>     > >
>
>

Re: [PyMOL] distance-based selection of the side-chains

[Ali S. K. <aku...@un...>]

Hi Enrico, 

I think it's because you are selecting side chains, glycine has no sidechain and alanine has single carbon atom side chain so this representation won't work for it. You would need to remove the sidechains from the selection to make it apply to the backbone atoms, i.e. cmd.select('rep lines and poly)

Cheers, 

Ali

On 27/1/22, 11:22 pm, "Enrico Martinez" <jms...@gm...> wrote:

    additional question in the same field:
    as I've mentioned before, before applying distance-based filtering, I
    would like to change the representation of the lines to ball-and-stick
    for the residues involved in the interactions:
    cmd.select('rep lines and sidechain')
    cmd.show_as('sticks', 'sele')
    cmd.set('stick_radius', '0.10')
    cmd.set('stick_ball', 'on')
    cmd.set('stick_ball_ratio', '2.2')

    I've just noticed that some residues remain their "line"
    representation, notably for hydrophobic (Gly, Ala) residues. How could
    it be fixed ?

    чт, 27 янв. 2022 г. в 12:38, Enrico Martinez <jms...@gm...>:
    >
    > Thank you very much, Ali!!
    > Cheers,
    > Enrico
    >
    > чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay <aku...@un...>:
    > >
    > > Hi Enrico,
    > >
    > > You need to use the byres or br. Selection (https://protect-au.mimecast.com/s/4MzUCROND2uvY6pqpi9A9Zw?domain=pymolwiki.org)
    > >
    > > I.e:
    > > cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
    > >
    > > Also, consider hiding all protein residues and showing only the ones near the protein, i.e.:
    > > cmd.show('sticks','br. poly within 4 of resn XXX')
    > > ^ Where 4 is the distance and XXX should be substituted with the residue name of the ligand
    > >
    > > Cheers,
    > >
    > > Ali
    > >
    > > On 27/1/22, 10:12 pm, "Enrico Martinez" <jms...@gm...> wrote:
    > >
    > >     Dear Pymol Users!
    > >     I am working on the visualization of the protein-ligand contacts
    > >     identified using
    > >     preset.ligand_cartoon('pdb',_self=cmd)
    > >     Since the command also displays some residues, which are not involved
    > >     in the interactions (with the radicals located too far away) with the
    > >     ligand, I need to filter the displayed side-chains focusing only on
    > >     the important interactions. I am using a distance-based criterion for
    > >     the selection of the residues which I am going to hide.
    > >
    > >     this is what I've already tried:
    > >
    > >     # display visible side chains as the sticks
    > >     cmd.select('rep lines and visible and sidechain')
    > >     cmd.show('sticks', 'sele')
    > >     # select all visible sticks of the sidechains far away from the ligand
    > >     cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
    > >     cmd.hide('everything', 'sele')
    > >
    > >     the problem is that the "select" command with such syntax, always
    > >     selects the ATOMS, but not the whole side-chains. Is it possible to
    > >     hide the whole side-chain using such syntax as well as it's displayed
    > >     label?
    > >     Many thanks in advance!
    > >     Enrico
    > >
    > >
    > >     _______________________________________________
    > >     PyMOL-users mailing list
    > >     Archives: https://protect-au.mimecast.com/s/_G8ICVARKgCxBJEoESz5b82?domain=mail-archive.com
    > >     Unsubscribe: https://protect-au.mimecast.com/s/LPL4CWLVXkU53EQmQIKfUJc?domain=sourceforge.net
    > >
    > >

Re: [PyMOL] distance-based selection of the side-chains

[Enrico M. <jms...@gm...>]

additional question in the same field:
as I've mentioned before, before applying distance-based filtering, I
would like to change the representation of the lines to ball-and-stick
for the residues involved in the interactions:
cmd.select('rep lines and sidechain')
cmd.show_as('sticks', 'sele')
cmd.set('stick_radius', '0.10')
cmd.set('stick_ball', 'on')
cmd.set('stick_ball_ratio', '2.2')

I've just noticed that some residues remain their "line"
representation, notably for hydrophobic (Gly, Ala) residues. How could
it be fixed ?

чт, 27 янв. 2022 г. в 12:38, Enrico Martinez <jms...@gm...>:
>
> Thank you very much, Ali!!
> Cheers,
> Enrico
>
> чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay <aku...@un...>:
> >
> > Hi Enrico,
> >
> > You need to use the byres or br. Selection (https://pymolwiki.org/index.php/Selection_Algebra)
> >
> > I.e:
> > cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
> >
> > Also, consider hiding all protein residues and showing only the ones near the protein, i.e.:
> > cmd.show('sticks','br. poly within 4 of resn XXX')
> > ^ Where 4 is the distance and XXX should be substituted with the residue name of the ligand
> >
> > Cheers,
> >
> > Ali
> >
> > On 27/1/22, 10:12 pm, "Enrico Martinez" <jms...@gm...> wrote:
> >
> >     Dear Pymol Users!
> >     I am working on the visualization of the protein-ligand contacts
> >     identified using
> >     preset.ligand_cartoon('pdb',_self=cmd)
> >     Since the command also displays some residues, which are not involved
> >     in the interactions (with the radicals located too far away) with the
> >     ligand, I need to filter the displayed side-chains focusing only on
> >     the important interactions. I am using a distance-based criterion for
> >     the selection of the residues which I am going to hide.
> >
> >     this is what I've already tried:
> >
> >     # display visible side chains as the sticks
> >     cmd.select('rep lines and visible and sidechain')
> >     cmd.show('sticks', 'sele')
> >     # select all visible sticks of the sidechains far away from the ligand
> >     cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
> >     cmd.hide('everything', 'sele')
> >
> >     the problem is that the "select" command with such syntax, always
> >     selects the ATOMS, but not the whole side-chains. Is it possible to
> >     hide the whole side-chain using such syntax as well as it's displayed
> >     label?
> >     Many thanks in advance!
> >     Enrico
> >
> >
> >     _______________________________________________
> >     PyMOL-users mailing list
> >     Archives: https://protect-au.mimecast.com/s/utRJClx1Nji2GrWxqIGRZsc?domain=mail-archive.com
> >     Unsubscribe: https://protect-au.mimecast.com/s/XwNECmO5glujXxVzLuOSHPJ?domain=sourceforge.net
> >
> >

Re: [PyMOL] distance-based selection of the side-chains

[Enrico M. <jms...@gm...>]

Thank you very much, Ali!!
Cheers,
Enrico

чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay <aku...@un...>:
>
> Hi Enrico,
>
> You need to use the byres or br. Selection (https://pymolwiki.org/index.php/Selection_Algebra)
>
> I.e:
> cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
>
> Also, consider hiding all protein residues and showing only the ones near the protein, i.e.:
> cmd.show('sticks','br. poly within 4 of resn XXX')
> ^ Where 4 is the distance and XXX should be substituted with the residue name of the ligand
>
> Cheers,
>
> Ali
>
> On 27/1/22, 10:12 pm, "Enrico Martinez" <jms...@gm...> wrote:
>
>     Dear Pymol Users!
>     I am working on the visualization of the protein-ligand contacts
>     identified using
>     preset.ligand_cartoon('pdb',_self=cmd)
>     Since the command also displays some residues, which are not involved
>     in the interactions (with the radicals located too far away) with the
>     ligand, I need to filter the displayed side-chains focusing only on
>     the important interactions. I am using a distance-based criterion for
>     the selection of the residues which I am going to hide.
>
>     this is what I've already tried:
>
>     # display visible side chains as the sticks
>     cmd.select('rep lines and visible and sidechain')
>     cmd.show('sticks', 'sele')
>     # select all visible sticks of the sidechains far away from the ligand
>     cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
>     cmd.hide('everything', 'sele')
>
>     the problem is that the "select" command with such syntax, always
>     selects the ATOMS, but not the whole side-chains. Is it possible to
>     hide the whole side-chain using such syntax as well as it's displayed
>     label?
>     Many thanks in advance!
>     Enrico
>
>
>     _______________________________________________
>     PyMOL-users mailing list
>     Archives: https://protect-au.mimecast.com/s/utRJClx1Nji2GrWxqIGRZsc?domain=mail-archive.com
>     Unsubscribe: https://protect-au.mimecast.com/s/XwNECmO5glujXxVzLuOSHPJ?domain=sourceforge.net
>
>

Re: [PyMOL] distance-based selection of the side-chains

[Ali S. K. <aku...@un...>]

Hi Enrico, 

You need to use the byres or br. Selection (https://pymolwiki.org/index.php/Selection_Algebra)

I.e:
cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')

Also, consider hiding all protein residues and showing only the ones near the protein, i.e.:
cmd.show('sticks','br. poly within 4 of resn XXX') 
^ Where 4 is the distance and XXX should be substituted with the residue name of the ligand 

Cheers, 

Ali

On 27/1/22, 10:12 pm, "Enrico Martinez" <jms...@gm...> wrote:

    Dear Pymol Users!
    I am working on the visualization of the protein-ligand contacts
    identified using
    preset.ligand_cartoon('pdb',_self=cmd)
    Since the command also displays some residues, which are not involved
    in the interactions (with the radicals located too far away) with the
    ligand, I need to filter the displayed side-chains focusing only on
    the important interactions. I am using a distance-based criterion for
    the selection of the residues which I am going to hide.

    this is what I've already tried:

    # display visible side chains as the sticks
    cmd.select('rep lines and visible and sidechain')
    cmd.show('sticks', 'sele')
    # select all visible sticks of the sidechains far away from the ligand
    cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
    cmd.hide('everything', 'sele')

    the problem is that the "select" command with such syntax, always
    selects the ATOMS, but not the whole side-chains. Is it possible to
    hide the whole side-chain using such syntax as well as it's displayed
    label?
    Many thanks in advance!
    Enrico


    _______________________________________________
    PyMOL-users mailing list
    Archives: https://protect-au.mimecast.com/s/utRJClx1Nji2GrWxqIGRZsc?domain=mail-archive.com
    Unsubscribe: https://protect-au.mimecast.com/s/XwNECmO5glujXxVzLuOSHPJ?domain=sourceforge.net