pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] About Pymol 2.3 Python Package

[Pedro L. <psl...@gm...>]

Hi,

Certainly you can use PyMOL as you want, it is open source (has few
restrictions). If you install from Ubuntu or Fedora repositories you can
use freely.

Don't worry, just share your code or session then your coworkers open as
they can. If is for your sole analysis don't worry as well.

(In fact seems that exists some proprietary version at pymol.org but I
don't know)

Em sáb, 2 de nov de 2019 20:51, halil ibrahim özdemir <
ozd...@gm...> escreveu:

> Dear Mr/Mrs,
>
>
>
> I am a fresh master's degree student in the computational biology
> department. Now working on my new standalone project about allosteric
> proteins. Actually i finished. But for visualization I used pymol2 and I
> heard that it is not free anymore. And i wrote my code in python 3. So I
> want to show my protein in Pymol. Is it possible or not that I want to ask?
> The program for academic, not commercial. Thank you very much for your
> understanding, kindness and precious time.
>
>
>
> Best regards,
>
> Halil İbrahim ÖZDEMİR
>
> Marmara University
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Pymol Qt Wayland

[RDirective <rdi...@gm...>]

Dear all,

I have a slight problem with Pymol on Fedora 31. The vanilla distribution
runs Gnome on Wayland.  Pymol complains that [qt.qpa.plugin: Could not find
the Qt platform plugin "wayland" in ""]. The GUI and 3D render will still
work but if I were to install qt5-qtwayland-devel to provide the plugin,
then the GUI will load but the 3D render no longer shows anything. It is
just a blank frame.  What can be done about this?

Best,
Quyen

[PyMOL] About Pymol 2.3 Python Package

[halil i. ö. <ozd...@gm...>]

Dear Mr/Mrs,



I am a fresh master's degree student in the computational biology
department. Now working on my new standalone project about allosteric
proteins. Actually i finished. But for visualization I used pymol2 and I
heard that it is not free anymore. And i wrote my code in python 3. So I
want to show my protein in Pymol. Is it possible or not that I want to ask?
The program for academic, not commercial. Thank you very much for your
understanding, kindness and precious time.



Best regards,

Halil İbrahim ÖZDEMİR

Marmara University

Re: [PyMOL] Get surface coordinates

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

Hi Pedro - 

The COLLADA option exports unlabeled mesh objects so I couldn't figure out which one is acceptor or donor.
Yes, you're correct about that.  This is due to the fact that COLLADA export uses geometry after it is prepared for ray tracing, which doesn't know about object names (see the primary function call).  It might be interesting/useful to export things in a more granular way using pre-ray-tracing information as it is stored in the PyMOL session, but that would involve substantial effort, and wasn't included when we planned this export feature.

If you wanted to know which mesh is which, you could export objects one-at-a-time by disabling all the others, although to me, the dump command output looks more helpful as it can be more easily parsed.

Just one more question, what are these normal values?

The normal values Thomas refers to are the 3 components of the vector indicating the direction toward the "outside" of the object, which is normal to the surface the triangle mesh attempts to approximate.  This is used in shading.

https://en.wikipedia.org/wiki/Vertex_normal

The cmd.get_volume_field() returns a sparse ndarray with unknow layout and all dimensions variables depending of the object. How to interpret such array?
On PyMOL 1.x it returned -1 but in 2.x returned the array.

The dump command worked (almost) like a charm.
I expect to extract the "dump" array from get_volume_field() so don't need to write the file just to be read and deleted afterwards. Is it possible?

I'm not familiar with `cmd.get_volume_field()`, so I'll defer to others on those questions.

Hope that helps.

Cheers,
Jared

Re: [PyMOL] Get surface coordinates

[Pedro L. <psl...@gm...>]

Just one more question, what are these normal values?

Em sex, 1 de nov de 2019 às 02:43, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi Thomas,
>
> The cmd.get_volume_field() returns a sparse ndarray with unknow layout and
> all dimensions variables depending of the object. How to interpret such
> array?
> On PyMOL 1.x it returned -1 but in 2.x returned the array.
>
> The dump command worked (almost) like a charm.
> I expect to extract the "dump" array from get_volume_field() so don't need
> to write the file just to be read and deleted afterwards. Is it possible?
>
> Hi Jared,
>
> The COLLADA option exports unlabeled mesh objects so I couldn't figure out
> which one is acceptor or donor.
>
>
> Em qua, 30 de out de 2019 às 15:20, Thomas Holder <
> tho...@sc...> escreveu:
>
>> Hi Pedro,
>>
>> There is a "dump" command which exports all surface points and normals to
>> a text file.
>>
>>   dump /tmp/dump.txt, acceptor_17
>>
>> Each line will have 6 numbers, 3 for the position, and 3 for the normal.
>>
>> For cmd.get_volume_field you need the map name, not the surface name.
>>
>>   data = cmd.get_volume_field('acceptor')
>>   print(data)
>>
>>
>> Hope that helps.
>>
>> Cheers,
>>   Thomas
>>
>>
>> > On Oct 30, 2019, at 6:42 AM, Pedro Lacerda <psl...@gm...> wrote:
>> >
>> > And cmd.get_volume_field is returning -1.
>> >
>> > Em qua, 30 de out de 2019 às 02:00, Pedro Lacerda <psl...@gm...>
>> escreveu:
>> > Hi,
>> >
>> > How can I access the underlying coordinates of acceptor, donor and
>> apolar surface objects on the given session given by the following server?
>> Coords akin to dot representation would suffice.
>> >
>> > http://fragment-hotspot-maps.ccdc.cam.ac.uk/results_table
>> > http://fragment-hotspot-maps.ccdc.cam.ac.uk/result/1542
>> >
>> > An example of session is attached.
>> >
>> > --
>> > Pedro Sousa Lacerda
>> >
>> > Laboratório de Bioinformática e Modelagem Molecular
>> > Faculdade de Farmácia / UFBA
>> >
>> > @pslacerda
>> > +55 71 9 9981-1856
>> >
>> >  ARSB_hotspots.pse
>> >
>> >
>> > --
>> > Pedro Sousa Lacerda
>> >
>> > Laboratório de Bioinformática e Modelagem Molecular
>> > Faculdade de Farmácia / UFBA
>> >
>> > @pslacerda
>> > +55 71 9 9981-1856
>> > _______________________________________________
>> > PyMOL-users mailing list
>> > Archives: http://www.mail-archive.com/pym...@li...
>> > Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
>>
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>


-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] Get surface coordinates

[Pedro L. <psl...@gm...>]

Hi Thomas,

The cmd.get_volume_field() returns a sparse ndarray with unknow layout and
all dimensions variables depending of the object. How to interpret such
array?
On PyMOL 1.x it returned -1 but in 2.x returned the array.

The dump command worked (almost) like a charm.
I expect to extract the "dump" array from get_volume_field() so don't need
to write the file just to be read and deleted afterwards. Is it possible?

Hi Jared,

The COLLADA option exports unlabeled mesh objects so I couldn't figure out
which one is acceptor or donor.


Em qua, 30 de out de 2019 às 15:20, Thomas Holder <
tho...@sc...> escreveu:

> Hi Pedro,
>
> There is a "dump" command which exports all surface points and normals to
> a text file.
>
>   dump /tmp/dump.txt, acceptor_17
>
> Each line will have 6 numbers, 3 for the position, and 3 for the normal.
>
> For cmd.get_volume_field you need the map name, not the surface name.
>
>   data = cmd.get_volume_field('acceptor')
>   print(data)
>
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
>
> > On Oct 30, 2019, at 6:42 AM, Pedro Lacerda <psl...@gm...> wrote:
> >
> > And cmd.get_volume_field is returning -1.
> >
> > Em qua, 30 de out de 2019 às 02:00, Pedro Lacerda <psl...@gm...>
> escreveu:
> > Hi,
> >
> > How can I access the underlying coordinates of acceptor, donor and
> apolar surface objects on the given session given by the following server?
> Coords akin to dot representation would suffice.
> >
> > http://fragment-hotspot-maps.ccdc.cam.ac.uk/results_table
> > http://fragment-hotspot-maps.ccdc.cam.ac.uk/result/1542
> >
> > An example of session is attached.
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> >
> >  ARSB_hotspots.pse
> >
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] View manger (and how to store arbitrary data on the session?)

[Pedro L. <psl...@gm...>]

Hi Jared,

Glad you liked and thank you for the patch and incentive. I'll pull it on
the repo and create a wiki page.

Best regards,
Pedro Lacerda


Em qua, 30 de out de 2019 14:16, Jared Sampson <jar...@co...>
escreveu:

> Hi Pedro -
>
> I just took a look at the plugin, and it seems quite convenient.  I
> imagine using this as a tool to complement PyMOL's default scenes, as a way
> of looking at different representations or objects from the same viewpoint.
>
> Looking at the code, I was curious about all the Q* global variable
> assignments near the top, and thought they might be cleaner and easier to
> maintain as imports.  (Plus many of them were unused in the plugin code.)
>  Apparently due to the way pymol.Qt is a wrapper for PyQt5, we can't do
> `from pymol.Qt.QtWidgets import *`, but the following does work:
>
> ```
> from pymol.Qt import QtWidgets, QtCore, QtGui
> ```
>
> then use e.g. `QtWidgets.QWidget()` in the body of the code; see the
> attached patch (I hope you don't mind my sending it!).  As a side note,
> this appears to be—at least unofficially—a preferred way to do it,
> according to an example plugin
> <https://github.com/Pymol-Scripts/pymol2-demo-plugin/blob/master/__init__.py#L51> by
> PyMOL lead developer Thomas Holder (speleo3).
>
> Also, I would encourage you to add your plugin to the PyMOL scripts repo
> <https://github.com/Pymol-Scripts/Pymol-script-repo> on Github, and to
> create a PyMOL Wiki page for it.
>
> Thanks for sharing!
>
> Cheers,
> Jared
>
> On October 26, 2019 at 12:39:35 PM, Pedro Lacerda (psl...@gm...)
> wrote:
>
> And the plugin, of course!
>
> Em sáb, 26 de out de 2019 às 13:37, Pedro Lacerda <psl...@gm...>
> escreveu:
>
>> Hi,
>>
>> I just made a graphical plugin to set and get views. It uses the set_view
>> and get_view functions.
>>
>> It is available in the last option ("Show views") on the "Scene" menu.
>> Double-click to rename a view. Erase it's name to delete it.
>>
>> In order to persist data in the PSE session it stores data into the
>> mesh_clear_selection setting. It was the only way I found.
>>
>> How to store arbitrary data on the session? Some "ostate" string settings
>> are preserved on the PSE session. But not all support set arbitrary data
>> (eg, bg_image_filename). It is very hackish and not a definite solution.
>>
>> Just wondering, maybe a hidden "setting" (not visible to can be be used
>> as a key-value store. It would hold serialized data (eg json or pickle) and
>> have a pair of functions set_key(key, obj) and get(key) that read and write
>> the setting.
>>
>> Another great addition would be able to set arbitrary strings to objects
>> and atoms. But in case of implementing a key-value store would be some
>> overlap.
>>
>> Best regards,
>>
>>
>> [image: image.png]
>>
>> --
>> Pedro Sousa Lacerda
>>
>>
>> *Laboratório de Bioinformática e Modelagem Molecular*
>> *Faculdade de Farmácia / UFBA*
>>
>> *@pslacerda*
>>
>> *+55 71 9 9981-1856*
>>
>
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubsc
> <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
>
>

Re: [PyMOL] Get surface coordinates

[Thomas H. <tho...@sc...>]

Hi Pedro,

There is a "dump" command which exports all surface points and normals to a text file.

  dump /tmp/dump.txt, acceptor_17

Each line will have 6 numbers, 3 for the position, and 3 for the normal.

For cmd.get_volume_field you need the map name, not the surface name.

  data = cmd.get_volume_field('acceptor')
  print(data)


Hope that helps.

Cheers,
  Thomas


> On Oct 30, 2019, at 6:42 AM, Pedro Lacerda <psl...@gm...> wrote:
> 
> And cmd.get_volume_field is returning -1.
> 
> Em qua, 30 de out de 2019 às 02:00, Pedro Lacerda <psl...@gm...> escreveu:
> Hi,
> 
> How can I access the underlying coordinates of acceptor, donor and apolar surface objects on the given session given by the following server? Coords akin to dot representation would suffice.
> 
> http://fragment-hotspot-maps.ccdc.cam.ac.uk/results_table
> http://fragment-hotspot-maps.ccdc.cam.ac.uk/result/1542
> 
> An example of session is attached.
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> 
>  ARSB_hotspots.pse
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Get surface coordinates

[Pedro L. <psl...@gm...>]

And cmd.get_volume_field is returning -1.

Em qua, 30 de out de 2019 às 02:00, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi,
>
> How can I access the underlying coordinates of acceptor, donor and apolar
> surface objects on the given session given by the following server? Coords
> akin to dot representation would suffice.
>
> http://fragment-hotspot-maps.ccdc.cam.ac.uk/results_table
> http://fragment-hotspot-maps.ccdc.cam.ac.uk/result/1542
>
> An example of session is attached.
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>
>  ARSB_hotspots.pse
> <https://drive.google.com/file/d/1os3t_yNQ556PrwgFEaRcyQZs-FVi3YEr/view?usp=drive_web>
>


-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

[PyMOL] Get surface coordinates

[Pedro L. <psl...@gm...>]

Hi,

How can I access the underlying coordinates of acceptor, donor and apolar
surface objects on the given session given by the following server? Coords
akin to dot representation would suffice.

http://fragment-hotspot-maps.ccdc.cam.ac.uk/results_table
http://fragment-hotspot-maps.ccdc.cam.ac.uk/result/1542

An example of session is attached.

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

 ARSB_hotspots.pse
<https://drive.google.com/file/d/1os3t_yNQ556PrwgFEaRcyQZs-FVi3YEr/view?usp=drive_web>

Re: [PyMOL] View manger (and how to store arbitrary data on the session?)

[Pedro L. <psl...@gm...>]

And the plugin, of course!

Em sáb, 26 de out de 2019 às 13:37, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi,
>
> I just made a graphical plugin to set and get views. It uses the set_view
> and get_view functions.
>
> It is available in the last option ("Show views") on the "Scene" menu.
> Double-click to rename a view. Erase it's name to delete it.
>
> In order to persist data in the PSE session it stores data into the
> mesh_clear_selection setting. It was the only way I found.
>
> How to store arbitrary data on the session? Some "ostate" string settings
> are preserved on the PSE session. But not all support set arbitrary data
> (eg, bg_image_filename). It is very hackish and not a definite solution.
>
> Just wondering, maybe a hidden "setting" (not visible to can be be used as
> a key-value store. It would hold serialized data (eg json or pickle) and
> have a pair of functions set_key(key, obj) and get(key) that read and write
> the setting.
>
> Another great addition would be able to set arbitrary strings to objects
> and atoms. But in case of implementing a key-value store would be some
> overlap.
>
> Best regards,
>
>
> [image: image.png]
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>


-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

[PyMOL] View manger (and how to store arbitrary data on the session?)

[Pedro L. <psl...@gm...>]

Hi,

I just made a graphical plugin to set and get views. It uses the set_view
and get_view functions.

It is available in the last option ("Show views") on the "Scene" menu.
Double-click to rename a view. Erase it's name to delete it.

In order to persist data in the PSE session it stores data into the
mesh_clear_selection setting. It was the only way I found.

How to store arbitrary data on the session? Some "ostate" string settings
are preserved on the PSE session. But not all support set arbitrary data
(eg, bg_image_filename). It is very hackish and not a definite solution.

Just wondering, maybe a hidden "setting" (not visible to can be be used as
a key-value store. It would hold serialized data (eg json or pickle) and
have a pair of functions set_key(key, obj) and get(key) that read and write
the setting.

Another great addition would be able to set arbitrary strings to objects
and atoms. But in case of implementing a key-value store would be some
overlap.

Best regards,


[image: image.png]

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

[PyMOL] Open position for PyMOL Software Engineer

[Thomas H. <tho...@sc...>]

Greetings,

Schrödinger is looking to hire a Software Engineer to join the PyMOL team in New York. We would be very excited if there is a talented member from the PyMOL community who can fill this position. Interested? Please follow the link:

https://hire.withgoogle.com/public/jobs/schrodingercom/view/P_AAAAAADAADpO9VyJDPz7O7

Cheers,
The PyMOL Team at Schrödinger

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] educational PyMOL 1.7.4.5 crashing with Mac Catalina OS 10.15

[Pedro L. <psl...@gm...>]

Recently I found that the trial version 2.x don't expires. You may have
some trouble with licensing, but it is fine for 30 days.

I had only some trouble with pse versions, but the pse_export_version
option did the job.

https://pymol.org/2/

Em sex, 18 de out de 2019 às 17:50, Amy C Rosenzweig <am...@no...>
escreveu:

> Students in a course I am teaching just updated to Mac Catalina OS 10.15
> and they are now unable to use the educational version of PyMOL (1.7.4.5).
> Does anyone know if there is a fix for this? Thanks!
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

[PyMOL] educational PyMOL 1.7.4.5 crashing with Mac Catalina OS 10.15

[Amy C R. <am...@no...>]

Students in a course I am teaching just updated to Mac Catalina OS 10.15 and they are now unable to use the educational version of PyMOL (1.7.4.5). Does anyone know if there is a fix for this? Thanks!

Re: [PyMOL] Drawing lines between residues

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

Hi Jorge,

I have written a script that will draw lines between arbitrary pairs of atoms using CGO cylinders.  The script is called "draw_links.py" and can be found on my script page:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Besides listing the pairs of atoms to connect you can control the colour and radius of the CGO cylinders with a command like:

draw_links mol1 & chain A & name CA & resi 1+6+7+8, mol1 & chain A & name CA & resi 10+16+17+18 

and that would connect the alpha carbons of residue 1 with 10, 6 with 16, 7 with 17 and 8 with 18.


Cheers,
Rob

On Thu, 2019-10-17 16:31  +0200,  Jorge Fernández de Cossío Díaz <j.c...@gm...> wrote:

> Hi all.
> 
> I have a list of pairs of residues. I want to draw lines between the
> residues in each pair. The lines can have different colors. So in the
> end I would like to achieve a figure like this one:
> 
> 
> [image: 2019-10-15.png]
> 
> What commands can I use to get this done in PyMOL?
> 
> Thanks



-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<rob...@qu...>  http://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] Drawing lines between residues

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

Hi Jorge and Blaine

Another was to do this is to take a measurement between the residues and then use the command, “set dash_gap, 0”
This will also allow you to control the thickness of the lines using the “set dash_radius” command

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
Email: aku...@un...

From: Jorge Fernández de Cossío Díaz <j.c...@gm...>
Date: Friday, 18 October 2019 at 1:34 am
To: "pym...@li..." <pym...@li...>
Subject: [PyMOL] Drawing lines between residues

Hi all.

I have a list of pairs of residues. I want to draw lines between the residues in each pair. The lines can have different colors. So in the end I would like to achieve a figure like this one:


[cid:image001.png@01D5856C.60197160]

What commands can I use to get this done in PyMOL?

Thanks

Re: [PyMOL] [EXTERNAL] Drawing lines between residues

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

Hi Jorge,

You can use the "bond" command if the structures to be linked are in the same molecular object.
You may have to use the "create" command with both objects in a selection to merge two objects into one. 

bond [atom1, atom2 [,order]]

You can control the bond thickness via the stick_radius setting.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Jorge Fernández de Cossío Díaz [j.c...@gm...]
Sent: Thursday, October 17, 2019 9:31 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Drawing lines between residues

Hi all.

I have a list of pairs of residues. I want to draw lines between the residues in each pair. The lines can have different colors. So in the end I would like to achieve a figure like this one:


[2019-10-15.png]

What commands can I use to get this done in PyMOL?

Thanks

[PyMOL] Drawing lines between residues

[Jorge F. de C. D. <j.c...@gm...>]

Hi all.

I have a list of pairs of residues. I want to draw lines between the
residues in each pair. The lines can have different colors. So in the end I
would like to achieve a figure like this one:


[image: 2019-10-15.png]

What commands can I use to get this done in PyMOL?

Thanks

Re: [PyMOL] dots with/without ray tracing

[Thomas H. <tho...@sc...>]

Hi Vaheh,

Try this:

set dot_radius, 0.1
set dot_as_spheres

Cheers,
  Thomas


> On Oct 15, 2019, at 9:53 PM, Oganesyan, Vaheh <vah...@as...> wrote:
> 
> Hello PyMOLers,
>  
> Figure that contains dots getting unwanted metamorphosis after ray tracing (figures before ray tracing and after are attached). Any suggestion how to overcome it?
> Thank you.
> Regards,
>  
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> ____________________________________________________________________
> AstraZeneca
> R&D | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T:  301-398-5851
> Vah...@as...
>  
> <details-with-ray.jpg><details-no-ray.jpg>_______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] feature request

[Thomas H. <tho...@sc...>]

Hi Jared and Vaheh -

We've implemented two modes and pushed the change to the github repository.

set internal_gui_name_color_mode, 
set internal_gui_name_color_mode, 2

Mode 1 is color by first carbon color. We think this is the most relevant use case and what the user typically would expect. This only affects molecular objects of course, other object types will appear in the default color (white).

Mode 2 is object color. It applies to all object types.

I learned that the "C > by element > ..." menu options also update the object color with the same color that is applied to carbons.

A neat way to transfer atom color to object color is with this command:

  iterate (name CA), cmd.set_object_color(model, color)

Other selections are possible of course.

Cheers,
  Thomas


> On Oct 2, 2019, at 7:31 PM, Jared Sampson <jar...@co...> wrote:
> 
> Hi Thomas - 
> 
>> When I said it's easy to implement, I was only thinking of object color. Among the various cases you describe, the "dominant color" is probably the most important one, as it might not be obvious to the user that object color can be different from atom colors.
> Indeed, I was among those for whom "it might not be obvious" that there are separate object and atom colors!  I had thought all coloring was done at the atom level (as you show using the selection), and didn't realize there is a separate object-level color, nor did I know about the `set_object_color` command.
> 
> Thanks for the explanation, Thomas!
> 
> Cheers,
> 
> Jared
> 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] dots with/without ray tracing

[Oganesyan, V. <vah...@as...>]

Hello PyMOLers,

Figure that contains dots getting unwanted metamorphosis after ray tracing (figures before ray tracing and after are attached). Any suggestion how to overcome it?
Thank you.
Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics
____________________________________________________________________
AstraZeneca
R&D | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
Vah...@as...<mailto:Oga...@me...>

[PyMOL] RMSD-based clustering tool

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

I was wondering does PyMol have a RMSD based clustering tool.

Many thanks,
Neena

[PyMOL] Help

[Vertika G. <var...@gm...>]

Hi!

I am new user.
>From a 3DRISM analysis
1. I want to show iso-surface of a potential map (.dx) and another
2. explicit distribution (.pdb) which should be colored by index from low
to high,(e.g. red to blue).


 Thanks in advance!
-- 
Vertika Gautam

Research Assistant
Drug Design and Development Research Group (DDDRG)
Department of Chemistry, Faculty of Science
University of Malaya



*e-mail address: var...@gm...
<var...@gm...>
var...@ho... <var...@ho...>
    01112294191*

Re: [PyMOL] [EXTERNAL] Mac installation error: clang++, segmentation fault 11

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

Hi Sumudu,

Homebrew gave a clang++ error.  This may be due a recent upgrade of Xcode 
which replaced MacOSX10.14.sdk with MacOSX10.15.sdk inside the Xcode.app.
If this happened to you, do the following:

cd /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs 
sudo ln -s MacOSX.sdk MacOSX10.14.sdk 

I am not sure about the origins of the segmentation fault in 
with the macports pymol. I install it last week successfully.
I had python3.7 already installed in macports. 
I installed the py37 variant of PyMOL. 

I had run the commands below a year earlier. 
I am not sure if these ports are necessary anymore. 

sudo port install tcl -corefoundation
sudo port install tk -quartz

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Sumudu Leelananda [sum...@gm...]
Sent: Friday, October 04, 2019 10:53 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Mac installation error: clang++, segmentation fault 11

Hi,

I was trying to get open source pymol installed on my Mac but was unable to do so. I tried brew and macports. I'm on Mojave 10.14.6. I attached the error I get with brew. With Macports, when I try to open Pymol it returns a segmentation fault 11 error.

Has anybody seen this before? Any suggestions?

Thank you!


brew install brewsci/bio/pymol




Updating Homebrew...

==> Auto-updated Homebrew!

Updated 4 taps (homebrew/core, homebrew/cask, homebrew/services and caskroom/cask).

==> Updated Formulae

cmake ✔           deno              ffsend            go@1.12           gspell            haproxy           iso-codes         node              rke               roswell           rust


==> Installing pymol from brewsci/bio

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==> Downloading https://files.pythonhosted.org/packages/11/74/2c151a13ef41ab9fb43b3c4ff9e788e0496ed7923b2078d42cab30622bdf/virtualenv-16.7.4.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_11_74_2c151a13ef41ab9fb43b3c4ff9e788e0496ed7923b2078d42cab30622bdf_virtualenv-2D16.7.4.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=a4dBdjqDiDnC10aVIUHN-v0TtjddjFC73iVBkKaHPO0&e=>

Already downloaded: /Users/sumudu/Library/Caches/Homebrew/downloads/507d2087bf24df82641b681a5fe4da778ef50ebe819a86ea1b584f70788f0f63--virtualenv-16.7.4.tar.gz

==> python3 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/pymol/2.3.0/libexec --install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin --single-version-externally-man

==> Downloading https://files.pythonhosted.org/packages/3a/20/c81632328b1a4e1db65f45c0a1350a9c5341fd4bbb8ea66cdd98da56fe2e/numpy-1.15.0.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_3a_20_c81632328b1a4e1db65f45c0a1350a9c5341fd4bbb8ea66cdd98da56fe2e_numpy-2D1.15.0.zip&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=g_9yGKFX3t1BaE8uAGJXLH3pC0Nm15JIF4-P-OTvkio&e=>

Already downloaded: /Users/sumudu/Library/Caches/Homebrew/downloads/c3591902b12abd9354b52438f4e5aa07974b9e83cf502a778095fd0fd6a1cc46--numpy-1.15.0.zip

==> python3 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/pymol/2.3.0/libexec --install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin --single-version-externally-man

==> Downloading https://files.pythonhosted.org/packages/13/ea/c6a302ccdfdcc1ab200bd2b7561e574329055d2974b1fb7939a7aa374da3/mmtf-python-1.1.2.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_13_ea_c6a302ccdfdcc1ab200bd2b7561e574329055d2974b1fb7939a7aa374da3_mmtf-2Dpython-2D1.1.2.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=ebk16SyRo7S3WRYtFn6A1gARpXPcseHuOSHU441C9bM&e=>

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==> python3 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/pymol/2.3.0/libexec --install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin --single-version-externally-man

==> Downloading https://files.pythonhosted.org/packages/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-0.6.1.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_81_9c_0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578_msgpack-2D0.6.1.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=cKfy9zqGkC2Htf63F3IsV9EbtrTyLLvFMxgtY32YfZo&e=>

Already downloaded: /Users/sumudu/Library/Caches/Homebrew/downloads/432b50d5f899f052d91eb12c17bb4fe7686828cd77a7f5d3b6e4f646b09eabf6--msgpack-0.6.1.tar.gz

==> python3 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/pymol/2.3.0/libexec --install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin --single-version-externally-man

==> Downloading https://files.pythonhosted.org/packages/8a/20/6eca772d1a5830336f84aca1d8198e5a3f4715cd1c7fc36d3cc7f7185091/msgpack-python-0.5.6.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_8a_20_6eca772d1a5830336f84aca1d8198e5a3f4715cd1c7fc36d3cc7f7185091_msgpack-2Dpython-2D0.5.6.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=AuTIyzeL2Z-Ti44j29R9ylqJsx-6SFwqLrLd45RnFmY&e=>

Already downloaded: /Users/sumudu/Library/Caches/Homebrew/downloads/49c4120b43aa86620eaebc552b359f6d897f72f59d979634a803f54088ea44d8--msgpack-python-0.5.6.tar.gz

==> python3 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/pymol/2.3.0/libexec --install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin --single-version-externally-man

==> Downloading https://files.pythonhosted.org/packages/73/0c/55e4294143ba6781936c799ff13181db9109b161a8d8fc9b50eec45e1134/msgpack-tool-0.0.1.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_73_0c_55e4294143ba6781936c799ff13181db9109b161a8d8fc9b50eec45e1134_msgpack-2Dtool-2D0.0.1.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=4jQJkEos6NKgVpw1a5gpmVOvP4DNLVt57MqOZnlKMu0&e=>

Already downloaded: /Users/sumudu/Library/Caches/Homebrew/downloads/cc8ecf250035cd7b706c464cf5a1be6cfdd1a92482350d209d6900918ec93b34--msgpack-tool-0.0.1.tar.gz

==> python3 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/pymol/2.3.0/libexec --install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin --single-version-externally-man

==> Downloading https://files.pythonhosted.org/packages/e7/20/8d0c4ba96a5fe62e1bcf2b8a212ccfecd67ad951e8f3e89cf147d63952aa/Pmw-2.0.1.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__files.pythonhosted.org_packages_e7_20_8d0c4ba96a5fe62e1bcf2b8a212ccfecd67ad951e8f3e89cf147d63952aa_Pmw-2D2.0.1.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=utv0f3_bZL9Yh3JfGRTMmdoNiQMxDPrGljDOtC1DBn0&e=>

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==> python3 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/pymol/2.3.0/libexec --install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin --single-version-externally-man

==> python3 setup.py install --install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin --install-lib=/usr/local/Cellar/pymol/2.3.0/libexec/lib/python3.7/site-packages --glut --use-msgpackc=c++11

Last 15 lines from /Users/sumudu/Library/Logs/Homebrew/pymol/08.python3:

            ^

contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: unused function 'whereami' [-Wunused-function]

static void whereami(FILE *file) {

            ^

contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: unused function 'replace_wavefunction' [-Wunused-function]

static void replace_wavefunction(qm_timestep_t *ts, int n) {

            ^

contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: unused function 'del_wavefunction' [-Wunused-function]

static void del_wavefunction(qm_timestep_t *ts) {

            ^

contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: unused function 'print_matrix4' [-Wunused-function]

static void print_matrix4(const float mat[16]) {

            ^

12 warnings generated.

error: command 'clang++' failed with exit status 1