pymol-users Mailing List for PyMOL Molecular Graphics System

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
> <" rel="nofollow">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
> <" rel="nofollow">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
> <" rel="nofollow">https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
>
>

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.

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
> <" rel="nofollow">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*

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

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*

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*

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.

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*

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!

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

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

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

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

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.

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.

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...>

Hello PyMOL users,

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

Many thanks,
Neena

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*

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

==> Downloading " rel="nofollow">https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_schrodinger_pymol-2Dopen-2Dsource_archive_v2.3.0.tar.gz&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=iz1aCl1CaOgWsfa1s3YdF7fusvmrg0uAYTPbFUs8yXI&s=Um_WhO1_-dwQYFKunIbXRV4fqmJsW65fMLP6bqDbMfc&e=>

Already downloaded: /Users/sumudu/Library/Caches/Homebrew/downloads/a51d46dea90ae24d275dac1d9efa7cf70025ab5fed71dc210ce3000d5d65219c--pymol-open-source-2.3.0.tar.gz

==> Downloading " rel="nofollow">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 " rel="nofollow">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 " rel="nofollow">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=>

Already downloaded: /Users/sumudu/Library/Caches/Homebrew/downloads/8184cd2975ddc6f5276f8aca6273b4b0e2e98a69ae60a94e8f087e2bf4f7fbc2--mmtf-python-1.1.2.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 " rel="nofollow">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 " rel="nofollow">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 " rel="nofollow">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 " rel="nofollow">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

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*

==> *Downloading
https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz
<*" rel="nofollow">https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz>*

Already downloaded:
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==> *Downloading
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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
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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
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Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/8184cd2975ddc6f5276f8aca6273b4b0e2e98a69ae60a94e8f087e2bf4f7fbc2--mmtf-python-1.1.2.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/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-0.6.1.tar.gz
<*" rel="nofollow">https://files.pythonhosted.org/packages/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-0.6.1.tar.gz>*

Already downloaded:
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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/8a/20/6eca772d1a5830336f84aca1d8198e5a3f4715cd1c7fc36d3cc7f7185091/msgpack-python-0.5.6.tar.gz
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Already downloaded:
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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/73/0c/55e4294143ba6781936c799ff13181db9109b161a8d8fc9b50eec45e1134/msgpack-tool-0.0.1.tar.gz
<*" rel="nofollow">https://files.pythonhosted.org/packages/73/0c/55e4294143ba6781936c799ff13181db9109b161a8d8fc9b50eec45e1134/msgpack-tool-0.0.1.tar.gz>*

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
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Already downloaded:
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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

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

Hi Jared and Vaheh -

Jared, you've put way more thought into this than I did :-) 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.

color blue, (obj)                    ;# only changes atom colors
color blue, obj                      ;# changes object and atom colors
cmd.set_object_color("obj", "blue")  ;# only changes object color

More complex situations like spectrum or per-representation colors can be neglected I think - I wouldn't know how to map those to a label color in a useful way.

As a first step, I can add internal_gui_name_color_mode=1 with object colors.

Cheers,
  Thomas


> On Oct 1, 2019, at 9:31 PM, Oganesyan, Vaheh <vah...@as...> wrote:
> 
> Thomas and Jared,
> I’m not sure what will be the best solution, but as a start, color of the object name may stay white if more than one color is used. Because you both found this as an interesting idea allows me to ask similar question now regarding labels. What if we can get label_color match the residue color. I vaguely remember something like this discussed x number of years ago, but do not remember why not. Could label become property of the object and not just a property of a session?
>  
> Thank you.
>  
>  
> From: Jared Sampson <jar...@co...> 
> Sent: Tuesday, October 1, 2019 2:45 PM
> To: Oganesyan, Vaheh <vah...@as...>; Thomas Holder <tho...@sc...>
> Cc: pymol-users <pym...@li...>
> Subject: Re: [PyMOL] feature request
>  
> Hi Thomas and Vaheh - 
>  
> This is indeed an interesting idea.  I was thinking about this in terms of implementation, and what the edge cases might be.  I wonder what would be the mechanism for assigning the color if the object is not just a single color.  Would it be the color that is the dominant color of the object over all (visible) representations?
>  
> What about a spectrum-colored object?  Would it be possible to color the object name according to the colors in the spectrum (like the "spectrum" and "rainbow" menu items already in the OpenGL menu)?
>  
> And what if there are different coloring schemes for the different representations—would there be a hierarchy in terms of choosing , e.g. surface > cartoon > stick > line, etc.?
>  
> I definitely like Thomas' idea of a global `internal_gui_name_color_mode` setting to turn the menu object name coloring on/off.  (Perhaps different modes could correspond to different ways of choosing the displayed color.)  It might also be useful to include object-level (or named-selection-level) settings to override the global setting and specify the color or spectrum directly, e.g.:
>  
>     set internal_gui_name_color, red, obj1
>     set internal_gui_name_spectrum, rainbow, obj1
>  
> Really interesting suggestion, Vaheh.  Looking forward to seeing how it might work!
>  
> Cheers,
> Jared
>  
> On October 1, 2019 at 5:13:07 AM, Thomas Holder (tho...@sc...) wrote:
> 
> Hi Vaheh,
> 
> I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?).
> 
> Cheers,
> Thomas
> 
> 
> > On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh <vah...@as...> wrote:
> > 
> > Thomas and other PyMOL developers,
> > 
> > It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't.
> > Anybody else think it might be helpful?
> > 
> > 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: 301-398-4640 M: 240-398-0046 
> > Vah...@as...
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: https://clicktime.symantec.com/3UV6BFZxvbLGNd6ZnGajdMx6H2?u=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net
> Unsubscribe: https://clicktime.symantec.com/3E9dosvp4WJ7Ck38g9VwWNV6H2?u=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Vaheh - 

Fortunately, `label_color` is an atom-level setting already.  For example:

```
PyMOL>fab AAAAA, ala_pep
PyMOL>label n. CA, f"{resn} {resi}"
 Label: labelled 5 atoms.
PyMOL>color white
 Executive: Colored 50 atoms.
PyMOL>set label_color, red, resi 1
 Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, orange, resi 2
 Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, yellow, resi 3
 Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, green, resi 4
 Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, blue, resi 5
 Setting: label_color set for 10 atoms in object "pep1".
```

Hope that helps.

Cheers,
Jared


On October 1, 2019 at 3:31:54 PM, Oganesyan, Vaheh (vah...@as...) wrote:

Thomas and Jared,

I’m not sure what will be the best solution, but as a start, color of the object name may stay white if more than one color is used. Because you both found this as an interesting idea allows me to ask similar question now regarding labels. What if we can get label_color match the residue color. I vaguely remember something like this discussed x number of years ago, but do not remember why not. Could label become property of the object and not just a property of a session?

 

Thank you.

 

 

From: Jared Sampson <jar...@co...>  
Sent: Tuesday, October 1, 2019 2:45 PM
To: Oganesyan, Vaheh <vah...@as...>; Thomas Holder <tho...@sc...>
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] feature request

 

Hi Thomas and Vaheh - 

 

This is indeed an interesting idea.  I was thinking about this in terms of implementation, and what the edge cases might be.  I wonder what would be the mechanism for assigning the color if the object is not just a single color.  Would it be the color that is the dominant color of the object over all (visible) representations?

 

What about a spectrum-colored object?  Would it be possible to color the object name according to the colors in the spectrum (like the "spectrum" and "rainbow" menu items already in the OpenGL menu)?

 

And what if there are different coloring schemes for the different representations—would there be a hierarchy in terms of choosing , e.g. surface > cartoon > stick > line, etc.?

 

I definitely like Thomas' idea of a global `internal_gui_name_color_mode` setting to turn the menu object name coloring on/off.  (Perhaps different modes could correspond to different ways of choosing the displayed color.)  It might also be useful to include object-level (or named-selection-level) settings to override the global setting and specify the color or spectrum directly, e.g.:

 

    set internal_gui_name_color, red, obj1

    set internal_gui_name_spectrum, rainbow, obj1

 

Really interesting suggestion, Vaheh.  Looking forward to seeing how it might work!

 

Cheers,

Jared

 

On October 1, 2019 at 5:13:07 AM, Thomas Holder (tho...@sc...) wrote:

Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?).

Cheers,
Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh <vah...@as...> wrote:
>  
> Thomas and other PyMOL developers,
>  
> It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't.
> Anybody else think it might be helpful?
>  
> 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: 301-398-4640 M: 240-398-0046  
> Vah...@as...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Thomas and Jared,
I’m not sure what will be the best solution, but as a start, color of the object name may stay white if more than one color is used. Because you both found this as an interesting idea allows me to ask similar question now regarding labels. What if we can get label_color match the residue color. I vaguely remember something like this discussed x number of years ago, but do not remember why not. Could label become property of the object and not just a property of a session?

Thank you.


From: Jared Sampson <jar...@co...>
Sent: Tuesday, October 1, 2019 2:45 PM
To: Oganesyan, Vaheh <vah...@as...>; Thomas Holder <tho...@sc...>
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] feature request

Hi Thomas and Vaheh -

This is indeed an interesting idea.  I was thinking about this in terms of implementation, and what the edge cases might be.  I wonder what would be the mechanism for assigning the color if the object is not just a single color.  Would it be the color that is the dominant color of the object over all (visible) representations?

What about a spectrum-colored object?  Would it be possible to color the object name according to the colors in the spectrum (like the "spectrum" and "rainbow" menu items already in the OpenGL menu)?

And what if there are different coloring schemes for the different representations—would there be a hierarchy in terms of choosing , e.g. surface > cartoon > stick > line, etc.?

I definitely like Thomas' idea of a global `internal_gui_name_color_mode` setting to turn the menu object name coloring on/off.  (Perhaps different modes could correspond to different ways of choosing the displayed color.)  It might also be useful to include object-level (or named-selection-level) settings to override the global setting and specify the color or spectrum directly, e.g.:

    set internal_gui_name_color, red, obj1
    set internal_gui_name_spectrum, rainbow, obj1

Really interesting suggestion, Vaheh.  Looking forward to seeing how it might work!

Cheers,
Jared


On October 1, 2019 at 5:13:07 AM, Thomas Holder (tho...@sc...<mailto:tho...@sc...>) wrote:
Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?).

Cheers,
Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> wrote:
>
> Thomas and other PyMOL developers,
>
> It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't.
> Anybody else think it might be helpful?
>
> 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: 301-398-4640 M: 240-398-0046
> Vah...@as...<mailto:Vah...@as...>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Hi Thomas and Vaheh - 

This is indeed an interesting idea.  I was thinking about this in terms of implementation, and what the edge cases might be.  I wonder what would be the mechanism for assigning the color if the object is not just a single color.  Would it be the color that is the dominant color of the object over all (visible) representations?

What about a spectrum-colored object?  Would it be possible to color the object name according to the colors in the spectrum (like the "spectrum" and "rainbow" menu items already in the OpenGL menu)?

And what if there are different coloring schemes for the different representations—would there be a hierarchy in terms of choosing , e.g. surface > cartoon > stick > line, etc.?

I definitely like Thomas' idea of a global `internal_gui_name_color_mode` setting to turn the menu object name coloring on/off.  (Perhaps different modes could correspond to different ways of choosing the displayed color.)  It might also be useful to include object-level (or named-selection-level) settings to override the global setting and specify the color or spectrum directly, e.g.:

    set internal_gui_name_color, red, obj1
    set internal_gui_name_spectrum, rainbow, obj1

Really interesting suggestion, Vaheh.  Looking forward to seeing how it might work!

Cheers,
Jared

On October 1, 2019 at 5:13:07 AM, Thomas Holder (tho...@sc...) wrote:

Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?).

Cheers,
Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh <vah...@as...> wrote:
>  
> Thomas and other PyMOL developers,
>  
> It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't.
> Anybody else think it might be helpful?
>  
> 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: 301-398-4640 M: 240-398-0046  
> Vah...@as...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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