pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] volume representation is extremely dark colored

[Stanevich, V. [JRDUS] <vst...@IT...>]

Thanks Thomas and Akbar! "set precomputed_lighting" did the trick and everything looks normal now.

Vitali



-----Original Message-----
From: Thomas Holder <tho...@sc...> 
Sent: Wednesday, May 27, 2020 2:24 AM
To: Stanevich, Vitali [JRDUS] <vst...@IT...>
Cc: Mooers, Blaine H.M. (HSC) <Bla...@ou...>; pym...@li...
Subject: [EXTERNAL] Re: [PyMOL] volume representation is extremely dark colored

Hi Vitali,

Try this:

  set precomputed_lighting

Or upgrade to the latest PyMOL version which has this setting by default.

It's an Intel Graphics driver issue, you can read about it in this bug report:
https://github.com/schrodinger/pymol-open-source/issues/15

Cheers,
  Thomas


> On May 27, 2020, at 4:26 AM, Stanevich, Vitali [JRDUS] via PyMOL-users <pym...@li...> wrote:
> 
> Hi Blaine,
> 
> Setting ambient to 0.1 didn't change anything. Setting to 0.4 and higher improves brightness but makes representation not very "esthetically pleasing" -  the color is definitively oversaturated.
> 
> Thanks,
> Vitali
> 
> -----Original Message-----
> From: Mooers, Blaine H.M. (HSC) <Bla...@ou...> 
> Sent: Tuesday, May 26, 2020 6:31 PM
> To: Stanevich, Vitali [JRDUS] <vst...@IT...>; pym...@li...
> Subject: [EXTERNAL] RE: volume representation is extremely dark colored
> 
> WARNING: This email originated from outside the company. Do not click on links unless you recognize the sender and have confidence the content is safe. If you have concerns about this email, send it as an attachment to 'Sus...@IT...'.
> 
> Hi Vitali,
> 
> Maybe ambient was set to a large negative value. 
> Doing so has not impact on line drawings.
> 
> Try resetting it to the default value.
> 
> set ambient, 0.1
> 
> 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: Stanevich, Vitali [JRDUS] via PyMOL-users [pym...@li...]
> Sent: Tuesday, May 26, 2020 4:32 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] volume representation is extremely dark colored
> 
> Hello everyone,
> 
> I have a problem of creating useful volume representations in Pymol version 1.8.6.2<https://urldefense.proofpoint.com/v2/url?u=http-3A__1.8.6.2&d=DwQFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=RPm4waFOpdYkr0DWzikqf33ejGbyEIpp1mroeQkUqjc&e=>. Lines representation behaves as expected, but anything volume related (sticks, surface, cartoon) is drawn as a very dark surface, see example image at the link below:
> https://www.dropbox.com/s/nc8vqs42ki5l0zs/vs1.png?dl=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_nc8vqs42ki5l0zs_vs1.png-3Fdl-3D0&d=DwMFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=Wug1vVUQk8jevkmDUEfqd8P7wnR8KN82kBpEqNiWbE8&e=>
> 
> Is there setting in Pymol which can bring volume-related representation to something more normal? Or do you think it's non-Pymol problem with drivers compatibility and etc issues?
> 
> Thanks in advance!
> 
> Vitali Stanevich, PhD
> Scientist
> Janssen R&D
> 
> 
> 
> _______________________________________________
> 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] volume representation is extremely dark colored

[Akbar S. <akb...@sc...>]

Can you try:

set precomputed_lighting, 1

set use_shaders, 0


*Akbar Shaikh* | Associate Scientist II
*P:* +91 9767217767
[image: Schrodinger Logo] <https://www.schrodinger.com/>Science and
Technology Support <https://www.schrodinger.com/supportcenter>


On Wed, May 27, 2020 at 8:11 AM Stanevich, Vitali [JRDUS] via PyMOL-users <
pym...@li...> wrote:

> Hi Blaine,
>
> Setting ambient to 0.1 didn't change anything. Setting to 0.4 and higher
> improves brightness but makes representation not very "esthetically
> pleasing" -  the color is definitively oversaturated.
>
> Thanks,
> Vitali
>
> -----Original Message-----
> From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
> Sent: Tuesday, May 26, 2020 6:31 PM
> To: Stanevich, Vitali [JRDUS] <vst...@IT...>;
> pym...@li...
> Subject: [EXTERNAL] RE: volume representation is extremely dark colored
>
> WARNING: This email originated from outside the company. Do not click on
> links unless you recognize the sender and have confidence the content is
> safe. If you have concerns about this email, send it as an attachment to '
> Sus...@IT...'.
>
> Hi Vitali,
>
> Maybe ambient was set to a large negative value.
> Doing so has not impact on line drawings.
>
> Try resetting it to the default value.
>
> set ambient, 0.1
>
> 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: Stanevich, Vitali [JRDUS] via PyMOL-users [
> pym...@li...]
> Sent: Tuesday, May 26, 2020 4:32 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] volume representation is extremely dark colored
>
> Hello everyone,
>
> I have a problem of creating useful volume representations in Pymol
> version 1.8.6.2<
> https://urldefense.proofpoint.com/v2/url?u=http-3A__1.8.6.2&d=DwQFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=RPm4waFOpdYkr0DWzikqf33ejGbyEIpp1mroeQkUqjc&e=>.
> Lines representation behaves as expected, but anything volume related
> (sticks, surface, cartoon) is drawn as a very dark surface, see example
> image at the link below:
> https://www.dropbox.com/s/nc8vqs42ki5l0zs/vs1.png?dl=0<
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_nc8vqs42ki5l0zs_vs1.png-3Fdl-3D0&d=DwMFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=Wug1vVUQk8jevkmDUEfqd8P7wnR8KN82kBpEqNiWbE8&e=
> >
>
> Is there setting in Pymol which can bring volume-related representation to
> something more normal? Or do you think it's non-Pymol problem with drivers
> compatibility and etc issues?
>
> Thanks in advance!
>
> Vitali Stanevich, PhD
> Scientist
> Janssen R&D
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Re: [PyMOL] volume representation is extremely dark colored

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

Hi Vitali,

Try this:

  set precomputed_lighting

Or upgrade to the latest PyMOL version which has this setting by default.

It's an Intel Graphics driver issue, you can read about it in this bug report:
https://github.com/schrodinger/pymol-open-source/issues/15

Cheers,
  Thomas


> On May 27, 2020, at 4:26 AM, Stanevich, Vitali [JRDUS] via PyMOL-users <pym...@li...> wrote:
> 
> Hi Blaine,
> 
> Setting ambient to 0.1 didn't change anything. Setting to 0.4 and higher improves brightness but makes representation not very "esthetically pleasing" -  the color is definitively oversaturated.
> 
> Thanks,
> Vitali
> 
> -----Original Message-----
> From: Mooers, Blaine H.M. (HSC) <Bla...@ou...> 
> Sent: Tuesday, May 26, 2020 6:31 PM
> To: Stanevich, Vitali [JRDUS] <vst...@IT...>; pym...@li...
> Subject: [EXTERNAL] RE: volume representation is extremely dark colored
> 
> WARNING: This email originated from outside the company. Do not click on links unless you recognize the sender and have confidence the content is safe. If you have concerns about this email, send it as an attachment to 'Sus...@IT...'.
> 
> Hi Vitali,
> 
> Maybe ambient was set to a large negative value. 
> Doing so has not impact on line drawings.
> 
> Try resetting it to the default value.
> 
> set ambient, 0.1
> 
> 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: Stanevich, Vitali [JRDUS] via PyMOL-users [pym...@li...]
> Sent: Tuesday, May 26, 2020 4:32 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] volume representation is extremely dark colored
> 
> Hello everyone,
> 
> I have a problem of creating useful volume representations in Pymol version 1.8.6.2<https://urldefense.proofpoint.com/v2/url?u=http-3A__1.8.6.2&d=DwQFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=RPm4waFOpdYkr0DWzikqf33ejGbyEIpp1mroeQkUqjc&e=>. Lines representation behaves as expected, but anything volume related (sticks, surface, cartoon) is drawn as a very dark surface, see example image at the link below:
> https://www.dropbox.com/s/nc8vqs42ki5l0zs/vs1.png?dl=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_nc8vqs42ki5l0zs_vs1.png-3Fdl-3D0&d=DwMFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=Wug1vVUQk8jevkmDUEfqd8P7wnR8KN82kBpEqNiWbE8&e=>
> 
> Is there setting in Pymol which can bring volume-related representation to something more normal? Or do you think it's non-Pymol problem with drivers compatibility and etc issues?
> 
> Thanks in advance!
> 
> Vitali Stanevich, PhD
> Scientist
> Janssen R&D
> 
> 
> 
> _______________________________________________
> 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] volume representation is extremely dark colored

[Stanevich, V. [JRDUS] <vst...@IT...>]

Hi Blaine,

Setting ambient to 0.1 didn't change anything. Setting to 0.4 and higher improves brightness but makes representation not very "esthetically pleasing" -  the color is definitively oversaturated.

Thanks,
Vitali

-----Original Message-----
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...> 
Sent: Tuesday, May 26, 2020 6:31 PM
To: Stanevich, Vitali [JRDUS] <vst...@IT...>; pym...@li...
Subject: [EXTERNAL] RE: volume representation is extremely dark colored

WARNING: This email originated from outside the company. Do not click on links unless you recognize the sender and have confidence the content is safe. If you have concerns about this email, send it as an attachment to 'Sus...@IT...'.

Hi Vitali,

Maybe ambient was set to a large negative value. 
Doing so has not impact on line drawings.

Try resetting it to the default value.

set ambient, 0.1

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: Stanevich, Vitali [JRDUS] via PyMOL-users [pym...@li...]
Sent: Tuesday, May 26, 2020 4:32 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] volume representation is extremely dark colored

Hello everyone,

I have a problem of creating useful volume representations in Pymol version 1.8.6.2<https://urldefense.proofpoint.com/v2/url?u=http-3A__1.8.6.2&d=DwQFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=RPm4waFOpdYkr0DWzikqf33ejGbyEIpp1mroeQkUqjc&e=>. Lines representation behaves as expected, but anything volume related (sticks, surface, cartoon) is drawn as a very dark surface, see example image at the link below:
https://www.dropbox.com/s/nc8vqs42ki5l0zs/vs1.png?dl=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_nc8vqs42ki5l0zs_vs1.png-3Fdl-3D0&d=DwMFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=Wug1vVUQk8jevkmDUEfqd8P7wnR8KN82kBpEqNiWbE8&e=>

Is there setting in Pymol which can bring volume-related representation to something more normal? Or do you think it's non-Pymol problem with drivers compatibility and etc issues?

Thanks in advance!

Vitali Stanevich, PhD
Scientist
Janssen R&D

Re: [PyMOL] volume representation is extremely dark colored

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

Hi Vitali,

Maybe ambient was set to a large negative value. 
Doing so has not impact on line drawings.

Try resetting it to the default value.

set ambient, 0.1

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: Stanevich, Vitali [JRDUS] via PyMOL-users [pym...@li...]
Sent: Tuesday, May 26, 2020 4:32 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] volume representation is extremely dark colored

Hello everyone,

I have a problem of creating useful volume representations in Pymol version 1.8.6.2<https://urldefense.proofpoint.com/v2/url?u=http-3A__1.8.6.2&d=DwQFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=RPm4waFOpdYkr0DWzikqf33ejGbyEIpp1mroeQkUqjc&e=>. Lines representation behaves as expected, but anything volume related (sticks, surface, cartoon) is drawn as a very dark surface, see example image at the link below:
https://www.dropbox.com/s/nc8vqs42ki5l0zs/vs1.png?dl=0<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dropbox.com_s_nc8vqs42ki5l0zs_vs1.png-3Fdl-3D0&d=DwMFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=BNWMZg9-_ltMi2O9nPtMsSvn01PANBYBXuDSFdm92O4&s=Wug1vVUQk8jevkmDUEfqd8P7wnR8KN82kBpEqNiWbE8&e=>

Is there setting in Pymol which can bring volume-related representation to something more normal? Or do you think it’s non-Pymol problem with drivers compatibility and etc issues?

Thanks in advance!

Vitali Stanevich, PhD
Scientist
Janssen R&D

[PyMOL] volume representation is extremely dark colored

[Stanevich, V. [JRDUS] <vst...@IT...>]

Hello everyone,

I have a problem of creating useful volume representations in Pymol version 1.8.6.2. Lines representation behaves as expected, but anything volume related (sticks, surface, cartoon) is drawn as a very dark surface, see example image at the link below:
https://www.dropbox.com/s/nc8vqs42ki5l0zs/vs1.png?dl=0

Is there setting in Pymol which can bring volume-related representation to something more normal? Or do you think it's non-Pymol problem with drivers compatibility and etc issues?

Thanks in advance!

Vitali Stanevich, PhD
Scientist
Janssen R&D

[PyMOL] Importing Non-Protein Structure Files

[Grace C. <go...@le...>]

Hello,
Is there a way to import a non-protein structure into PyMol for a binding
assay (similar to importing a PDB for proteins)? Particularly I'd like to
study how my protein of interest interacts with a small inorganic molecule.
Thanks,
Grace

Re: [PyMOL] DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL

[Xiang-Jun Lu <3d...@gm...>]

>
> I thought that some of the list members may be interested in the paper,
> titled "DSSR-enabled innovative schematics of 3D nucleic acid structures
> with PyMOL", recently published in _Nucleic Acids Research_ (
> https://doi.org/10.1093/nar/gkz1222).


*Sorry* about the wrong link to nar/gkz1222 -- I was reading that
interesting paper on the U•A-U-rich RNA triple helix.

The correct URL to the DSSR-PyMOL NAR paper is:
https://doi.org/10.1093/nar/gkaa426

Best regards,

Xiang-Jun

--
Xiang-Jun Lu (Ph.D.)
Email: xia...@x3...
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/


On Sat, May 23, 2020 at 1:41 PM Xiang-Jun Lu <3d...@gm...> wrote:

> I am glad to announce that the paper, titled "DSSR-enabled innovative
> schematics of 3D nucleic acid structures with PyMOL", has recently been
> published in _Nucleic Acids Research_ (https://doi.org/10.1093/nar/gkz1222).
>
>
> The DSSR program creates schematic block representations in diverse styles
> that can be seamlessly integrated into PyMOL and complement its other
> popular visualization options. In addition to portraying individual base
> blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the
> minor-groove edges. Notably, DSSR can dramatically simplify the depiction
> of G-quadruplexes by automatically detecting G-tetrads and treating them as
> large square blocks. The DSSR-enabled innovative schematics with PyMOL are
> aesthetically pleasing and highly informative: the base identity, pairing
> geometry, stacking interactions, double-helical stems, and G-quadruplexes
> are immediately obvious. These features can be accessed via four
> interfaces: the command-line interface, the DSSR plugin for PyMOL (written
> by Thomas Holder; http://pymolwiki.org/index.php/dssr_block), the web
> application (http://skmatic.x3dna.org/), and the web application
> programming interface.
>
> The web application interface (http://skmatic.x3dna.org/) also provides
> pre-calculated schematics and meta information of nucleic-acid-containing
> structures in the PDB. Here are some examples:
>
> * http://skmatic.x3dna.org/pdb/2lx1
> * http://skmatic.x3dna.org/pdb/2grb
> * http://skmatic.x3dna.org/pdb/6vu1
> * http://skmatic.x3dna.org/pdb_entries  # 12 random entries
> * http://skmatic.x3dna.org/pdb_entries/recent-week
> * http://skmatic.x3dna.org/pdb_entries/recent-month
>
> The supplemental PDF (http://skmatic.x3dna.org/gkaa426-supp.pdf) has been
> written to serve as a practical guide, with complete and reproducible
> examples.
>
> Best regards,
>
> Xiang-Jun
>
> --
> Xiang-Jun Lu (Ph.D.)
> Email: xia...@x3...
> Web: http://x3dna.org/
> Forum: http://forum.x3dna.org/
>

[PyMOL] DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL

[Xiang-Jun Lu <3d...@gm...>]

I am glad to announce that the paper, titled "DSSR-enabled innovative
schematics of 3D nucleic acid structures with PyMOL", has recently been
published in _Nucleic Acids Research_ (https://doi.org/10.1093/nar/gkz1222).


The DSSR program creates schematic block representations in diverse styles
that can be seamlessly integrated into PyMOL and complement its other
popular visualization options. In addition to portraying individual base
blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the
minor-groove edges. Notably, DSSR can dramatically simplify the depiction
of G-quadruplexes by automatically detecting G-tetrads and treating them as
large square blocks. The DSSR-enabled innovative schematics with PyMOL are
aesthetically pleasing and highly informative: the base identity, pairing
geometry, stacking interactions, double-helical stems, and G-quadruplexes
are immediately obvious. These features can be accessed via four
interfaces: the command-line interface, the DSSR plugin for PyMOL (written
by Thomas Holder; http://pymolwiki.org/index.php/dssr_block), the web
application (http://skmatic.x3dna.org/), and the web application
programming interface.

The web application interface (http://skmatic.x3dna.org/) also provides
pre-calculated schematics and meta information of nucleic-acid-containing
structures in the PDB. Here are some examples:

* http://skmatic.x3dna.org/pdb/2lx1
* http://skmatic.x3dna.org/pdb/2grb
* http://skmatic.x3dna.org/pdb/6vu1
* http://skmatic.x3dna.org/pdb_entries  # 12 random entries
* http://skmatic.x3dna.org/pdb_entries/recent-week
* http://skmatic.x3dna.org/pdb_entries/recent-month

The supplemental PDF (http://skmatic.x3dna.org/gkaa426-supp.pdf) has been
written to serve as a practical guide, with complete and reproducible
examples.

Best regards,

Xiang-Jun

--
Xiang-Jun Lu (Ph.D.)
Email: xia...@x3...
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/

Re: [PyMOL] Structure allignmnet in Pymol

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

Hi Maryam,

You can easily align two proteins in Pymol to compare their structures. Read both protein structures into the same window under the action option, choose align and select which one you want. E.g align to molecule (via alpha carbons)
Hope this is what you wanted
J

[cid:image001.png@01D630FC.D30D62D0]

From: mta...@ch... <mta...@ch...>
Sent: Saturday, 23 May 2020 11:18 am
To: pym...@li...
Subject: [PyMOL] Structure allignmnet in Pymol

Dear All,
I am a new user in PyMoL and I have a question regarding the structure alignment in PyMOL.
I have a protein that its crystal structure is not known. So I used "Modeller" software to predict the structure of its closet hit. ( I can easily visualize the structure of the closet hit in PyMOL)
Now I want to visualize the structure of initial protein (the one that its  crystal structure was not known) based on the structure of its closest hit.
I tried that with "Chimera" software using structure alignment. I would like to know if PyMoL is able to do that?
Any suggestion would greatly be appreciated.
Best regards
Maryam

[PyMOL] Structure allignmnet in Pymol

[<mta...@ch...>]

Dear All,
I am a new user in PyMoL and I have a question regarding the structure
alignment in PyMOL.
I have a protein that its crystal structure is not known. So I used
"Modeller" software to predict the structure of its closet hit. ( I can
easily visualize the structure of the closet hit in PyMOL)
Now I want to visualize the structure of initial protein (the one that its
crystal structure was not known) based on the structure of its closest hit.
I tried that with "Chimera" software using structure alignment. I would
like to know if PyMoL is able to do that?
Any suggestion would greatly be appreciated.
Best regards
Maryam

[PyMOL] Updating to 2.4

[Grace C. <go...@le...>]

Hello,
Is there a way to update my PyMol software to version 2.4 without
redownloading the software?
Grace

Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

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

Yes correct, the numbers should be like that. I don't see anything wrong with your approach.

Thanks for the background info. Maybe you can give us an update once the study is over, sounds interesting!

Cheers,
  Thomas



> On May 22, 2020, at 12:41 AM, Thomas Evangelidis <te...@gm...> wrote:
> 
> So, Thomas, you don't see anything wrong in the way I compute the surfaces? The numbers should be like that, right?
> 
> The reason I need both the molecular surface and the SASA in not directly related to a physical quantity. I do SQM scoring of compounds bound to proteins, but the bulkier molecules, which are usually non-binders, tend to yield lower interaction free energies. Thus, I thought to try these two surface types of both the protein and the ligand as descriptors in a machine learning-based attempt to balance these differences and improve the scoring. It remains to be seen in practice which of these two types (molecular surface or SASA) are more useful for my purpose. I also use other molecular descriptors, but I don't want to elaborate on this because it's out of topic.
> 
> Best,
> Thomas
> 
> 
> On Thu, 21 May 2020 at 21:57, Thomas Holder <tho...@sc...> wrote:
> Hi Thomas and Blaine,
> 
> SASA is probably the correct feature to evaluate here, not molecular surface. Of course it may depend the actual goal of this exercise, but typically when talking about interface surface, you're putting that into context with binding energy or solvation effects, and only SASA is meaningful for that as far as I know.
> 
> The difference between SASA and molecular surface is a matter of size and shape. For a very uneven shape (lots of small pockets or protuberances), going from molecular surface to SASA will flatten the surface, which can result in a smaller area, even though the volume is increased.
> 
> You may be interested to check out PISA for this task, it's the tool the PDB uses to determine biological assemblies: https://www.ebi.ac.uk/pdbe/pisa/
> 
> PyMOL's and PISA's results should be similar, but PyMOL is probably easier to handle :-)
> 
> Cheers,
>   Thomas
> 
> 
> > On May 21, 2020, at 4:37 AM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:
> > 
> > Hi Thomas,
> > 
> > If you display the SASA of the protein in PyMOL's viewport, 
> > you will see that it and that of the ligand have huge overlaps
> > How do you define the interface in such a situation and how 
> > do you interpret it? 
> > 
> > The interface of the molecular surfaces seems easier to interpret. 
> > 
> > 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: Thomas Evangelidis [te...@gm...]
> > Sent: Wednesday, May 20, 2020 9:14 AM
> > To: pymol mailinglist
> > Subject: [EXTERNAL] [PyMOL] How to compute the interface surface between ligand and protein?
> > 
> > Greetings,
> > 
> > I want to compute the interface surface between the ligand and the protein in batch mode for hundreds of thousands of PDBs, like the attached one (sample.pdb). I am interested in the interface surface of both of them. First I create two new molecules, the protein, and the ligand, and I work with them because the results I get when working with the original molecule (which contains both protein and ligand) are different.
> > 
> > load sample.pdb
> > create protein, polymer
> > create ligand, resn LIG
> > delete sample
> > 
> > select prot_interface, protein within 3.5 of ligand;
> > set dot_solvent, 0;
> > get_area prot_interface;
> > set dot_solvent, 1;
> > get_area prot_interface;
> > 
> > select lig_interface, ligand within 3.5 of protein;
> > set dot_solvent, 0;
> > get_area lig_interface;
> > set dot_solvent, 1;
> > get_area lig_interface;
> > 
> > protein interface molecular surface = 1216.239 Angstroms^2
> > protein interface SASA = 763.095 Angstroms^2
> > ligand interface molecular surface = 748.867 Angstroms^2
> > ligand interface SASA = 977.608 Angstroms^2
> > 
> > I still don't understand why the interface molecular surface of the ligand is smaller than the interface SASA, while the opposite happens with the protein. Could someone please explain this to me and verify that I am computing the interface surfaces correctly?
> > 
> > I thank you in advance.
> > Thomas
> > 
> > 
> > 
> > --
> > 
> > ======================================================================
> > 
> > Dr. Thomas Evangelidis
> > 
> > Research Scientist
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> 
> -- 
> ======================================================================
> Dr. Thomas Evangelidis
> Research Scientist
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
>   & 
> CEITEC - Central European Institute of Technology, Brno, Czech Republic 
> 
> email: te...@gm..., Twitter: tevangelidis, LinkedIn: Thomas Evangelidis
> website: https://sites.google.com/site/thomasevangelidishomepage/
> 
> 
> 
> 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

[Thomas E. <te...@gm...>]

So, Thomas, you don't see anything wrong in the way I compute the surfaces?
The numbers should be like that, right?

The reason I need both the molecular surface and the SASA in not directly
related to a physical quantity. I do SQM scoring of compounds bound to
proteins, but the bulkier molecules, which are usually non-binders, tend to
yield lower interaction free energies. Thus, I thought to try these two
surface types of both the protein and the ligand as descriptors in a
machine learning-based attempt to balance these differences and improve
the scoring. It remains to be seen in practice which of these two types
(molecular surface or SASA) are more useful for my purpose. I also use
other molecular descriptors, but I don't want to elaborate on this because
it's out of topic.

Best,
Thomas


On Thu, 21 May 2020 at 21:57, Thomas Holder <tho...@sc...>
wrote:

> Hi Thomas and Blaine,
>
> SASA is probably the correct feature to evaluate here, not molecular
> surface. Of course it may depend the actual goal of this exercise, but
> typically when talking about interface surface, you're putting that into
> context with binding energy or solvation effects, and only SASA is
> meaningful for that as far as I know.
>
> The difference between SASA and molecular surface is a matter of size and
> shape. For a very uneven shape (lots of small pockets or protuberances),
> going from molecular surface to SASA will flatten the surface, which can
> result in a smaller area, even though the volume is increased.
>
> You may be interested to check out PISA for this task, it's the tool the
> PDB uses to determine biological assemblies:
> https://www.ebi.ac.uk/pdbe/pisa/
>
> PyMOL's and PISA's results should be similar, but PyMOL is probably easier
> to handle :-)
>
> Cheers,
>   Thomas
>
>
> > On May 21, 2020, at 4:37 AM, Mooers, Blaine H.M. (HSC) <
> Bla...@ou...> wrote:
> >
> > Hi Thomas,
> >
> > If you display the SASA of the protein in PyMOL's viewport,
> > you will see that it and that of the ligand have huge overlaps
> > How do you define the interface in such a situation and how
> > do you interpret it?
> >
> > The interface of the molecular surfaces seems easier to interpret.
> >
> > 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: Thomas Evangelidis [te...@gm...]
> > Sent: Wednesday, May 20, 2020 9:14 AM
> > To: pymol mailinglist
> > Subject: [EXTERNAL] [PyMOL] How to compute the interface surface between
> ligand and protein?
> >
> > Greetings,
> >
> > I want to compute the interface surface between the ligand and the
> protein in batch mode for hundreds of thousands of PDBs, like the attached
> one (sample.pdb). I am interested in the interface surface of both of them.
> First I create two new molecules, the protein, and the ligand, and I work
> with them because the results I get when working with the original molecule
> (which contains both protein and ligand) are different.
> >
> > load sample.pdb
> > create protein, polymer
> > create ligand, resn LIG
> > delete sample
> >
> > select prot_interface, protein within 3.5 of ligand;
> > set dot_solvent, 0;
> > get_area prot_interface;
> > set dot_solvent, 1;
> > get_area prot_interface;
> >
> > select lig_interface, ligand within 3.5 of protein;
> > set dot_solvent, 0;
> > get_area lig_interface;
> > set dot_solvent, 1;
> > get_area lig_interface;
> >
> > protein interface molecular surface = 1216.239 Angstroms^2
> > protein interface SASA = 763.095 Angstroms^2
> > ligand interface molecular surface = 748.867 Angstroms^2
> > ligand interface SASA = 977.608 Angstroms^2
> >
> > I still don't understand why the interface molecular surface of the
> ligand is smaller than the interface SASA, while the opposite happens with
> the protein. Could someone please explain this to me and verify that I am
> computing the interface surfaces correctly?
> >
> > I thank you in advance.
> > Thomas
> >
> >
> >
> > --
> >
> > ======================================================================
> >
> > Dr. Thomas Evangelidis
> >
> > Research Scientist
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 

======================================================================

Dr. Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
  &
CEITEC - Central European Institute of Technology
<https://www.ceitec.eu/>, Brno,
Czech Republic

email: te...@gm..., Twitter: tevangelidis
<https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis
<https://www.linkedin.com/in/thomas-evangelidis-495b45125/>

website: https://sites.google.com/site/thomasevangelidishomepage/

Re: [PyMOL] tertiary structure/protein folding

[KurtYilmaz, N. <Nes...@um...>]

Hi Grace,
You may want to use a protein homology modeling software for more advanced structure building, such as Modeller.
https://salilab.org/modeller/

Nese

________________________________
From: Grace Ciabattoni <go...@le...>
Sent: Thursday, May 21, 2020 12:49 PM
To: pym...@li... <pym...@li...>
Subject: [PyMOL] tertiary structure/protein folding

Hello,
I am trying to model my protein of interest using the builder function in version 2.3. Is there a way to induce protein folding to properly mimic tertiary structure, or is secondary structure the highest manipulatable level of protein order in PyMol?
Thank you,
Grace

Re: [PyMOL] tertiary structure/protein folding

[Tamas H. <bio...@gm...>]

Hi,

Predicting tertiary structure with high accuracy is the holy grail...
I can suggest to perform homology modeling. See Modeller.
If your target is small, you can use molecular dynamics (w replica 
exchange).

Tamas

On 2020. 05. 21. 18:49, Grace Ciabattoni wrote:
> Hello,
> I am trying to model my protein of interest using the builder function 
> in version 2.3. Is there a way to induce protein folding to properly 
> mimic tertiary structure, or is secondary structure the highest 
> manipulatable level of protein order in PyMol?
> Thank you,
> Grace
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


-- 
This email has been checked for viruses by AVG.
https://www.avg.com

Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

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

Hi Thomas and Blaine,

SASA is probably the correct feature to evaluate here, not molecular surface. Of course it may depend the actual goal of this exercise, but typically when talking about interface surface, you're putting that into context with binding energy or solvation effects, and only SASA is meaningful for that as far as I know.

The difference between SASA and molecular surface is a matter of size and shape. For a very uneven shape (lots of small pockets or protuberances), going from molecular surface to SASA will flatten the surface, which can result in a smaller area, even though the volume is increased.

You may be interested to check out PISA for this task, it's the tool the PDB uses to determine biological assemblies: https://www.ebi.ac.uk/pdbe/pisa/

PyMOL's and PISA's results should be similar, but PyMOL is probably easier to handle :-)

Cheers,
  Thomas


> On May 21, 2020, at 4:37 AM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:
> 
> Hi Thomas,
> 
> If you display the SASA of the protein in PyMOL's viewport, 
> you will see that it and that of the ligand have huge overlaps
> How do you define the interface in such a situation and how 
> do you interpret it? 
> 
> The interface of the molecular surfaces seems easier to interpret. 
> 
> 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: Thomas Evangelidis [te...@gm...]
> Sent: Wednesday, May 20, 2020 9:14 AM
> To: pymol mailinglist
> Subject: [EXTERNAL] [PyMOL] How to compute the interface surface between ligand and protein?
> 
> Greetings,
> 
> I want to compute the interface surface between the ligand and the protein in batch mode for hundreds of thousands of PDBs, like the attached one (sample.pdb). I am interested in the interface surface of both of them. First I create two new molecules, the protein, and the ligand, and I work with them because the results I get when working with the original molecule (which contains both protein and ligand) are different.
> 
> load sample.pdb
> create protein, polymer
> create ligand, resn LIG
> delete sample
> 
> select prot_interface, protein within 3.5 of ligand;
> set dot_solvent, 0;
> get_area prot_interface;
> set dot_solvent, 1;
> get_area prot_interface;
> 
> select lig_interface, ligand within 3.5 of protein;
> set dot_solvent, 0;
> get_area lig_interface;
> set dot_solvent, 1;
> get_area lig_interface;
> 
> protein interface molecular surface = 1216.239 Angstroms^2
> protein interface SASA = 763.095 Angstroms^2
> ligand interface molecular surface = 748.867 Angstroms^2
> ligand interface SASA = 977.608 Angstroms^2
> 
> I still don't understand why the interface molecular surface of the ligand is smaller than the interface SASA, while the opposite happens with the protein. Could someone please explain this to me and verify that I am computing the interface surfaces correctly?
> 
> I thank you in advance.
> Thomas
> 
> 
> 
> --
> 
> ======================================================================
> 
> Dr. Thomas Evangelidis
> 
> Research Scientist

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

[Chen, Q. <qi...@pi...>]

I tried that.
that is actually how I found this is a way to color them according the CA color assigned in the spectrum.

Charles

________________________________
From: Olson, Linda <lo...@mc...>
Sent: Thursday, May 21, 2020 12:24 PM
To: Chen, Qiang <qi...@pi...>
Subject: Re: Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

Have you tried going to the first option under the color by menu which colors c alpha by whatever they are asigned?

Linda Olson, PhD
Assistant Professor/
x-Ray Facility Manager
Dept. Biochemistry
Medical College of Wisconsin
8701 Watertown Plank Rd
Milwaukee, WI 53226

phone 414-955-8545
fax      414-456-6510
________________________________
From: Chen, Qiang <qi...@pi...>
Sent: Thursday, May 21, 2020 10:20:11 AM
To: Mooers, Blaine H.M. (HSC) <Bla...@ou...>; pym...@li... <pym...@li...>
Subject: Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

ATTENTION: This email originated from a sender outside of MCW. Use caution when clicking on links or opening attachments.
________________________________
Thanks, Prof. Mooers.

I tried your script. It did not report any error. but the selected residues are colored as the default, green for carbon.

Then I figured out I made things complicated.

I created a new object (cnsp) for the cartoon representation colored with spectrum.

Then I selected residues with chain A and resi 10+20+30, and showed them as sticks. I guess, the color info of CAs from the spectrum is missing at this step.

If I selected the residues with cnsp and chain A and resi 10+20+30, then showed them with sticks, the color of sidechain is matching with CA color in the spectrum.

All I need is just util.cnc.

The working script is like the following

select cnsp, chain A
spectrum count, magenta_cyan, cnsp, byres=1
select sre, cnsp and resi 10+20+30
show sticks, sre,
util.cnc sre

Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Thursday, May 21, 2020 9:19 AM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

Hi Charles,

This pml script does want you want,

# Color the carvons atoms of the sidechain the same as the color of the CA atom
col=[]
# >>>> edit resi here
iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color)))
# Define the colors ca10, ca20, and ca40
[cmd.set_color('ca'+co[1],list(co[3]) ) for co in col]
# >>>>>>Edit color names here
colorList =['ca10','ca20','ca30']
# Check this list
[print(cmd.get_color_tuple(co)) for co in colorList]
#make a list of residues
resList = [co[1] for co in col]
# Check the list
print(resList)
# Now zip the list of colors and the list of residues
pairs = list(zip(colorList,resList))
# Check the list of lists
print(pairs)
# Check the atom selection syntax
[print('resi ' + str(pairs[i][1]) + ' and (sidechain and name c*)') for i in range(0,len(pairs))]
# Apply the pairs after defining the indices
[cmd.color(pairs[i][0], 'resi ' + str(pairs[i][1]) + ' and (sidechain and name c*)') for i in range(0,len(pairs))]

The print statements are sanity checks.
You can delete them and the comments if you want a more concise script.

You can also copy and paste this compound command onto the command line to get the get effect.
You the up arrow key to get back the command and edit the list of residues and the colorList.

col=[];iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color)));colorList =['ca10','ca20','ca30'];resList = [co[1] for co in col];pairs = list(zip(colorList,resList));[cmd.color(pairs[i][0], 'resi ' + str(pairs[i][1]) + ' and (sidechain and name c*)') for i in range(0,len(pairs))]

When you enter help color, you will see that the first argument of color is the color, which is a string.
That string is a name or number. The number is an integer that is internally mapped to a color name.
You can see these by entering the following: print(cmd.get_color_indices()).

Your col object is a list of tuples.
This is not of the data type that the color command expects.
The third line of your code returns an error because col is a list of tuples and not a string.
That number is not the same as your color tuple.
You want to apply your color tuple.
I am not sure how to do apply the color tuple because PyMOL will take the RGB values as list of integers, not as a tuple.
The returned  tuple is for use in an external program.
The above script converts the tuple into a list of integers that PyMOL can work with.
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: Chen, Qiang [qi...@pi...]
Sent: Wednesday, May 20, 2020 7:50 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

Hi, Pymol-users

I have my protein shown as cartoon and colored with spectrum. Now I would like to show several residues at different places with sticks representation. when I tried, I can not get the color consistent between the backbone CA and the carbons on the sidechain.

I searched the archives, and tried something like this.

col=[]
iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color)))
cmd.color(col,"all")
util.cnc("all")

The first two lines will get me a color_tuple of the selected residues (CA)
The third line will color all atoms as the same color of CA.
The fourth line will color all none carbon atoms with the default colors.

However, this does not work as I thought.

Would anyone point out what mistakes I made here? Or any other solution to get the consistence between CA and the sidechain?

Your help is high appreciated!

Thanks!

Charles

[PyMOL] tertiary structure/protein folding

[Grace C. <go...@le...>]

Hello,
I am trying to model my protein of interest using the builder function in
version 2.3. Is there a way to induce protein folding to properly mimic
tertiary structure, or is secondary structure the highest manipulatable
level of protein order in PyMol?
Thank you,
Grace

Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

[Chen, Q. <qi...@pi...>]

Thanks, Prof. Mooers.

I tried your script. It did not report any error. but the selected residues are colored as the default, green for carbon.

Then I figured out I made things complicated.

I created a new object (cnsp) for the cartoon representation colored with spectrum.

Then I selected residues with chain A and resi 10+20+30, and showed them as sticks. I guess, the color info of CAs from the spectrum is missing at this step.

If I selected the residues with cnsp and chain A and resi 10+20+30, then showed them with sticks, the color of sidechain is matching with CA color in the spectrum.

All I need is just util.cnc.

The working script is like the following

select cnsp, chain A
spectrum count, magenta_cyan, cnsp, byres=1
select sre, cnsp and resi 10+20+30
show sticks, sre,
util.cnc sre

Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: Thursday, May 21, 2020 9:19 AM
To: Chen, Qiang <qi...@pi...>; pym...@li... <pym...@li...>
Subject: RE: Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

Hi Charles,

This pml script does want you want,

# Color the carvons atoms of the sidechain the same as the color of the CA atom
col=[]
# >>>> edit resi here
iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color)))
# Define the colors ca10, ca20, and ca40
[cmd.set_color('ca'+co[1],list(co[3]) ) for co in col]
# >>>>>>Edit color names here
colorList =['ca10','ca20','ca30']
# Check this list
[print(cmd.get_color_tuple(co)) for co in colorList]
#make a list of residues
resList = [co[1] for co in col]
# Check the list
print(resList)
# Now zip the list of colors and the list of residues
pairs = list(zip(colorList,resList))
# Check the list of lists
print(pairs)
# Check the atom selection syntax
[print('resi ' + str(pairs[i][1]) + ' and (sidechain and name c*)') for i in range(0,len(pairs))]
# Apply the pairs after defining the indices
[cmd.color(pairs[i][0], 'resi ' + str(pairs[i][1]) + ' and (sidechain and name c*)') for i in range(0,len(pairs))]

The print statements are sanity checks.
You can delete them and the comments if you want a more concise script.

You can also copy and paste this compound command onto the command line to get the get effect.
You the up arrow key to get back the command and edit the list of residues and the colorList.

col=[];iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color)));colorList =['ca10','ca20','ca30'];resList = [co[1] for co in col];pairs = list(zip(colorList,resList));[cmd.color(pairs[i][0], 'resi ' + str(pairs[i][1]) + ' and (sidechain and name c*)') for i in range(0,len(pairs))]

When you enter help color, you will see that the first argument of color is the color, which is a string.
That string is a name or number. The number is an integer that is internally mapped to a color name.
You can see these by entering the following: print(cmd.get_color_indices()).

Your col object is a list of tuples.
This is not of the data type that the color command expects.
The third line of your code returns an error because col is a list of tuples and not a string.
That number is not the same as your color tuple.
You want to apply your color tuple.
I am not sure how to do apply the color tuple because PyMOL will take the RGB values as list of integers, not as a tuple.
The returned  tuple is for use in an external program.
The above script converts the tuple into a list of integers that PyMOL can work with.
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: Chen, Qiang [qi...@pi...]
Sent: Wednesday, May 20, 2020 7:50 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

Hi, Pymol-users

I have my protein shown as cartoon and colored with spectrum. Now I would like to show several residues at different places with sticks representation. when I tried, I can not get the color consistent between the backbone CA and the carbons on the sidechain.

I searched the archives, and tried something like this.

col=[]
iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color)))
cmd.color(col,"all")
util.cnc("all")

The first two lines will get me a color_tuple of the selected residues (CA)
The third line will color all atoms as the same color of CA.
The fourth line will color all none carbon atoms with the default colors.

However, this does not work as I thought.

Would anyone point out what mistakes I made here? Or any other solution to get the consistence between CA and the sidechain?

Your help is high appreciated!

Thanks!

Charles

Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

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

Hi Charles,

This pml script does want you want, 

# Color the carvons atoms of the sidechain the same as the color of the CA atom
col=[]
# >>>> edit resi here
iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color)))
# Define the colors ca10, ca20, and ca40
[cmd.set_color('ca'+co[1],list(co[3]) ) for co in col]
# >>>>>>Edit color names here
colorList =['ca10','ca20','ca30']
# Check this list
[print(cmd.get_color_tuple(co)) for co in colorList]
#make a list of residues
resList = [co[1] for co in col]
# Check the list
print(resList)
# Now zip the list of colors and the list of residues
pairs = list(zip(colorList,resList))
# Check the list of lists
print(pairs)
# Check the atom selection syntax
[print('resi ' + str(pairs[i][1]) + ' and (sidechain and name c*)') for i in range(0,len(pairs))]
# Apply the pairs after defining the indices
[cmd.color(pairs[i][0], 'resi ' + str(pairs[i][1]) + ' and (sidechain and name c*)') for i in range(0,len(pairs))]

The print statements are sanity checks. 
You can delete them and the comments if you want a more concise script.

You can also copy and paste this compound command onto the command line to get the get effect. 
You the up arrow key to get back the command and edit the list of residues and the colorList.

col=[];iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color)));colorList =['ca10','ca20','ca30'];resList = [co[1] for co in col];pairs = list(zip(colorList,resList));[cmd.color(pairs[i][0], 'resi ' + str(pairs[i][1]) + ' and (sidechain and name c*)') for i in range(0,len(pairs))]

When you enter help color, you will see that the first argument of color is the color, which is a string. 
That string is a name or number. The number is an integer that is internally mapped to a color name.
You can see these by entering the following: print(cmd.get_color_indices()).  

Your col object is a list of tuples.
This is not of the data type that the color command expects.
The third line of your code returns an error because col is a list of tuples and not a string.
That number is not the same as your color tuple. 
You want to apply your color tuple. 
I am not sure how to do apply the color tuple because PyMOL will take the RGB values as list of integers, not as a tuple. 
The returned  tuple is for use in an external program.
The above script converts the tuple into a list of integers that PyMOL can work with.
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: Chen, Qiang [qi...@pi...]
Sent: Wednesday, May 20, 2020 7:50 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

Hi, Pymol-users

I have my protein shown as cartoon and colored with spectrum. Now I would like to show several residues at different places with sticks representation. when I tried, I can not get the color consistent between the backbone CA and the carbons on the sidechain.

I searched the archives, and tried something like this.

col=[]
iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color)))
cmd.color(col,"all")
util.cnc("all")

The first two lines will get me a color_tuple of the selected residues (CA)
The third line will color all atoms as the same color of CA.
The fourth line will color all none carbon atoms with the default colors.

However, this does not work as I thought.

Would anyone point out what mistakes I made here? Or any other solution to get the consistence between CA and the sidechain?

Your help is high appreciated!

Thanks!

Charles

[PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

[Chen, Q. <qi...@pi...>]

Hi, Pymol-users

I have my protein shown as cartoon and colored with spectrum. Now I would like to show several residues at different places with sticks representation. when I tried, I can not get the color consistent between the backbone CA and the carbons on the sidechain.

I searched the archives, and tried something like this.

col=[]
iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color)))
cmd.color(col,"all")
util.cnc("all")

The first two lines will get me a color_tuple of the selected residues (CA)
The third line will color all atoms as the same color of CA.
The fourth line will color all none carbon atoms with the default colors.

However, this does not work as I thought.

Would anyone point out what mistakes I made here? Or any other solution to get the consistence between CA and the sidechain?

Your help is high appreciated!

Thanks!

Charles

Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

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

Hi Thomas,

If you display the SASA of the protein in PyMOL's viewport, 
you will see that it and that of the ligand have huge overlaps
How do you define the interface in such a situation and how 
do you interpret it? 

The interface of the molecular surfaces seems easier to interpret. 

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: Thomas Evangelidis [te...@gm...]
Sent: Wednesday, May 20, 2020 9:14 AM
To: pymol mailinglist
Subject: [EXTERNAL] [PyMOL] How to compute the interface surface between ligand and protein?

Greetings,

I want to compute the interface surface between the ligand and the protein in batch mode for hundreds of thousands of PDBs, like the attached one (sample.pdb). I am interested in the interface surface of both of them. First I create two new molecules, the protein, and the ligand, and I work with them because the results I get when working with the original molecule (which contains both protein and ligand) are different.

load sample.pdb
create protein, polymer
create ligand, resn LIG
delete sample

select prot_interface, protein within 3.5 of ligand;
set dot_solvent, 0;
get_area prot_interface;
set dot_solvent, 1;
get_area prot_interface;

select lig_interface, ligand within 3.5 of protein;
set dot_solvent, 0;
get_area lig_interface;
set dot_solvent, 1;
get_area lig_interface;

protein interface molecular surface = 1216.239 Angstroms^2
protein interface SASA = 763.095 Angstroms^2
ligand interface molecular surface = 748.867 Angstroms^2
ligand interface SASA = 977.608 Angstroms^2

I still don't understand why the interface molecular surface of the ligand is smaller than the interface SASA, while the opposite happens with the protein. Could someone please explain this to me and verify that I am computing the interface surfaces correctly?

I thank you in advance.
Thomas



--

======================================================================

Dr. Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.uochb.cz_web_structure_31.html-3Flang-3Den&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kgJ3ggEDW_MHgArC60SMFo77wMerMvyyPjI3lu1Fj8U&s=_57VI-rsaa_XreiW4XyCB4JCeYxIgxYQMzE2-4tSVZY&e=>, Prague, Czech Republic

  &
CEITEC - Central European Institute of Technology<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ceitec.eu_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kgJ3ggEDW_MHgArC60SMFo77wMerMvyyPjI3lu1Fj8U&s=A2aVI7iISZXV0okVxr2DaiNghbfhZnUYoT3Yoev5S9U&e=>, Brno, Czech Republic


email: te...@gm...<mailto:te...@gm...>, Twitter: tevangelidis<https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_tevangelidis&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kgJ3ggEDW_MHgArC60SMFo77wMerMvyyPjI3lu1Fj8U&s=xm1YlcM5Yu2NrXsLFcftypRirhta1tskIsgqE4aGA0U&e=>, LinkedIn: Thomas Evangelidis<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_thomas-2Devangelidis-2D495b45125_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kgJ3ggEDW_MHgArC60SMFo77wMerMvyyPjI3lu1Fj8U&s=attBDYWqEeZXqfolM-a1fEo5S7h671troeIdMmvv6Wo&e=>

website: https://sites.google.com/site/thomasevangelidishomepage/<https://urldefense.proofpoint.com/v2/url?u=https-3A__sites.google.com_site_thomasevangelidishomepage_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kgJ3ggEDW_MHgArC60SMFo77wMerMvyyPjI3lu1Fj8U&s=B9x_aKai1Ed5wAeUbu0U8rN9y2bjXnsT6Cv8QC-UCqs&e=>

[PyMOL] How to compute the interface surface between ligand and protein?

[Thomas E. <te...@gm...>]

Greetings,

I want to compute the interface surface between the ligand and the protein
in batch mode for hundreds of thousands of PDBs, like the attached one
(sample.pdb). I am interested in the interface surface of both of them.
First I create two new molecules, the protein, and the ligand, and I work
with them because the results I get when working with the original molecule
(which contains both protein and ligand) are different.

load sample.pdb
> create protein, polymer
> create ligand, resn LIG
> delete sample
>
> select prot_interface, protein within 3.5 of ligand;
> set dot_solvent, 0;
> get_area prot_interface;
> set dot_solvent, 1;
> get_area prot_interface;
>
> select lig_interface, ligand within 3.5 of protein;
> set dot_solvent, 0;
> get_area lig_interface;
> set dot_solvent, 1;
> get_area lig_interface;


protein interface molecular surface = 1216.239 Angstroms^2
protein interface SASA = 763.095 Angstroms^2
ligand interface molecular surface = 748.867 Angstroms^2
ligand interface SASA = 977.608 Angstroms^2

I still don't understand why the interface molecular surface of the ligand
is smaller than the interface SASA, while the opposite happens with the
protein. Could someone please explain this to me and verify that I am
computing the interface surfaces correctly?

I thank you in advance.
Thomas



-- 

======================================================================

Dr. Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
  &
CEITEC - Central European Institute of Technology
<https://www.ceitec.eu/>, Brno,
Czech Republic

email: te...@gm..., Twitter: tevangelidis
<https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis
<https://www.linkedin.com/in/thomas-evangelidis-495b45125/>

website: https://sites.google.com/site/thomasevangelidishomepage/

[PyMOL] PyMOL 2.4 released

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

Greetings,

We are happy to announce the release of PyMOL 2.4. Download ready-to-use bundles from https://pymol.org/ or update your installation with "conda install -c schrodinger pymol".

Highlights:

- Incentive PyMOL only:
  - Support for https://lookingglassfactory.com/schrodinger 
  - Pi-Pi and Pi-Cation interactions (A > find > pi-interactions)
  - WaterMap result presets (A > preset > WaterMap ...)
  - APBS Plugin improvements (multi-state assemblies, propka pH calculation)

- Open-Source and Incentive PyMOL:
  - Distinguish .mrc and .ccp4 formats (origin interpretation)
  - Trajectory handling improvements
  - Improved error handling in Python API with exceptions
  - ... many bug fixes

This will be the last release with support for Python 2.7.

Find the complete release notes at:
https://pymol.org/d/media:new24 

We welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schrödinger

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.