pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Combine two states into one state?

[Nicholas G. <dom...@gm...>]

Dear PyMOL users,

I have an antibody-antigen structure where the authors have put the antigen
atoms in state 1 and put the antibody atoms in state 2.  Is there a good
way via command line to collapse state 1 and 2 into a single state, where
both antibody and antigen atoms are viewable together?

Sincerely,
Nicholas Gao

Re: [PyMOL] Extract H-bond angle

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

Hello PyMOL users,

With "list_hbonds analyte" command, PyMOL gives the list of all H-bonds
with distances in a protein.
I was wondering how to also extract H-bond angle information for those
h-bonds. Is there a command line for this?

Thank you so much,
Neena

On Thu, 3 Mar 2022 at 19:10, Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> With "list_hbonds analyte" command, PyMOL gives the list of all H-bonds
> with distances in a protein.
> I was wondering how to also extract H-bond angle information for those
> h-bonds. Is there a command line for this?
>
> Thank you so much,
> Neena
>

Re: [PyMOL] Virtual Annual CCP4/APS Crystallographic School (2022) in the US

[Qingping Xu <qx...@an...>]

Dear Colleagues,

Just a friendly reminder that the registration of the upcoming CCP4/APS 
virtual school is open. If you plan to attend the school, please submit 
your application before the Apr 15th, 2022 deadline, preferably sooner.

The school schedule is available on the CCP4 school website 
(https://www.ccp4.ac.uk/schools/APS-2022/index.php).

Charles, Andrey, Garib and Qingping


On 1/24/22 10:07, Qingping Xu wrote:
>
> Dear Colleagues,
>
> We are pleased to announce the virtual annual CCP4/APS 
> crystallographic school “From data collection to structure refinement 
> and beyond” will be held on June 13-24, 2022 at the Advanced Photon 
> Source (APS), Argonne National Laboratory (ANL), near Chicago, 
> Illinois, USA. All details can be found at the school website: 
> http://www.ccp4.ac.uk/schools/APS-2022/index.php.
>
> Dates: June 6 (Bioinformatics & setup) and June 13 through 24, 2022 
> (with a weekend break on June 18 and 19th)
>
> Location: Virtual/Remote
>
> The school comprises two parts: remote data collection workshop and 
> virtual crystallographic computing workshop. Data collection workshop 
> includes beamline training, data collection on GM/CA at APS beamlines 
> 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors 
> respectively, and data processing. For data collection, only the 
> participants’ crystals will be used. Crystallographic computation 
> workshop will feature many modern crystallographic software packages 
> taught by authors and other experts. The daily schedule will be 
> organized in three sections – lectures, tutorials, and hands-on 
> (interactive troubleshooting of the technical difficulties the 
> participants face in their projects). We have had considerable success 
> resolving these problems in past years, attested by resulting 
> publications (see 
> http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft of 
> the program, contact info and other details can be found at the School 
> website. Note that for the virtual school, an additional day (June 
> 6th, 2022) was scheduled to prepare for the main event, with lectures 
> on generating AlphaFold models to use in later part of the school.
>
> Applicants: Graduate students, postdoctoral researchers and 
> early-career faculty, along with commercial/industrial researchers are 
> encouraged to apply. Only about 20 applicants will be selected for 
> participation. Participants of the workshop are strongly encouraged to 
> bring their own problem data sets or crystals so the problems can be 
> addressed during data collection and/or computation workshops.
>
> Application: Application deadline is April 15th, 2022. To apply, visit 
> https://www.ccp4.ac.uk/schools/APS-2022/application.php.
>
> Fees: There is no fee for attending the virtual school for the chosen 
> applicants.
>
> We hope to see you at the school.
>
> Charles, Andrey, Garib and Qingping
>

Re: [PyMOL] Pymol-Alignment Module

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

Hi Ecem -

If I understand correctly, you first want to align on one set of residues
and calculate their RMSD, then to calculate the RMSD for the remaining
residues without moving the structures.  This is straightforward using
PyMOL's internal command line.

```
# Create two selections called "sel1" and "sel2"
select sel1, resi 1-20
select sel2, resi 30-100

# Note: if the numbering is different between the structures, you may need
something like this instead:
# select sel1, (struc1 and resi 1-20) or (struc2 and resi 2-21)

# Superimpose the structures (this prints the RMSD to the console)
super struc1 and sel1, struc2 and sel1

# Calculate the "in-place" RMSD for the remaining residues (also printed to
the console)
rms_cur struc1 and sel2, struc2 and sel2
```

Note that if there are any residues with alternate conformations, or if the
numbering is different between the two structures, the `rms_cur` step may
need to be modified as indicated in the examples on its wiki page
<https://pymolwiki.org/index.php/Rms_cur#Examples>.

Hope that helps.

Cheers,
Jared


On Fri, Mar 4, 2022 at 5:37 AM Ecem Güngör <ece...@gm...> wrote:

> Dear Pymol community,
>
> I have a question about alignment module of Pymol. I have two different
> pdb ids and each have about 100 amino acid long. I would like to align the
> specific parts of these proteins and see both how the rest of the proteins
> and also these specific parts superimpose with each other. In other words,
> if I align the proteins based on their 20-30 amino acids, I would like to
> first see what the RMSD is for these specific regions (20-30 aa) and then
> the RMSD of the rest (1-20 and 30-100) is. I truly appreciate your
> suggestions and guidance on this. Thank you!
>
> Have a great week/weekend,
> Ecem
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] saving info regarding protein-ligand interactions in the log

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

Dear Pymol users!
I am using a multi-model pdb containing the 80 predicted docking
solutions as well as the receptor (the both presented in each frame).
I need to calculate all hydrogen bonds (and possible other
interactions) observed in each frame (=docking solution)? I've already
used pymol for the visualizations of the interactions, and find it
very useful for the visual inspection. May I use some pymol script in
order that I could save the information regarding the observed
interactions in the log file?
Many thanks in advance
Cheers,
Enrico

[PyMOL] Pymol-Alignment Module

[Ecem G. <ece...@gm...>]

Dear Pymol community,

I have a question about alignment module of Pymol. I have two different pdb
ids and each have about 100 amino acid long. I would like to align the
specific parts of these proteins and see both how the rest of the proteins
and also these specific parts superimpose with each other. In other words,
if I align the proteins based on their 20-30 amino acids, I would like to
first see what the RMSD is for these specific regions (20-30 aa) and then
the RMSD of the rest (1-20 and 30-100) is. I truly appreciate your
suggestions and guidance on this. Thank you!

Have a great week/weekend,
Ecem

[PyMOL] Extract H-bond angle

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

Hello PyMOL users,

With "list_hbonds analyte" command, PyMOL gives the list of all H-bonds
with distances in a protein.
I was wondering how to also extract H-bond angle information for those
h-bonds. Is there a command line for this?

Thank you so much,
Neena

[PyMOL] Query about inserting ligand at preferred base pairs of DNA

[Sneha K. <Sne...@ug...>]

Hello Team,

I need help in inserting ligand to base pair in DNA. I have a drug molecule and want to insert in between the base pairs I am interested in ( it is 12-mer dsDNA). I tried to follow the tutorials but cannot find something where I can insert ligand into the custom DNA sequence I have generated.

I will appreciate if you can please help me or guide me where I can study and understand how to do it.

Thank you,
Sneha

[PyMOL] undefined symbol: H5Pset_fapl_ros3

[amirhossein t. <tag...@gm...>]

Hello,

I am trying to install the pymol with "conda install -c conda-forge -c
schrodinger pymol-bundle".
package is installed without error messages but it fails to start:

I tried the latest libnetcdf "conda install -c conda-forge libnetcdf"
and a clean install but failed again.

Could you please let me know how to solve this?

Best,
Amir

cannot import name addmenuitemqt
Unable to initialize plugin 'fingernat-pymol-plugin-0-4'
(pmg_tk.startup.fingernat-pymol-plugin-0-4).
cannot import name addmenuitemqt
Unable to initialize plugin 'fingernat-pymol-plugin-main'
(pmg_tk.startup.fingernat-pymol-plugin-main).
 PyMOL: normal program termination.

[PyMOL] Align with axis and rewrite coordinates

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

Is there a way to open a crystal structure and realign the structure with an axis, then save the transformed coordinates?  I want all atoms to remain in the same position with respect to each other...just not with respect to the crystallographically defined x, y, z.  I have tried alter_state command with rebuild....but I only seem to be able to find commands that translate along the x, y, z. The rebuild does rewrite the coordinates, so that bit is working.  I have tried rotating, but this only rotates around an already defined axis.  I need to move the structure away from the predefined axis positions; the easiest way I could think would be to align with a current axis, but open to other ideas. For example, if there is a way to incorporate sine and cosine into the alter_state function...

Thanks in advance!


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

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

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

I have tried to do it in the same way and saw the same errors. I may
think that it does not work with the latest pymol.. May someone
suggest to me some other plugin which could be useful to describe
protein-ligand contacts (electrostatic, vdW etc )?
Many thanks !!
Enrico

пт, 18 февр. 2022 г. в 13:49, Saurabh Gayali <sau...@gm...>:
>
> I was able to install it by downloading the zip file for the web version link and installing inside pymol for the local file.
>
>
> However, it shows an error for initialization:
>
> When using Fetch URl mode, it shows charmap error.
>
> ________________________________
>
> Saurabh Gayali / Post Doctoral Fellow
> sau...@gm... / +91 8800412916
>
>
> Noida, UP, India
>
>
>
> Sender notified by
> Mailtrack 18/02/22, 06:19:03 pm
>
> On Thu, Feb 17, 2022 at 4:16 PM Enrico Martinez <jms...@gm...> wrote:
>>
>> Dear Pymol Users!
>> I am looking for some pymol plugin for the detailed analysis of
>> protein-ligand interactions. I have already seen:
>> http://mordred.bioc.cam.ac.uk/intermezzo/
>> but I could not understand how I could install it ( I am using pymol
>> 2.4 pro installed on my MACBOOK and it seems to me that the package
>> had been developed for the previous release).
>>
>> On the site I found:
>>
>> "Additionally, it will soon also be possible to install the plugin
>> using the "Install from PyMOLWiki" and "Install from Repository"
>> sections."
>>
>> but eventually I could not find it in pymolWIKI.
>>
>> May you suggest some other solutions which would work with my pymol version ?
>>
>> Many thanks in advance
>> Enrico
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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

[Saurabh G. <sau...@gm...>]

I was able to install it by downloading the zip file for the web version
link and installing inside pymol for the local file.
[image: image.png]

However, it shows an error for initialization:
[image: image.png]
When using Fetch URl mode, it shows charmap error.
[image: image.png]
------------------------------

*Saurabh Gayali* / Post Doctoral Fellow
sau...@gm... / +91 8800412916


<http://example.com/>Noida, UP, India


[image: Mailtrack]
<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&>
Sender
notified by
Mailtrack
<https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&>
18/02/22,
06:19:03 pm

On Thu, Feb 17, 2022 at 4:16 PM Enrico Martinez <jms...@gm...>
wrote:

> Dear Pymol Users!
> I am looking for some pymol plugin for the detailed analysis of
> protein-ligand interactions. I have already seen:
> http://mordred.bioc.cam.ac.uk/intermezzo/
> but I could not understand how I could install it ( I am using pymol
> 2.4 pro installed on my MACBOOK and it seems to me that the package
> had been developed for the previous release).
>
> On the site I found:
>
> "Additionally, it will soon also be possible to install the plugin
> using the "Install from PyMOLWiki" and "Install from Repository"
> sections."
>
> but eventually I could not find it in pymolWIKI.
>
> May you suggest some other solutions which would work with my pymol
> version ?
>
> Many thanks in advance
> Enrico
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

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

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

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

On the site I found:

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

but eventually I could not find it in pymolWIKI.

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

Many thanks in advance
Enrico

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

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

Hi James,

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

Best,

Jarrett Johnson

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

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



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

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

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

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




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

Hi James,

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

Best,

Jarrett Johnson

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

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

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

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


Thanks in advance !
Jim Procter.

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

The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


--

Jarrett Johnson | Senior Developer, PyMOL

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

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

Re: [PyMOL] CGO object code structure

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

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

Hope that helps.

Cheers,
Jared

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

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

Re: [PyMOL] Installing in Linux

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

Hello Peter,

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

  sudo apt-get install pymol

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

Cheers,
Rob

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

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



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

[PyMOL] Align with Axis and Rewrite Coordinates

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

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

Thanks,

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

[PyMOL] Installing in Linux

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

Greetings,

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

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

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

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

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

Dear pymol-users

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

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

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


Thanks in advance !
Jim Procter.

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

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

Re: [PyMOL] CGO object code structure

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

Hi Marcelo -

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

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

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

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

Hope that helps.

Cheers,
Jared

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

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

Re: [PyMOL] CGO object code structure

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

Thank you Jared,

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

Best regards,
--
Marcelo

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

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

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

Re: [PyMOL] CGO object code structure

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

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

    set cgo_transparency, 0.5, my_cgo_object

Cheers,
Jared

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

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

Re: [PyMOL] CGO object code structure

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

Hi Marcelo -

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

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

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

Hope that helps.

Cheers,
Jared


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

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

[PyMOL] CGO object code structure

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

Hi all,

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

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

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

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