pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Structure alignment -- general question

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

extra_fit command will work in this scenario.

More information in documentation here:
https://pymolwiki.org/index.php/Extra_fit

------------------------------

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

*CSIR-IGIB*
<http://example.com/>New Delhi, India


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04/01/22,
04:18:41 pm

On Tue, Jan 4, 2022 at 3:18 PM George Tzotzos via PyMOL-users <
pym...@li...> wrote:

> I’m dealing with 4 heterogeneous structures belonging to the same fold.
> I’d like to compare some conserved structural features and for this purpose
> it would be useful that the structures are aligned and then visualised in a
> grid.
>
> I understand that the align command works for 2 structures only. Is there
> another way achieve what I described above.
>
> Looking forward to any suggestions
>
> Many thanks in advance and all the best for 2022
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Structure alignment -- general question

[George T. <gtz...@me...>]

I’m dealing with 4 heterogeneous structures belonging to the same fold. I’d like to compare some conserved structural features and for this purpose it would be useful that the structures are aligned and then visualised in a grid.

I understand that the align command works for 2 structures only. Is there another way achieve what I described above.

Looking forward to any suggestions

Many thanks in advance and all the best for 2022

[PyMOL] Analysis of protein-ligand interactions

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

Dear Pymol users!
I am performing analysis of protein-ligand interactions for the ligand
pose established in protein-docking and comparing it with the pattern
observed in the X-ray structure for the same complex.
Is it possible to use some Pymol command in the pymol's command line
to save (in the text log) all of the non-bonded interactions
established between ligand and all of the surrounded groups of the
receptor for two different selections:
(1) between the conformation used for docking and the best docking pose
(2) between the X-ray structure + it's (native) ligand pose

assuming that ((1): two different objects for receptor.pdb and the
ensemble of docking conformations) and ((2): one object consisting of
ligand and receptor together) are loaded in Pymol.
Many thanks in advance!
Cheers
Enrico

[PyMOL] Unable to run pymol from Linux command line

[Max L. <ma...@ya...>]

Hi, 

I installed pymol on Ubuntu 20.04 on WSL (Windows 10) using:

sudo apt-get install -y pymol

However, when I run pymol on the command line, I get this error:

<string>:1: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
qt.qpa.xcb: could not connect to display
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb.
Aborted

What should I do to get pymol to work?  

Best regards, 
Max

[PyMOL] Distorted 3-10 helix

[Bonsor, D. (NIH/N. [C] <dan...@ni...>]

Dear All,

My latest structure has several 3-10 helices present, however, a few of them in cartoon form shows the starting residue of the helix to be distorted/twisted.

The structure is 2.2Ang and I can clearly see the position of the amide bond and the direction of carbonyl, but I cannot stop the twisting of the cartoon.

I have tried altering that residue ss to a loop which “works” (as in the problem goes away) but I really wish to show the full helix. I have also run DSSPtoPDB and force it not to recognize the 3-10 helices as helices but in cartoon form you can see they are helices.

Do anyone have suggestions or a way to force it to be a helix?
[A close up of a toy  Description automatically generated with low confidence]
Thanks,

Daniel


[Text Frederick National Laboratory on a teal background]

[LinkedIn icon]<https://www.linkedin.com/company/frederick-national-laboratory-for-cancer-research/> [Twitter icon] <https://twitter.com/FredNatLab>   [Facebook icon] <https://www.facebook.com/FredNatLab>   [Instagram icon] <https://www.instagram.com/frednatlab/>
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RAS Structural Biology


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Re: [PyMOL] Can i find a specific sequence in pymol?

[Mirna D. <mir...@uc...>]

Hello,

Can I please unsubscribe from the mail lists?

Best,
Mirna

From: Ambbar Aballay González <amb...@gm...>
Sent: December 15, 2021 12:06 PM
To: Thomas Holder <th...@th...>
Cc: he...@sc...; pymol-users <pym...@li...>
Subject: Re: [PyMOL] Can i find a specific sequence in pymol?

[△EXTERNAL]

Thank you very much.


Ambbar


El mié, 15 dic 2021 a las 16:02, Thomas Holder (<th...@th...<mailto:th...@th...>>) escribió:
Hi Ambbar,

To select sequence "ACDEF", you can do:

select mysele, pepseq ACDEF

See also https://pymolwiki.org/index.php/Selection_Algebra

Cheers,
  Thomas

On Wed, Dec 15, 2021 at 7:54 PM Ambbar Aballay González
<amb...@gm...<mailto:amb...@gm...>> wrote:
>
> Dear friends,
> How can I find and select a specific sequence in pymol, while displaying the PDB?
>
> have a nice day
>
> Kinds Regards
>
> Ambbar Aballay González
> Universidad de Concepción, Chile.
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Can i find a specific sequence in pymol?

[Thomas H. <th...@th...>]

Hi Ambbar,

To select sequence "ACDEF", you can do:

select mysele, pepseq ACDEF

See also https://pymolwiki.org/index.php/Selection_Algebra

Cheers,
  Thomas

On Wed, Dec 15, 2021 at 7:54 PM Ambbar Aballay González
<amb...@gm...> wrote:
>
> Dear friends,
> How can I find and select a specific sequence in pymol, while displaying the PDB?
>
> have a nice day
>
> Kinds Regards
>
> Ambbar Aballay González
> Universidad de Concepción, Chile.
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Can i find a specific sequence in pymol?

[Ambbar A. G. <amb...@gm...>]

Thank you very much.


Ambbar



El mié, 15 dic 2021 a las 16:02, Thomas Holder (<th...@th...>)
escribió:

> Hi Ambbar,
>
> To select sequence "ACDEF", you can do:
>
> select mysele, pepseq ACDEF
>
> See also https://pymolwiki.org/index.php/Selection_Algebra
>
> Cheers,
>   Thomas
>
> On Wed, Dec 15, 2021 at 7:54 PM Ambbar Aballay González
> <amb...@gm...> wrote:
> >
> > Dear friends,
> > How can I find and select a specific sequence in pymol, while displaying
> the PDB?
> >
> > have a nice day
> >
> > Kinds Regards
> >
> > Ambbar Aballay González
> > Universidad de Concepción, Chile.
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

[PyMOL] Can i find a specific sequence in pymol?

[Ambbar A. G. <amb...@gm...>]

Dear friends,
How can I find and select a specific sequence in pymol, while displaying
the PDB?

have a nice day

Kinds Regards

Ambbar Aballay González
Universidad de Concepción, Chile.

[PyMOL] Ruge problem visualization of PDBQT file on pymol

[EDUARDO J. A. C. <ed...@ep...>]

Dear friends
how are you? I hope you are doing well
I am using autodock vina for virtual screening.. I used the LigPret to
prepare my ligands into mol2 file, however when MGLTools convert the mol2
to PDBQT and specially the vina output file in PDBQT has become a very
anomalous and strange molecule structure.
This file attached is ZINC100199761 molecule structure in mol2 generated
from SMILE sequence using LigPrep. After LigPrep I pass it
through the Avogadro to obtain the best geometry optimization
Only after that I make the PDBQT conversion using the MGLTools and so the
molecular docking using vina.

Well did you know what is happening?? Is it a pymol visualization problem
with pdqbt files?
Could Anyone could know what the problem is and how to fix it?
Thanks a lot!!

have a nice end year

Kinds Regards

Eduardo Jose Azevedo Correa
from Brazil
-- 

*Eduardo José Azevedo Corrêa*

Biólogo| Professor e Pesquisador


(37)9997-5771

(37)3271-4673

*www.epamig.br <http://www.epamig.br/>*

*EPAMIG Pitangui*
Rodovia BR - MG352 Km35 Zona Rural

Caixa Postal 43

CEP 35650-000 - Pitangui - MG

[PyMOL] Problem Compiling PyMOL in WSL2/Debian Bullseye

[Stephen P. M. <s.m...@sb...>]

I have installed Debian Bullseye on my Windows 10 Laptop using WSL2 and 
have encountered a problem with PyMOL-2.6.a0a.

I compiled the source code using the instructions in the PyMOL Wiki.

Unfortunately, there were errors when I attempted running PyMOL:

Please wait...

Qt not available (pymol.Qt), using GLUT/Tk interface
Traceback (most recent call last):
   File "/home/comp/Apps/PyMOL-2.6.a0a/lib/python/pymol/__init__.py", 
line 73, in <module>
     sys.exit(pymol.launch(args))
   File "/home/comp/Apps/PyMOL-2.6.a0a/lib/python/pymol/__init__.py", 
line 429, in launch
     _cmd.runpymol(None, block_input_hook)
NotImplementedError: compile with --glut

 >>>> END OF COMMAND <<<<

The build commands and build log are attached.

I should mention that I have comp[iled PyMOL quite a few times in 
multiple Linux distros without this particular problem.

A solution will be appreciated.

Thanks in advance.

-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1

[PyMOL] drawing small organic molecules

[Janos D. <jan...@gm...>]

Dear All,

I am searching for some features in pymol, I hope these are implemented
features:
I would like to:
-add crosses on spheres like:
https://www.cylview.org/ewExternalFiles/CYLview_manual_revC.pdf (page 1.)
or
https://rb.gy/gru47s

-increase the stick diameter for H atoms from commandline like:

Setting: stick_h_scale set to 1.00000. (Settings/ lines and sticks /
hydrogen scale: 1)
-add and remove bonds from commandline
-add dashed bonds from commandline


Many thanks in advance!

Best,

Janos

Re: [PyMOL] PyMOL for M1 macs

[Florian N. <mai...@na...>]

Hi,

You can install the open source version 2.5 of PyMOL using homebrew and it will be M1 native (see https://brew.sh)

But frankly, the intel version is already so fast with rosetta2 on the M1 that it does not worth it except if you do really fancy stuff.

Florian

> On 6 Dec 2021, at 08:00, Chris Swain via PyMOL-users <pym...@li...> wrote:
> 
> Hi,
> 
> Thanks all will give it a try
> 
> Cheers,
> 
> Chris
> 
>> On 6 Dec 2021, at 06:08, Jarrett Johnson <jar...@sc... <mailto:jar...@sc...>> wrote:
>> 
>> IIRC when we tried with Rosetta2, PyMOL was still faster (about 2x I think) than the previous x86. Your mileage may vary.
>> 
>> Best,
>> Jarrett J
>> 
>> On Mon, Dec 6, 2021 at 12:46 AM Xin Yu <xin...@gm... <mailto:xin...@gm...>> wrote:
>> It looks like while you can’t run it natively on M1, maybe you can do it through rosetta2 translation via Conda install?
>> See here: https://pymol.org/2/support.html? <https://pymol.org/2/support.html?>
>> Supported platform states M1 with rosetta2. Perhaps with some penalty for efficiency though. Anyone tried?
>> 
>> Sent from my iPhone
>> 
>>> On Dec 5, 2021, at 10:27 PM, Jarrett Johnson <jar...@sc... <mailto:jar...@sc...>> wrote:
>>> 
>>> 
>>> Hi Chris,
>>> 
>>> We haven't released any official Incentive PyMOL builds yet for M1 ARM mac yet but it's on our radar to do so soon.
>>> 
>>> Best,
>>> 
>>> Jarrett J
>>> 
>>> On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users <pym...@li... <mailto:pym...@li...>> wrote:
>>> Hi,
>>> 
>>> Is there a build of PyMOL for M1 Macs yet?
>>> 
>>> Cheers,
>>> 
>>> Chris
>>> 
>>> 
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
>>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
>>> 
>>> 
>>> -- 
>>> Jarrett Johnson | Senior Developer, PyMOL
>>> 
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
>>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
>> 
>> -- 
>> Jarrett Johnson | Senior Developer, PyMOL
>> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Missing structure

[Dr. K. M J. <kj...@st...>]

Looks like the nucleic acid sits on a 2-fold crystallographic symmetry axis. You can generate symmetry-related molecules using symexp:

https://pymolwiki.org/index.php/Symexp

Alternatively, from the rcsb page for the structure, click “Download Files > Biological Assembly” or fetch it in pymol with:
Fetch 1bg1, type=pdb1


From: JJ Oliveira <joa...@gm...>
Date: Wednesday, December 8, 2021 at 9:57 AM
To: PYMOLBB <PyM...@li...>
Subject: [PyMOL] Missing structure
Hi there

PyMol doesn't show the full PDB file 1BG1 (TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX) as shown in rcsb.org<http://rcsb.org> (2nd attached image).

How do I fix that?

Thank you!

[cid:image001.png@01D7EC1D.B053FD20]
[cid:image002.png@01D7EC1D.B053FD20]

Re: [PyMOL] Missing structure

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

Hello,

The top image from the RCSB site is illustrating the entire biological
assembly. From what I see, the PDB file includes data for the
asymmetric unit.

To get the whole assembly:

`set assembly, 1`
`fetch 1bg1`

should get you what you want.


Best,
Jarrett J.

On Wed, Dec 8, 2021 at 12:56 PM JJ Oliveira <joa...@gm...> wrote:

> Hi there
>
> PyMol doesn't show the full PDB file 1BG1 (TRANSCRIPTION FACTOR STAT3B/DNA
> COMPLEX) as shown in rcsb.org (2nd attached image).
>
> How do I fix that?
>
> Thank you!
>
> [image: image.png]
> [image: image.png]
> _______________________________________________
> 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] Missing structure

[CRAIG A B. <cab...@wi...>]

You need to download the biological assembly

[cid:image001.png@01D7EC2C.356AB220]

From: joa...@gm... <joa...@gm...>
Date: Wednesday, December 8, 2021 at 11:56 AM
To: PYMOLBB <PyM...@li...>
Subject: [PyMOL] Missing structure
Hi there

PyMol doesn't show the full PDB file 1BG1 (TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX) as shown in rcsb.org<http://rcsb.org> (2nd attached image).

How do I fix that?

Thank you!

[cid:image002.png@01D7EC2C.356AB220]
[cid:image003.png@01D7EC2C.356AB220]

Re: [PyMOL] Missing structure

[Marko H. <mh...@ca...>]

Looks like you have half a dimer in asymmetric unit which is what PDB depositions would have. You can either see if you can download the biological complex or, within PyMOL, you can find symmetry mates from Action menu for the object. After that you need to remove those that are not related to dimeric complex.

Best, Marko

----
Marko Hyvonen
Department of Biochemistry
University of Cambridge
https://hyvonen.bioc.cam.ac.uk
@HyvonenGroup
mh...@ca...
________________________________
From: JJ Oliveira <joa...@gm...>
Sent: Wednesday, December 8, 2021 2:54:31 PM
To: PYMOLBB <PyM...@li...>
Subject: [PyMOL] Missing structure

Hi there

PyMol doesn't show the full PDB file 1BG1 (TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX) as shown in rcsb.org<http://rcsb.org> (2nd attached image).

How do I fix that?

Thank you!

[image.png]
[image.png]

[PyMOL] Missing structure

[JJ O. <joa...@gm...>]

Hi there

PyMol doesn't show the full PDB file 1BG1 (TRANSCRIPTION FACTOR STAT3B/DNA
COMPLEX) as shown in rcsb.org (2nd attached image).

How do I fix that?

Thank you!

[image: image.png]
[image: image.png]

Re: [PyMOL] PyMOL for M1 macs

[Chris S. <sw...@ma...>]

Hi,

Thanks all will give it a try

Cheers,

Chris

> On 6 Dec 2021, at 06:08, Jarrett Johnson <jar...@sc...> wrote:
> 
> IIRC when we tried with Rosetta2, PyMOL was still faster (about 2x I think) than the previous x86. Your mileage may vary.
> 
> Best,
> Jarrett J
> 
> On Mon, Dec 6, 2021 at 12:46 AM Xin Yu <xin...@gm... <mailto:xin...@gm...>> wrote:
> It looks like while you can’t run it natively on M1, maybe you can do it through rosetta2 translation via Conda install?
> See here: https://pymol.org/2/support.html? <https://pymol.org/2/support.html?>
> Supported platform states M1 with rosetta2. Perhaps with some penalty for efficiency though. Anyone tried?
> 
> Sent from my iPhone
> 
>> On Dec 5, 2021, at 10:27 PM, Jarrett Johnson <jar...@sc... <mailto:jar...@sc...>> wrote:
>> 
>> 
>> Hi Chris,
>> 
>> We haven't released any official Incentive PyMOL builds yet for M1 ARM mac yet but it's on our radar to do so soon.
>> 
>> Best,
>> 
>> Jarrett J
>> 
>> On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users <pym...@li... <mailto:pym...@li...>> wrote:
>> Hi,
>> 
>> Is there a build of PyMOL for M1 Macs yet?
>> 
>> Cheers,
>> 
>> Chris
>> 
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
>> 
>> 
>> -- 
>> Jarrett Johnson | Senior Developer, PyMOL
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
> 
> -- 
> Jarrett Johnson | Senior Developer, PyMOL
> 

Re: [PyMOL] PyMOL for M1 macs

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

IIRC when we tried with Rosetta2, PyMOL was still faster (about 2x I think)
than the previous x86. Your mileage may vary.

Best,
Jarrett J

On Mon, Dec 6, 2021 at 12:46 AM Xin Yu <xin...@gm...> wrote:

> It looks like while you can’t run it natively on M1, maybe you can do it
> through rosetta2 translation via Conda install?
> See here: https://pymol.org/2/support.html?
> Supported platform states M1 with rosetta2. Perhaps with some penalty for
> efficiency though. Anyone tried?
>
> Sent from my iPhone
>
> On Dec 5, 2021, at 10:27 PM, Jarrett Johnson <
> jar...@sc...> wrote:
>
> 
> Hi Chris,
>
> We haven't released any official Incentive PyMOL builds yet for M1 ARM mac
> yet but it's on our radar to do so soon.
>
> Best,
>
> Jarrett J
>
> On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users <
> pym...@li...> wrote:
>
>> Hi,
>>
>> Is there a build of PyMOL for M1 Macs yet?
>>
>> Cheers,
>>
>> Chris
>>
>>
>> _______________________________________________
>> 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
>
> _______________________________________________
> 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] PyMOL for M1 macs

[Xin Yu <xin...@gm...>]

It looks like while you can’t run it natively on M1, maybe you can do it through rosetta2 translation via Conda install?
See here: https://pymol.org/2/support.html?
Supported platform states M1 with rosetta2. Perhaps with some penalty for efficiency though. Anyone tried?

Sent from my iPhone

> On Dec 5, 2021, at 10:27 PM, Jarrett Johnson <jar...@sc...> wrote:
> 
> 
> Hi Chris,
> 
> We haven't released any official Incentive PyMOL builds yet for M1 ARM mac yet but it's on our radar to do so soon.
> 
> Best,
> 
> Jarrett J
> 
>> On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users <pym...@li...> wrote:
>> Hi,
>> 
>> Is there a build of PyMOL for M1 Macs yet?
>> 
>> Cheers,
>> 
>> Chris
>> 
>> 
>> _______________________________________________
>> 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
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] PyMOL for M1 macs

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

Hi Chris,

We haven't released any official Incentive PyMOL builds yet for M1 ARM mac
yet but it's on our radar to do so soon.

Best,

Jarrett J

On Sun, Dec 5, 2021 at 2:09 PM Chris Swain via PyMOL-users <
pym...@li...> wrote:

> Hi,
>
> Is there a build of PyMOL for M1 Macs yet?
>
> Cheers,
>
> Chris
>
>
> _______________________________________________
> 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

[PyMOL] PyMOL for M1 macs

[Chris S. <sw...@ma...>]

Hi,

Is there a build of PyMOL for M1 Macs yet?

Cheers,

Chris

Re: [PyMOL] Loading chempy objects into PyMOL 2.4.0

[R M. <rau...@us...>]

Dear Thomas,

Thanks! That solved the problem (I actually used load_coordset, so I could
keep my coordinates in their original order.

Cheers!

On Wed, Dec 1, 2021 at 6:44 PM Thomas Holder <th...@th...>
wrote:

> Hi Raul,
>
> I suggest to use cmd.load_coords() to add trajectory frames to your model.
>
> https://pymolwiki.org/index.php/Load_coords
>
> Cheers,
>   Thomas
>
>
> On Nov 30, 2021, at 21:49, R Mera <rau...@us...> wrote:
>
> Dear all,
>
> I am trying to implement a reader for a trajectory format.
> I use cmd.get_model to get the "reference" structure, and then iterate
> over the trajectory frames, everytime replacing the coordinates of my model
> with the ones from the trajectory, and then loading the modified model back
> into PyMOL with cmd.load_model, changing the state every time.
>
> The issue is, I can't get the sequence view to work correctly (i.e. to
> display the one-letter code of each residue). This happens even if I don't
> modify the coordinates at all, like here:
>
> #This doesn't display the sequence
> for i in range(9):
>    m=cmd.get_model("sele")
>    cmd.load_model(m,"sele2",state=i+1)
>
> On the other hand, if I load only one state for the object, the sequence
> is displayed correctly:
>
> #this DOES display the sequence
> for i in range(1):
>    m=cmd.get_model("sele")
>    cmd.load_model(m,"sele2",state=i+1)
>
>
>
> I have tried with the Wiki help and even looking at the cmd code, but I
> can't find any way of getting this to work. The options for load_model, for
> instance, have no effect. What I _can_ do is to use:
>
> cmd.set("seq_view_discrete_by_state",0)
>
> Which will show the sequence correctly (apparently, the first state always
> gets the sequence, the others don't).  It is not a good solution, though,
> as you can't use that sequence to select residues (it will only select them
> on the first state, _and_ it will take you back to that state).
>
> Is this possible at all to do? Is it an issue with my PyMOL version? (I am
> using PyMOL on Fedora [Linux], and it i the version from the Fedora 32
> repositories, by the way, although I don't think I am doing anything
> OS-dependent).
>
> Thanks!
>
> Raul
>
>
> --
>
> Prof. Dr. Raúl Mera Adasme
>
> Facultad de Química y Biología ,
> Universidad de Santiago de Chile (USACH).
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>

-- 

Prof. Dr. Raúl Mera Adasme

Facultad de Química y Biología ,
Universidad de Santiago de Chile (USACH).

Re: [PyMOL] Loading chempy objects into PyMOL 2.4.0

[Thomas H. <th...@th...>]

Hi Raul,

I suggest to use cmd.load_coords() to add trajectory frames to your model.

https://pymolwiki.org/index.php/Load_coords <https://pymolwiki.org/index.php/Load_coords>

Cheers,
  Thomas


> On Nov 30, 2021, at 21:49, R Mera <rau...@us...> wrote:
> 
> Dear all,
> 
> I am trying to implement a reader for a trajectory format.
> I use cmd.get_model to get the "reference" structure, and then iterate over the trajectory frames, everytime replacing the coordinates of my model with the ones from the trajectory, and then loading the modified model back into PyMOL with cmd.load_model, changing the state every time.
> 
> The issue is, I can't get the sequence view to work correctly (i.e. to display the one-letter code of each residue). This happens even if I don't modify the coordinates at all, like here:
> 
> #This doesn't display the sequence
> for i in range(9):
>    m=cmd.get_model("sele")
>    cmd.load_model(m,"sele2",state=i+1)
> 
> On the other hand, if I load only one state for the object, the sequence is displayed correctly:
> 
> #this DOES display the sequence
> for i in range(1):
>    m=cmd.get_model("sele")
>    cmd.load_model(m,"sele2",state=i+1)
> 
> 
> 
> I have tried with the Wiki help and even looking at the cmd code, but I can't find any way of getting this to work. The options for load_model, for instance, have no effect. What I _can_ do is to use:
> 
> cmd.set("seq_view_discrete_by_state",0)
> 
> Which will show the sequence correctly (apparently, the first state always gets the sequence, the others don't).  It is not a good solution, though, as you can't use that sequence to select residues (it will only select them on the first state, _and_ it will take you back to that state).
> 
> Is this possible at all to do? Is it an issue with my PyMOL version? (I am using PyMOL on Fedora [Linux], and it i the version from the Fedora 32 repositories, by the way, although I don't think I am doing anything OS-dependent). 
> 
> Thanks!
> 
> Raul
>  
> 
> -- 
> 
> Prof. Dr. Raúl Mera Adasme
> 
> Facultad de Química y Biología ,
> Universidad de Santiago de Chile (USACH).
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe