pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] how to make selected residues blurry?

[sunyeping <sun...@al...>]

Hi, Paul,

Thank you for your reply. I think the ‘set transparency’ command is on the correct direction, but there is another problem. In order to apply the ‘set transparency’, we should use  "create" or "extract" command to make a new objective for the selected atoms. However, after I select the atoms that I want to make transparent, and use the command "extract":
     extract new_obj, sele
I find the new object is broken from the rest part of the structure. And then I use the commend:
 set cartoon_transparency, 0.7, new_obj
The breaking between the new objective (the transparent part) and the rest part become more obvious. Please see the figure at the line (https://drive.google.com/file/d/1XQqGeN7JRLfSlexk4J7ufESWhnTJM3bW/view?usp=sharing).
    Could you help me with the "breaking" problem?

Best regards,

Yeping



------------------------------------------------------------------
From:Smith, Paul <pau...@kc...>
Send Time:2018 Dec 3 (Mon) 20:38
To:孙业平 <sun...@al...>; pymol-users <pym...@li...>
Subject:RE: [PyMOL] how to make selected residues blurry?


Hi,
The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’.
Cheers,
Paul
From: sunyeping via PyMOL-users
Sent: 03 December 2018 03:02
To: pymol-users
Subject: [PyMOL] how to make selected residues blurry?
Dear all,


Could you please check this figure at the following link?
https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing


The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. 

I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
    set transparency, 0.8, sele
but it doesn't work.

Could anyone help me figure it out？ With sincere thanks.

Re: [PyMOL] how to make selected residues blurry?

[Smith, P. <pau...@kc...>]

Hi,

The ‘set transparency’ command will set the transparency of a surface (e.g. the interface between a protein and the surrounding water). I think the command you’re after is ‘set cartoon_transparency’ (https://pymolwiki.org/index.php/Cartoon#Various_Transparency_Levels). Depending on your choice of representation, see also ‘set sphere_transparency’ and ‘set stick_transparency’.

Cheers,
Paul


From: sunyeping via PyMOL-users<mailto:pym...@li...>
Sent: 03 December 2018 03:02
To: pymol-users<mailto:pym...@li...>
Subject: [PyMOL] how to make selected residues blurry?

Dear all,


Could you please check this figure at the following link?
https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0%2Fview%3Fusp%3Dsharing&data=01%7C01%7Cpaul.smith%40kcl.ac.uk%7C2bf336b34d554aedf37e08d658cbb9c8%7C8370cf1416f34c16b83c724071654356%7C0&sdata=tgPlIectw3pV9ppkv9IeX6YsqnRepi%2Bmb75aB0UzGPk%3D&reserved=0>


The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry.

I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
    set transparency, 0.8, sele
but it doesn't work.

Could anyone help me figure it out？ With sincere thanks.

[PyMOL] how to make selected residues blurry?

[sunyeping <sun...@al...>]

Dear all,

Could you please check this figure at the following link?
https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing

The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. 

I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
    set transparency, 0.8, sele
but it doesn't work.

Could anyone help me figure it out？ With sincere thanks.

Re: [PyMOL] getting transformation matrix

[Fedaa N. <fed...@ya...>]

 here what I did ..
using pymol1- I loaded post and pre-processing object2- I aligned them together3- I tried to get the transformation matrix with this commandprint cmd.get_object_matrix("pre-processing object")and this step returns a 4*4 matrices(-0.017042629420757294, 0.6273888349533081, -0.7785196304321289, -27.565351122804373, 0.15071848034858704, 0.7713475823402405, 0.6183096766471863, -142.13367787636093, 0.9884297847747803, -0.1067996621131897, -0.10770488530397415, -81.02178268868633, 0.0, 0.0, 0.0, 1.0)I am not sure if this is the right way or not?and if it is right what should I do in order to apply it to the post-processing object ? should I apply it as it is or the inverse of it?
Thank you, Fedaa Ali 
    On Saturday, December 1, 2018, 5:59:37 PM GMT+2, Fedaa Nada via PyMOL-users <pym...@li...> wrote:  
 
 After optimizing the structure the coordinates transforms to another frame, what I need to do is to transfer back to the original coordinates by getting the transformation matrix when I tried to get this matrix using pymol, I got an error and I can't figure out the problem because I am new to pymol.
please, could anyone help me how to get the transformation matrix? 

Thank you Fedaa Ali   _______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe  

[PyMOL] getting transformation matrix

[Fedaa N. <fed...@ya...>]

After optimizing the structure the coordinates transforms to another frame, what I need to do is to transfer back to the original coordinates by getting the transformation matrix when I tried to get this matrix using pymol, I got an error and I can't figure out the problem because I am new to pymol.
please, could anyone help me how to get the transformation matrix? 

Thank you Fedaa Ali   

Re: [PyMOL] how to make selected residues blurry?

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

Hi Arthur -

The `transparency` setting affects only surface representations.  I believe you're looking for `set cartoon_transparency, 0.8, sele`.   https://pymolwiki.org/index.php/Cartoon_transparency

Hope that helps.

Cheers,
Jared


On November 30, 2018 at 3:41:57 AM, sunyeping via PyMOL-users (pym...@li...) wrote:

Dear all,

Could you please check this figure at the following link?
https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing

The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. 

I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
    set transparency, 0.8, sele
but it doesn't work.

Could anyone help me figure it out？ With sincere thanks.

Arthur
_______________________________________________  
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-users Digest, Vol 150, Issue 13

[ahoneg <ann...@uz...>]

> 
> Today's Topics:
> 
>   1. how to make selected residues blurry? (sunyeping)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 30 Nov 2018 12:14:21 +0800
> From: "sunyeping" <sun...@al...>
> To: "pymol-users" <pym...@li...>
> Subject: [PyMOL] how to make selected residues blurry?
> Message-ID:
> 	<87e...@al...>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear all,
> 
> Could you please check this figure at the following link?
> https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing
> 
> The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. 
> 
> I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
>    set transparency, 0.8, sele
> but it doesn't work.
> 
> Could anyone help me figure it out? With sincere thanks.
> 
> Arthur

The residues that are farther back from the viewer are increasingly transparent. 
The effect is called depth cueing, basically causing  the residues farther back to appear to get  lost in the fog. 

set depth_cue, 1  # turn on depth cueing
 
will switch the effect on. The front and back clipping planes  define  the range, although you can keep more of the front unfogged 
by additionally adjusting the  fog_start value

see https://pymolwiki.org/index.php/Depth_cue

Annemarie

____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12     

[PyMOL] how to make selected residues blurry?

[sunyeping <sun...@al...>]

Dear all,

Could you please check this figure at the following link?
https://drive.google.com/file/d/1Uh9JRh7x0sjv-zGp_0ZKPc1cnWotkZA0/view?usp=sharing

The structure in blue in this figure is prepared from chain A of pdb id 4gms. Some residues are highlighted and look sharp ( as indicated in the figure: 130-loop, 150-loop, 190-helix and 220-loop, and the corresponding residues are:  residues 134-138, 155-163, 188-195, 221-228, respectively), while other part of the structure look blurry. 

I wish to repeat this visual effect but don't know how. I try to select the residues and use "set transparency" command:
    set transparency, 0.8, sele
but it doesn't work.

Could anyone help me figure it out？ With sincere thanks.

Arthur

Re: [PyMOL] Linux pymol issues

[Evgeny O. <joe...@gm...>]

Hi, Thomas,
Thanks,

bash> export QT_SCALE_FACTOR=1
bash> pymol

works wonderful!

ср, 28 нояб. 2018 г. в 15:35, Thomas Holder <tho...@sc...>:

> Hi Evgeny,
>
> Is any of the QT_*_SCALE_FACTOR variables set in your environment? Does it
> help if you set for example QT_SCALE_FACTOR=1? In a bash terminal that
> would be:
>
> bash> export QT_SCALE_FACTOR=1
> bash> pymol
>
> See also:
> http://doc.qt.io/qt-5/highdpi.html#high-dpi-support-in-qt
>
> Cheers,
>   Thomas
>
> > On Nov 27, 2018, at 7:50 PM, Evgeny Osipov <joe...@gm...> wrote:
> >
> > Dear Pymol community,
> >  I stumbled upon strange GUI issue with Pymol 2 and Maestro on my linux
> laptop ( Xubuntu 18.04 HP Probook 440 G5): it looks like GUI elements have
> different scale so it looks rather strange and very inconvenient for work.
> Problem appears  only at 1920x1080 resolution and everything is fine at
> lower resolution. I have uploaded screenshots from pymol 2 at 1920x1080
> (highDPI) and 1680x1050 (lowDPI) here:
> > https://imgur.com/a/Tlp79Kq
> >
> > Do anyone have a clue how to fix this?
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Re: [PyMOL] Pandas module in Pymol

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

Hi Andreas,

Looks like a known pandas issue, see:

https://github.com/pandas-dev/pandas/issues/16536

According to that issue, upgrading pandas could help.

Cheers,
  Thomas


> On Nov 21, 2018, at 5:01 PM, Andreas Tosstorff <and...@cu...> wrote:
> 
> Hi all,
> 
> I am trying to use pandas in a script in pymol.
> 
> These are the first lines of the script:
> 
> from pymol import cmd, stored, math
> import pandas as pd 
> 
> 
> I get the following error message when running the script:
> 
> 'module 'pandas' has no attribute 'plotting'
> 
> 
>   File "/home/andt88/anaconda3/lib/python3.6/site-packages/pmg_qt/pymol_qt_gui.py", line 863, in file_run
>     self.cmd.run(fname)
>   File "/home/andt88/anaconda3/lib/python3.6/site-packages/pymol/parsing.py", line 484, in run
>     run_(path, ns_pymol, ns_pymol)
>   File "/home/andt88/anaconda3/lib/python3.6/site-packages/pymol/parsing.py", line 533, in run_file
>     execfile(file,global_ns,local_ns)
>   File "/home/andt88/anaconda3/lib/python3.6/site-packages/pymol/parsing.py", line 528, in execfile
>     exec(co, global_ns, local_ns)
>   File "/home/andt88/Dropbox/PhD/IFN/Excipient_Screen/IFN_ES_2/NMR/NMR-Data/andreas/nmr/PPI-30 TEMPOL 250718/loadBfacts.py", line 2, in <module>
>     import pandas as pd
>   File "/home/andt88/anaconda3/lib/python3.6/site-packages/pandas/__init__.py", line 51, in <module>
>     plot_params = pandas.plotting._style._Options(deprecated=True)
> 
> I'd really appreciate your help with this!
> Kind regards,
> Andreas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Linux pymol issues

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

Hi Evgeny,

Is any of the QT_*_SCALE_FACTOR variables set in your environment? Does it help if you set for example QT_SCALE_FACTOR=1? In a bash terminal that would be:

bash> export QT_SCALE_FACTOR=1
bash> pymol

See also:
http://doc.qt.io/qt-5/highdpi.html#high-dpi-support-in-qt

Cheers,
  Thomas

> On Nov 27, 2018, at 7:50 PM, Evgeny Osipov <joe...@gm...> wrote:
> 
> Dear Pymol community,
>  I stumbled upon strange GUI issue with Pymol 2 and Maestro on my linux laptop ( Xubuntu 18.04 HP Probook 440 G5): it looks like GUI elements have different scale so it looks rather strange and very inconvenient for work. Problem appears  only at 1920x1080 resolution and everything is fine at lower resolution. I have uploaded screenshots from pymol 2 at 1920x1080 (highDPI) and 1680x1050 (lowDPI) here:
> https://imgur.com/a/Tlp79Kq
> 
> Do anyone have a clue how to fix this?

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Linux pymol issues

[Evgeny O. <joe...@gm...>]

Dear Pymol community,
 I stumbled upon strange GUI issue with Pymol 2 and Maestro on my linux
laptop ( Xubuntu 18.04 HP Probook 440 G5): it looks like GUI elements have
different scale so it looks rather strange and very inconvenient for work.
Problem appears  only at 1920x1080 resolution and everything is fine at
lower resolution. I have uploaded screenshots from pymol 2 at 1920x1080
(highDPI) and 1680x1050 (lowDPI) here:
https://imgur.com/a/Tlp79Kq

Do anyone have a clue how to fix this?

[PyMOL] Announcing 2018/2019 PyMOL Open Source Fellows

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

Greetings PyMOL users,

Please join me in congratulating Mateusz Bieniek, Paul Smith, and Blaine Mooers, who have been awarded the Warren L. DeLano Memorial PyMOL Open Source Fellowship for 2018-2019.

Mateusz and Paul will be working as a team on tools for molecular dynamics trajectory handling and analysis. They are graduate students at King’s College in London and use molecular dynamics simulations in their own research.

Blaine is a crystallographer and long-time PyMOL user who has introduced hundreds of students to molecular visualization with PyMOL. He will be working on a snippet library of PyMOL scripts with a searchable thumbnail gallery frontend for efficient discoverability of relevant snippets.

The Warren L. DeLano Memorial PyMOL Open-Source Fellowship is awarded by Schrӧdinger to supplement the income of an outstanding member of the PyMOL open-source community so that s/he can continue to develop free resources to help scientific progress and the community as a whole. You can read more about the PyMOL Open Source Fellowship Program and the fellows at https://pymol.org/fellowship

Cheers,
  The PyMOL Team at Schrödinger

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Viewing trajectories in pymol

[Istvan K. <iko...@gm...>]

Yes, when it comes to trajectory visualization, vmd is just much better
than Pymol.

intra_fit can be used for example this way:
print cmd.intra_fit("my-traj////CA", 1)
where my-traj is an object with all the frames and the macro in quotes can
be used to define any selection, in this example CA atoms. The 1 means fit
every state/frame on state number 1, and of course that can be any frame.

   Istvan

On Wed, Nov 21, 2018 at 7:58 PM Floris van Eerden <
flo...@bi...> wrote:

> Dear Ivan,
>
> Thanks for the suggestion. However it has the same result as what I tried
> before. The slider does the job, but is not responsive enough for intense
> scrolling through trajectories (not sure if it is because the rendering
> take to much CPU or because the slider is just not designed for that
> purpose). Anyway thanks for the suggestion.
>
> @Nese, there is the intra_fit command, you could try to use it on a
> selection only.
>
> On 22 Nov 2018, at 0:37, KurtYilmaz, Nese wrote:
>
> Hi,
>
> What is the best way to align the snapshots of a trajectory when viewing
> in pymol? Is it possible to align using a selection, say on a few selected
> residues?
>
> Nese
>
> ------------------------------
> *From:* Istvan Kolossvary [iko...@gm...]
> *Sent:* Tuesday, November 20, 2018 11:43 PM
> *To:* pym...@li...
> *Subject:* Re: [PyMOL] Viewing trajectories in pymol
>
> You can add a slider to the movie panel.
> # Set a movie slider
> set movie_panel=1
> #movie.add_state_sweep(1,0,start=1)
> movie.add_state_loop(1,0,start=1)
>
> Best,
>
>    Istvan
>
> On Tue, Nov 20, 2018 at 5:02 AM Floris van Eerden <
> flo...@bi...> wrote:
>
>> Dear Pymol community,
>>
>> Is there a way to *easily* view trajectories with pymol? In VMD there is
>> some kind of scrollbar, with which it is really easy to scroll through a
>> simulation. Is some similar functionality available somehow in pymol. The
>> only similar thing is the movie_panel in conjunction with the mset command.
>> However this does not provide as a smooth experience.
>>
>> Best wishes,
>>
>> Floris van Eerden
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=eSbvS1GcfWuUjgAauHz0g1f0A5qNz0rc2THr_TQr2tE&m=LnAnOCDh--BadJSQ541BIMtEwWIoRVYaYk7uOciE6pY&s=pS7H7gNmctghTtZt5IH7nLM7QIwzgVWu7HCJYcvo4tU&e=>
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=eSbvS1GcfWuUjgAauHz0g1f0A5qNz0rc2THr_TQr2tE&m=LnAnOCDh--BadJSQ541BIMtEwWIoRVYaYk7uOciE6pY&s=vRNaSYdcXcUbLgLChWpKz-URDV2Fi3TVRpMraAhUw_Y&e=>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Viewing trajectories in pymol

[Floris v. E. <flo...@bi...>]

Dear Ivan,

Thanks for the suggestion. However it has the same result as what I tried before. The slider does the job, but is not responsive enough for intense scrolling through trajectories (not sure if it is because the rendering take to much CPU or because the slider is just not designed for that purpose). Anyway thanks for the suggestion.

@Nese, there is the intra_fit command, you could try to use it on a selection only.

On 22 Nov 2018, at 0:37, KurtYilmaz, Nese wrote:

Hi,

What is the best way to align the snapshots of a trajectory when viewing in pymol? Is it possible to align using a selection, say on a few selected residues?

Nese

________________________________
From: Istvan Kolossvary [iko...@gm...]
Sent: Tuesday, November 20, 2018 11:43 PM
To: pym...@li...
Subject: Re: [PyMOL] Viewing trajectories in pymol

You can add a slider to the movie panel.
# Set a movie slider
set movie_panel=1
#movie.add_state_sweep(1,0,start=1)
movie.add_state_loop(1,0,start=1)

Best,

   Istvan

On Tue, Nov 20, 2018 at 5:02 AM Floris van Eerden <flo...@bi...<mailto:flo...@bi...>> wrote:

Dear Pymol community,

Is there a way to easily view trajectories with pymol? In VMD there is some kind of scrollbar, with which it is really easy to scroll through a simulation. Is some similar functionality available somehow in pymol. The only similar thing is the movie_panel in conjunction with the mset command. However this does not provide as a smooth experience.

Best wishes,

Floris van Eerden

_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=eSbvS1GcfWuUjgAauHz0g1f0A5qNz0rc2THr_TQr2tE&m=LnAnOCDh--BadJSQ541BIMtEwWIoRVYaYk7uOciE6pY&s=pS7H7gNmctghTtZt5IH7nLM7QIwzgVWu7HCJYcvo4tU&e=>
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=eSbvS1GcfWuUjgAauHz0g1f0A5qNz0rc2THr_TQr2tE&m=LnAnOCDh--BadJSQ541BIMtEwWIoRVYaYk7uOciE6pY&s=vRNaSYdcXcUbLgLChWpKz-URDV2Fi3TVRpMraAhUw_Y&e=>

_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Viewing trajectories in pymol

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

Hi,

What is the best way to align the snapshots of a trajectory when viewing in pymol? Is it possible to align using a selection, say on a few selected residues?

Nese

________________________________
From: Istvan Kolossvary [iko...@gm...]
Sent: Tuesday, November 20, 2018 11:43 PM
To: pym...@li...
Subject: Re: [PyMOL] Viewing trajectories in pymol

You can add a slider to the movie panel.
# Set a movie slider
set movie_panel=1
#movie.add_state_sweep(1,0,start=1)
movie.add_state_loop(1,0,start=1)

Best,

   Istvan

On Tue, Nov 20, 2018 at 5:02 AM Floris van Eerden <flo...@bi...<mailto:flo...@bi...>> wrote:

Dear Pymol community,

Is there a way to easily view trajectories with pymol? In VMD there is some kind of scrollbar, with which it is really easy to scroll through a simulation. Is some similar functionality available somehow in pymol. The only similar thing is the movie_panel in conjunction with the mset command. However this does not provide as a smooth experience.

Best wishes,

Floris van Eerden

_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=eSbvS1GcfWuUjgAauHz0g1f0A5qNz0rc2THr_TQr2tE&m=LnAnOCDh--BadJSQ541BIMtEwWIoRVYaYk7uOciE6pY&s=pS7H7gNmctghTtZt5IH7nLM7QIwzgVWu7HCJYcvo4tU&e=>
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=eSbvS1GcfWuUjgAauHz0g1f0A5qNz0rc2THr_TQr2tE&m=LnAnOCDh--BadJSQ541BIMtEwWIoRVYaYk7uOciE6pY&s=vRNaSYdcXcUbLgLChWpKz-URDV2Fi3TVRpMraAhUw_Y&e=>

[PyMOL] Pandas module in Pymol

[Andreas T. <and...@cu...>]

Hi all,

I am trying to use pandas in a script in pymol.

These are the first lines of the script:

from pymol import cmd, stored, math import pandas as pd

I get the following error message when running the script:

'module 'pandas' has no attribute 'plotting'

File 
"/home/andt88/anaconda3/lib/python3.6/site-packages/pmg_qt/pymol_qt_gui.py", 
line 863, in file_run

self.cmd.run(fname)

File 
"/home/andt88/anaconda3/lib/python3.6/site-packages/pymol/parsing.py", 
line 484, in run

run_(path, ns_pymol, ns_pymol)

File 
"/home/andt88/anaconda3/lib/python3.6/site-packages/pymol/parsing.py", 
line 533, in run_file

execfile(file,global_ns,local_ns)

File 
"/home/andt88/anaconda3/lib/python3.6/site-packages/pymol/parsing.py", 
line 528, in execfile

exec(co, global_ns, local_ns)

File 
"/home/andt88/Dropbox/PhD/IFN/Excipient_Screen/IFN_ES_2/NMR/NMR-Data/andreas/nmr/PPI-30 
TEMPOL 250718/loadBfacts.py", line 2, in <module>

import pandas as pd

File 
"/home/andt88/anaconda3/lib/python3.6/site-packages/pandas/__init__.py", 
line 51, in <module>

plot_params = pandas.plotting._style._Options(deprecated=True)

I'd really appreciate your help with this!

Kind regards,

Andreas

Re: [PyMOL] Viewing trajectories in pymol

[Istvan K. <iko...@gm...>]

You can add a slider to the movie panel.
# Set a movie slider
set movie_panel=1
#movie.add_state_sweep(1,0,start=1)
movie.add_state_loop(1,0,start=1)

Best,

   Istvan

On Tue, Nov 20, 2018 at 5:02 AM Floris van Eerden <
flo...@bi...> wrote:

> Dear Pymol community,
>
> Is there a way to *easily* view trajectories with pymol? In VMD there is
> some kind of scrollbar, with which it is really easy to scroll through a
> simulation. Is some similar functionality available somehow in pymol. The
> only similar thing is the movie_panel in conjunction with the mset command.
> However this does not provide as a smooth experience.
>
> Best wishes,
>
> Floris van Eerden
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Viewing trajectories in pymol

[Floris v. E. <flo...@bi...>]

Dear Pymol community,

Is there a way to easily view trajectories with pymol? In VMD there is some kind of scrollbar, with which it is really easy to scroll through a simulation. Is some similar functionality available somehow in pymol. The only similar thing is the movie_panel in conjunction with the mset command. However this does not provide as a smooth experience.

Best wishes,

Floris van Eerden

Re: [PyMOL] x-forwarding doesn't display bottom panel but displays menu bar and shell output

[Tan, S. <Sop...@uc...>]

Hi Thomas,



vgl works well, thanks for your help!

________________________________
From: Thomas Holder <tho...@sc...>
Sent: Monday, November 19, 2018 12:31:09 PM
To: Tan, Sophia
Cc: pym...@li...
Subject: Re: [PyMOL] x-forwarding doesn't display bottom panel but displays menu bar and shell output

Hi Sophia,

Regarding X forwarding on macOS: It turns out iglx is disabled by default since XQuartz 2.7.10. After enabling it, PyMOL works. I've put this information on the PyMOLWiki:

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

Cheers,
  Thomas

> On Nov 19, 2018, at 1:36 PM, Thomas Holder <tho...@sc...> wrote:
>
> Hi Sophia,
>
> This works on my old Mac with macOS 10.9 and XQuartz 2.7.7. However, on a newer Mac with macOS 10.12 and XQuartz 2.7.11 ssh forwarding of OpenGL apps doesn't work at all for me. Not even the "glxgears" test program works.
>
> The good news is: VirtualGL works really well, using macOS 10.12 as the client and a Linux workstation as the server.
>
> mac # /opt/VirtualGL/bin/vglconnect linux
> linux # vglrun pymol
>
> See also:
> https://virtualgl.org/vgldoc/2_2_1/#hd004003
>
> Cheers,
>  Thomas
>
>> On Nov 17, 2018, at 4:12 AM, Tan, Sophia <Sop...@uc...> wrote:
>>
>> Hi developers,
>>
>> I'm using PyMOL (2.2.3) on a Linux remote workstation, and am using X forwarding on my Mac by "ssh -Y etc."
>> The X forwarding works on other applications, but for PyMOL, only the top menu bar with the command line shell output is displayed; the bottom display is all white, no matter what I try to load.
>>
>> How can I get the bottom display to work ?
>>
>> Thank you,
>> Sophia

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] x-forwarding doesn't display bottom panel but displays menu bar and shell output

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

Hi Sophia,

Regarding X forwarding on macOS: It turns out iglx is disabled by default since XQuartz 2.7.10. After enabling it, PyMOL works. I've put this information on the PyMOLWiki:

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

Cheers,
  Thomas

> On Nov 19, 2018, at 1:36 PM, Thomas Holder <tho...@sc...> wrote:
> 
> Hi Sophia,
> 
> This works on my old Mac with macOS 10.9 and XQuartz 2.7.7. However, on a newer Mac with macOS 10.12 and XQuartz 2.7.11 ssh forwarding of OpenGL apps doesn't work at all for me. Not even the "glxgears" test program works.
> 
> The good news is: VirtualGL works really well, using macOS 10.12 as the client and a Linux workstation as the server.
> 
> mac # /opt/VirtualGL/bin/vglconnect linux
> linux # vglrun pymol
> 
> See also:
> https://virtualgl.org/vgldoc/2_2_1/#hd004003
> 
> Cheers,
>  Thomas
> 
>> On Nov 17, 2018, at 4:12 AM, Tan, Sophia <Sop...@uc...> wrote:
>> 
>> Hi developers, 
>> 
>> I'm using PyMOL (2.2.3) on a Linux remote workstation, and am using X forwarding on my Mac by "ssh -Y etc." 
>> The X forwarding works on other applications, but for PyMOL, only the top menu bar with the command line shell output is displayed; the bottom display is all white, no matter what I try to load. 
>> 
>> How can I get the bottom display to work ?
>> 
>> Thank you,
>> Sophia

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] x-forwarding doesn't display bottom panel but displays menu bar and shell output

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

Hi Sophia,

This works on my old Mac with macOS 10.9 and XQuartz 2.7.7. However, on a newer Mac with macOS 10.12 and XQuartz 2.7.11 ssh forwarding of OpenGL apps doesn't work at all for me. Not even the "glxgears" test program works.

The good news is: VirtualGL works really well, using macOS 10.12 as the client and a Linux workstation as the server.

mac # /opt/VirtualGL/bin/vglconnect linux
linux # vglrun pymol

See also:
https://virtualgl.org/vgldoc/2_2_1/#hd004003

Cheers,
  Thomas

> On Nov 17, 2018, at 4:12 AM, Tan, Sophia <Sop...@uc...> wrote:
> 
> Hi developers, 
> 
> I'm using PyMOL (2.2.3) on a Linux remote workstation, and am using X forwarding on my Mac by "ssh -Y etc." 
> The X forwarding works on other applications, but for PyMOL, only the top menu bar with the command line shell output is displayed; the bottom display is all white, no matter what I try to load. 
> 
> How can I get the bottom display to work ?
> 
> Thank you,
> Sophia 
> <Screen Shot 2018-11-16 at 6.58.48 PM.png>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] [HELP]Unable to import pymol as library

[Aureliano G. <gue...@gm...>]

Hi all,

I'm new here. My name is Aureliano Guedes.
I'd like your help.

I was trying to import pymol inside to python script to use to align
all-vs-all a list of structures.

I have a full pymol's installation working well installed with linux brew.
$ pymol --version
PyMOL 2.2.0 Open-Source
$ which pymol
/home/linuxbrew/.linuxbrew/bin/pymol

$ cat $(which pymol)
#!/bin/sh
export
PYMOL_PATH="/home/linuxbrew/.linuxbrew/Cellar/pymol/2.2.0/libexec/lib/python3.7/site-packages/pymol/pymol_path"
"/home/linuxbrew/.linuxbrew/opt/python/bin/python3.7"
"/home/linuxbrew/.linuxbrew/Cellar/pymol/2.2.0/libexec/lib/python3.7/site-packages/pymol/__init__.py"
"$@"

But when I try import it (using the same python installation) I got a error
reporting that no library called pymol was founded.

So, I would like to how to access pymol as module to use its
functionalities.

Thanks in advance,
acpguedes

-- 
Aureliano Guedes
skype: aureliano.guedes
contato:  (11) 94292-6110
whatsapp +5511942926110

[PyMOL] x-forwarding doesn't display bottom panel but displays menu bar and shell output

[Tan, S. <Sop...@uc...>]

Hi developers,

I'm using PyMOL (2.2.3) on a Linux remote workstation, and am using X forwarding on my Mac by "ssh -Y etc."
The X forwarding works on other applications, but for PyMOL, only the top menu bar with the command line shell output is displayed; the bottom display is all white, no matter what I try to load.

How can I get the bottom display to work ?

Thank you,
Sophia

Re: [PyMOL] issue with label command as in: label *, name; color red

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

Hi Xiang-Jun,

Some commands accept the semicolon in their argument list and thus cannot be followed by other commands on the same line. The "label" command is one of them.

See this table and the last column with "parsing.LITERAL1":
https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/keywords.py#L140

You could work around this by using Python syntax:

cmd.label("*", "name");cmd.color("red")

Cheers,
  Thomas

> On Nov 15, 2018, at 12:23 AM, Xiang-Jun Lu <3d...@gm...> wrote:
> 
> I am surprised by the PyMOL error message with the following commands:
> 
> # this is fine
> color red; label *, name 
> 
> # reversing the order causes problems
> label *, name; color red
> 
> =================================
> PyMOL>label *, name; color red
>   File "", line 1
>     name; color red
>         ^
> SyntaxError: invalid syntax
> Label-Error: failed to compile expression
>  Label: labelled 0 atoms.
> =================================
> 
> Replacing 'name' with 'resi' or 'resn' etc has the same result.
> 
> Issuing each command separately works as expected. The error message shows up only if "label *, name" is followed by another command, on the same line.
> 
> I am using "Version 1.8.7.0 Open-Source" on macOS.
> 
> Any ideas?
> 
> Thanks,
> 
> Xiang-Jun
> 
> --
> Xiang-Jun Lu (Ph.D.)
> Email: xia...@x3...
> Web: http://x3dna.org/
> Forum: http://forum.x3dna.org/

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.