pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Errors in "Label" page on PyMOL Wiki

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

Hi PyMOLers -

I'm currently not able to access the label
<https://pymolwiki.org/index.php/Label> page on PyMOL Wiki, which prints
out a string of PHP errors. Weirdly, it appears to be specific to that
page, as others (off the top of my head, I visited load
<https://pymolwiki.org/index.php/Load> and save
<https://pymolwiki.org/index.php/Save>) appear to be working fine.

Can anyone else confirm this?  If so, I wonder if it can be fixed by an
admin.

Cheers,
Jared

Re: [PyMOL] How to label secondary structures in pymol

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

Hi sunyeping - 

Yes, it is possible.  You can pick one atom to label in each SS element.  See this old thread: https://sourceforge.net/p/pymol/mailman/message/30823352/. 

You can also adjust the label position/size/style using the various label settings as well.  I would normally direct you to the label wiki page, but that appears (at least to me) to be broken at the moment.  So here, instead, is a link to a few-years-old archive of that page.

Hope that helps.

Cheers,
Jared


On July 7, 2019 at 1:38:15 PM, sunyeping via PyMOL-users (pym...@li...) wrote:

Dear all,

Is it possible to label  secondary structures directly in pymol? I mean add a text near local structures which tells the types and numbers of their secondary structures, such as "α1", "β1",  "α2", "β2", etc..

Thank you in advance.
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[PyMOL] How to label secondary structures in pymol

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

Dear all,

Is it possible to label  secondary structures directly in pymol? I mean add a text near local structures which tells the types and numbers of their secondary structures, such as "α1", "β1",  "α2", "β2", etc..

Thank you in advance.

Re: [PyMOL] How to color stick and surface representation separately

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

Hi, 

Thank you. I think a third method is to create a new object of the protein and display the stick in this new object, and display surface of the original object, so I can color them separately.

Best regards



------------------------------------------------------------------
From:Saurabh Gayali <sau...@gm...>
Sent At:2019 Jul. 6 (Sat.) 18:20
To:孙业平 <sun...@al...>
Cc:pymol-users <pym...@li...>
Subject:Re: [PyMOL] How to color stick and surface representation separately

there are two ways to achieve this (might not be correct ways, but it will give you results)
1. Open the molucule and choose show as Surface
[image.png]

This will show complete molecule as a surface. Remember choosing show as surface after choosing line or cartoon will remove former from viewport.
-
Now choose parts you want to keep and color them before moving on to next part
Next select the same molecule and enable line
[image.png]
remember to not choose line in show as menu but directly from show menu
This will keep the old object and add the new line visualization.
This way you can show both custom color surface and default color of line/cartoon
this way has limitation that you cannot color the second scheme but have to use the default coloring way.

2. Copy the molecule you want to load and create a copy in the folder
Load both moleculaes [You won't even need to align them]
now You can choose any visualization for both moleculaes as they are separate files.



Regards,Saurabh Gayali
---------------------------------------------------------------------


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On Sat, Jul 6, 2019 at 2:29 PM sunyeping via PyMOL-users <pym...@li...> wrote:
Dear all,

I color a protein as blue, display it by surface and cartoon simultaneously, and set the surface transperant so that the cartoon representation inside the surface can be seen. I display one residue as stick. I want to color the stick by element, but keep the surface representation as blue. However, I don't know how to do this. I can color the residue (please see the  Gln in the yellow circle at https://drive.google.com/open?id=1bviFQGUKgqLdbE-cUNDtzDZSdabc0N4Z), but both the stick and the surface representations are colored by element. Could anyone tell me how to color stick representation of this Gln by element but keep its surface representation as blue?

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

Re: [PyMOL] How to color stick and surface representation separately

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

there are two ways to achieve this (might not be correct ways, but it will
give you results)
1. Open the molucule and choose show as Surface
[image: image.png]

This will show complete molecule as a surface. Remember choosing show as
surface after choosing line or cartoon will remove former from viewport.
-
Now choose parts you want to keep and color them before moving on to next
part
Next select the same molecule and enable line
[image: image.png]
remember to not choose line in show as menu but directly from show menu
This will keep the old object and add the new line visualization.
This way you can show both custom color surface and default color of
line/cartoon
this way has limitation that you cannot color the second scheme but have to
use the default coloring way.

2. Copy the molecule you want to load and create a copy in the folder
Load both moleculaes [You won't even need to align them]
now You can choose any visualization for both moleculaes as they are
separate files.



Regards,
*Saurabh Gayali*
---------------------------------------------------------------------


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<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Sat, Jul 6, 2019 at 2:29 PM sunyeping via PyMOL-users <
pym...@li...> wrote:

> Dear all,
>
> I color a protein as blue, display it by surface and cartoon
> simultaneously, and set the surface transperant so that the cartoon
> representation inside the surface can be seen. I display one residue as
> stick. I want to color the stick by element, but keep the surface
> representation as blue. However, I don't know how to do this. I can color
> the residue (please see the  Gln in the yellow circle at
> https://drive.google.com/open?id=1bviFQGUKgqLdbE-cUNDtzDZSdabc0N4Z), but
> both the stick and the surface representations are colored by element.
> Could anyone tell me how to color stick representation of this Gln by
> element but keep its surface representation as blue?
>
> Thank you in advance
> Yeping
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] How to color stick and surface representation separately

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

Dear all,

I color a protein as blue, display it by surface and cartoon simultaneously, and set the surface transperant so that the cartoon representation inside the surface can be seen. I display one residue as stick. I want to color the stick by element, but keep the surface representation as blue. However, I don't know how to do this. I can color the residue (please see the  Gln in the yellow circle at https://drive.google.com/open?id=1bviFQGUKgqLdbE-cUNDtzDZSdabc0N4Z), but both the stick and the surface representations are colored by element. Could anyone tell me how to color stick representation of this Gln by element but keep its surface representation as blue?

Thank you in advance
Yeping

[PyMOL] Search error in PyMOLWiki

[Timofey T. <tyu...@ni...>]

Any search queries seem to result in errors:

Internal error

[46e930f3565a588ed0a5526d] 
/index.php?search=search&title=Special%3ASearch&fulltext=Search Error 
from line 56 of 
/var/www/pymolwiki_v1.31.1/extensions/MWSearch/MWSearch_body.php: Call 
to undefined function wfProfileIn()

Backtrace:

#0 /var/www/pymolwiki_v1.31.1/includes/specials/SpecialSearch.php(316): 
LuceneSearch->replacePrefixes(string)
#1 /var/www/pymolwiki_v1.31.1/includes/specials/SpecialSearch.php(185): 
SpecialSearch->showResults(string)
#2 /var/www/pymolwiki_v1.31.1/includes/specialpage/SpecialPage.php(522): 
SpecialSearch->execute(NULL)
#3 
/var/www/pymolwiki_v1.31.1/includes/specialpage/SpecialPageFactory.php(568): 
SpecialPage->run(NULL)
#4 /var/www/pymolwiki_v1.31.1/includes/MediaWiki.php(288): 
SpecialPageFactory::executePath(Title, RequestContext)
#5 /var/www/pymolwiki_v1.31.1/includes/MediaWiki.php(861): 
MediaWiki->performRequest()
#6 /var/www/pymolwiki_v1.31.1/includes/MediaWiki.php(524): MediaWiki->main()
#7 /var/www/pymolwiki_v1.31.1/index.php(42): MediaWiki->run()
#8 {main}

Re: [PyMOL] .

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

If typing pymol in commandline can start pymol in real, its in the path.

Regards,
*Saurabh Gayali*
---------------------------------------------------------------------


On Wed, Jul 3, 2019 at 6:01 PM O.L. Simpson <ori...@gm...> wrote:

>
> How do I ensure that PyMol is in my path as pymol?
>
> Thank you for the help in advance.
>
> Best
>
> m.o.l.s.
>
>
>
> On 3 Jul 2019, at 14:18, Saurabh Gayali <sau...@gm...> wrote:
>
> IPyMOL allows you to control PyMOL <https://www.pymol.org/> sessions via
> IPython. This tool is ideal for situations where you’d like to present your
> work neatly in a Jupyter Notebook <https://jupyter.org/> or conveniently
> prototype PyMOL scripts.
>
> https://pypi.org/project/ipymol/
>
>
> Regards,
> *Saurabh Gayali*
> ---------------------------------------------------------------------
>
>
> On Wed, Jul 3, 2019 at 5:50 PM O.L. Simpson <ori...@gm...>
> wrote:
>
>> Dear Pymol Users,
>>
>> How can I integrate PyMOL into Jupiter notebooks to visualise structures?
>>
>> Best
>>
>> m.o.l.s
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>
>

Re: [PyMOL] .

[O.L. S. <ori...@gm...>]

How do I ensure that PyMol is in my path as pymol? 


Thank you for the help in advance. 

Best

m.o.l.s.



> On 3 Jul 2019, at 14:18, Saurabh Gayali <sau...@gm...> wrote:
> 
> IPyMOL allows you to control PyMOL <https://www.pymol.org/> sessions via IPython. This tool is ideal for situations where you’d like to present your work neatly in a Jupyter Notebook <https://jupyter.org/> or conveniently prototype PyMOL scripts.
> 
> https://pypi.org/project/ipymol/ <https://pypi.org/project/ipymol/>
> 
> 
> Regards,
> Saurabh Gayali
> ---------------------------------------------------------------------
> 
> 
> On Wed, Jul 3, 2019 at 5:50 PM O.L. Simpson <ori...@gm... <mailto:ori...@gm...>> wrote:
> Dear Pymol Users, 
> 
> How can I integrate PyMOL into Jupiter notebooks to visualise structures? 
> 
> Best
> 
> m.o.l.s
> 
> 
> _______________________________________________
> 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>

Re: [PyMOL] .

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

IPyMOL allows you to control PyMOL <https://www.pymol.org/> sessions via
IPython. This tool is ideal for situations where you’d like to present your
work neatly in a Jupyter Notebook <https://jupyter.org/> or conveniently
prototype PyMOL scripts.

https://pypi.org/project/ipymol/


Regards,
*Saurabh Gayali*
---------------------------------------------------------------------


On Wed, Jul 3, 2019 at 5:50 PM O.L. Simpson <ori...@gm...> wrote:

> Dear Pymol Users,
>
> How can I integrate PyMOL into Jupiter notebooks to visualise structures?
>
> Best
>
> m.o.l.s
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

[PyMOL] .

[O.L. S. <ori...@gm...>]

Dear Pymol Users, 

How can I integrate PyMOL into Jupiter notebooks to visualise structures? 

Best

m.o.l.s

Re: [PyMOL] Export molecule does not keep COLOUR* changes - RESOLVED

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

A similar thing happen in 3d software where generic .Obj files do not have
any information of material analogous to colors in this case. They bypass
this limitation by having a software specific saving file format containing
all information or a separate file for material. In pymol phool scripting
file can help stor coloring informatiomation for the molecules as it is
highly unlikely to store color information in its generic pdb/cif format.
In another approach such information can be hidden in comments in specific
format that pymol would develop to parse on load event.

On Thu, 27 Jun 2019, 20:09 Sarameri, Jesse, <jes...@he...>
wrote:

> Hello,
>
>
> That might also explain why the same molecule loaded in LiteMol gives
> different colouring.
>
> So the conclusion is that the colors are not defined in molecules but
> instead in programs
>
> that displays them.
>
>
> Thank you!
>
>
> Regards,
>
> Jesse Sarameri
>
>
> ------------------------------
> *Lähettäjä:* Ali Kusay <aku...@un...>
> *Lähetetty:* tiistai 25. kesäkuuta 2019 20.52.33
> *Vastaanottaja:* Sarameri, Jesse
> *Kopio:* pym...@li...
> *Aihe:* Re: [PyMOL] Export molecule does not keep changes
>
>
> Hi Jesse,
>
>
>
> I am not aware of a structure file (i.e. PDB) which can store information
> such as color and thus when you load a PDB file pymol applies the default
> colors to it.
>
>
>
> You can however make it so that all proteins loaded into pymol are
> automatically assigned the grey colour, this is done by editing the pymolrc.
>
>
>
> In the menu go:
>
> File -> Edit -> pymolrc (will create file) -> type “set cartoon_color,
> grey80”
>
>
>
> When you close and reopen pymol, this will ensure that all proteins loaded
> into pymol are given the grey80 colour, you can make any additional edits
> to the pymolrc file as you please i.e stick color is still default
>
>
>
> Cheers,
>
>
>
> Ali
>
>
>
> *Ali Kusay *| BPharm (Hons) | PhD Candidate & Pharmacist
>
> *Supervised by *A/Prof Thomas Balle
>
> The University of Sydney School of Pharmacy | Faculty of Medicine and
> Health
>
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
>
> *From: *"Sarameri, Jesse" <jes...@he...>
> *Date: *Wednesday, 26 June 2019 at 6:34 pm
> *To: *"pym...@li..." <
> pym...@li...>
> *Subject: *[PyMOL] Export molecule does not keep changes
>
>
>
> Hello!
>
> (English is not my native language; please excuse typing errors.)
>
> Goal is to recolor molecule so it stays that way after the edit.
>
>
>
> This is how I thought it would work:
>
> Lets start by opening any molecule (like downloading 5jh0.cif from
> https://www.rcsb.org/structure/5jh0)
>
> Changed the color of the molecule to grey, save as session (.pse file),
> open it and still grey, great!
>
> But if I want to export to molecule (.pdb for example), open the molecule,
> no changes applied.
>
> Tried to change Saved state settings and different formats but no effect.
>
> No error messages either.
>
>
>
>  I did RTFM and STFW not able to find answer.
>
> (If I missed it, feel free to send pics with red circles and arrows to
> highlight it.)
>
>
>
> Software and hardware used:
>
> Open source PyMOL version 2.1.0.
>
> Windows 10
>
> Lenovo X280 Laptop
>
>
>
> Many thanks for help incase someone else might encounter this problem.
>
>
>
> Regards,
>
> Jesse Sarameri
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Multi-snapshot superimposition

[James S. <jms...@gm...>]

update:

for the realisation I have tried to use sep_state script with python version

so I modified sep_state adding superimposition
# pymol_save.py#
from pymol import cmd
import glob
import re

def save_sep(prefix=''):
  obj_list = cmd.get_names("public_objects")
  if obj_list:
    for i in range(len(obj_list)):
      obj_name = "%s%s.pdb" % (prefix, obj_list[i])
      cmd.save(obj_name, obj_list[i])
      print "Saving %s" %  obj_name
  else:
    print "No objects found"

cmd.extra_fit('name CA', '*', 'super')
cmd.extend('save_sep', save_sep)


and use it with my pdbs
pymol ${output}/*.pdb -ckqr pymol_save.py > ${output}/!temp/rmsf_fit.log

it align ensemble but did not save the resulted pdbs in separate
files. Finally, the same happenes when I open it in Pymol GUI
pymol-2.2.0 *.pdb pymol_save.py
remarkably when I use in this GUI session just a command 'save_sep' it
saves the files within the same directory (Which is ok!)
however cmd.extend('prefix', save_sep)does not work :(

чт, 27 июн. 2019 г. в 11:48, James Starlight <jms...@gm...>:
>
> Dear Pymol users!
>
> I have a folder with many pdb files. I would like to use pymol in
> no-gui mode in order to i)load all pdb within the pymol; ii)
> superimpose each pdb agains the first (top) pdb; iii) save sperimposed
> pdbs into the new folder under the SAME names of pdbs.
>
> Here is model of my script, which should be modified according to the
> indicated commentaries (mostly on the step of saving results).
>
> ${pymol} -c -d "
>   from pymol import cmd
>   # we open at once all pdbs which have "B-factors" suffix in its name!
>   cmd.load('${output}/!temp/B-factors*')
>   # it do almost what I want in terms of the superimposition, however
> not all snapshots are aligned properly
>   cmd.extra_fit('name CA', '*', 'super')
>  # here the most tricky part that should be modified since I need to
> save snapshots using some command keeping its original names!
>   cmd.save('output' + '.pdb')
>   "
>
> so the task is that I would like to use it in one command rather then
> to put inside the loop (e.g. opening 2 snapshots for each time to make
> mobile, reference superimposition, which is more easy way).
>
> Thank you in advance!
> James

[PyMOL] Multi-snapshot superimposition

[James S. <jms...@gm...>]

Dear Pymol users!

I have a folder with many pdb files. I would like to use pymol in
no-gui mode in order to i)load all pdb within the pymol; ii)
superimpose each pdb agains the first (top) pdb; iii) save sperimposed
pdbs into the new folder under the SAME names of pdbs.

Here is model of my script, which should be modified according to the
indicated commentaries (mostly on the step of saving results).

${pymol} -c -d "
  from pymol import cmd
  # we open at once all pdbs which have "B-factors" suffix in its name!
  cmd.load('${output}/!temp/B-factors*')
  # it do almost what I want in terms of the superimposition, however
not all snapshots are aligned properly
  cmd.extra_fit('name CA', '*', 'super')
 # here the most tricky part that should be modified since I need to
save snapshots using some command keeping its original names!
  cmd.save('output' + '.pdb')
  "

so the task is that I would like to use it in one command rather then
to put inside the loop (e.g. opening 2 snapshots for each time to make
mobile, reference superimposition, which is more easy way).

Thank you in advance!
James

[PyMOL] `selection` argument in load_traj

[brisvag <br...@gm...>]

Hi Thomas,

I see! Is it supposed to work with other formats too? Or at least, is
it planned to be expanded? I'm trying to switch to PyMOL to view
GROMACS `.xtc` trajectories, and this feature would be a great
addition.

Cheers,
Lorenzo

Re: [PyMOL] `selection` argument in load_traj

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

Hi Lorenzo,

You are correct, it's doing nothing for most trajectory formats. Only the implementation for AMBER .trj files uses it. It looks like it allows selecting a subset of atoms.

Cheers,
  Thomas

> On Jun 25, 2019, at 4:05 PM, Lorenzo Gaifas <br...@gm...> wrote:
> 
> Dear pymol users,
> 
> What is the purpose of the `selection` argument in the `load_traj` command?
> 
> My intuition would say that it allows to somehow select which atoms to load into pymol before the actual loading happens. However, it seems to do nothing whatsoever. What am I missing?
> 
> Thanks,
> Lorenzo
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Export molecule does not keep COLOUR* changes - RESOLVED

[Sarameri, J. <jes...@he...>]

Hello,


That might also explain why the same molecule loaded in LiteMol gives different colouring.

So the conclusion is that the colors are not defined in molecules but instead in programs

that displays them.


Thank you!


Regards,

Jesse Sarameri


________________________________
Lähettäjä: Ali Kusay <aku...@un...>
Lähetetty: tiistai 25. kesäkuuta 2019 20.52.33
Vastaanottaja: Sarameri, Jesse
Kopio: pym...@li...
Aihe: Re: [PyMOL] Export molecule does not keep changes


Hi Jesse,



I am not aware of a structure file (i.e. PDB) which can store information such as color and thus when you load a PDB file pymol applies the default colors to it.



You can however make it so that all proteins loaded into pymol are automatically assigned the grey colour, this is done by editing the pymolrc.



In the menu go:

File -> Edit -> pymolrc (will create file) -> type “set cartoon_color, grey80”



When you close and reopen pymol, this will ensure that all proteins loaded into pymol are given the grey80 colour, you can make any additional edits to the pymolrc file as you please i.e stick color is still default



Cheers,



Ali



Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist

Supervised by A/Prof Thomas Balle

The University of Sydney School of Pharmacy | Faculty of Medicine and Health

424, Brain and Mind Centre | The University of Sydney | NSW 2050



From: "Sarameri, Jesse" <jes...@he...>
Date: Wednesday, 26 June 2019 at 6:34 pm
To: "pym...@li..." <pym...@li...>
Subject: [PyMOL] Export molecule does not keep changes



Hello!

(English is not my native language; please excuse typing errors.)

Goal is to recolor molecule so it stays that way after the edit.



This is how I thought it would work:

Lets start by opening any molecule (like downloading 5jh0.cif from https://www.rcsb.org/structure/5jh0)

Changed the color of the molecule to grey, save as session (.pse file), open it and still grey, great!

But if I want to export to molecule (.pdb for example), open the molecule, no changes applied.

Tried to change Saved state settings and different formats but no effect.

No error messages either.



 I did RTFM and STFW not able to find answer.

(If I missed it, feel free to send pics with red circles and arrows to highlight it.)



Software and hardware used:

Open source PyMOL version 2.1.0.

Windows 10

Lenovo X280 Laptop



Many thanks for help incase someone else might encounter this problem.



Regards,

Jesse Sarameri

Re: [PyMOL] Thermal ellipsoid plot

[koji n. <pas...@gm...>]

 Mr. Thomas Holder,

Many thanks for your help.
I can manage it.

Best regards,
Koji

2019年6月26日(水) 18:56 Thomas Holder <tho...@sc...>:

> Hi Koji,
>
> Yes it is my understanding that sphere_scale 1.1932 would correspond to
> 30% probability.
>
> Cheers,
>   Thomas
>
> > On Jun 25, 2019, at 12:26 PM, koji naka <pas...@gm...> wrote:
> >
> > Dear Mr. Thomas Holder,
> >
> > Thank you very much for your kind reply.
> > I am very happy to know the scale factor for the 50% probability, but I
> don't understand well.
> > From the table, can I take a value the scale? For example, in case of
> 30% probability, is it ok to set " set sphere_scale,  1.1932"? or not?
> >
> > I am sorry for bothering you again.
> >
> > Best regards,
> > Koji
> >
> > 2019年6月25日(火) 18:49 Thomas Holder <tho...@sc...>:
> > Hi Koji,
> >
> > Interesting question, I wasn't aware of the ellipsoid_probability
> setting.
> >
> > The probability to radius conversion is done with a lookup table, see:
> >
> https://github.com/schrodinger/pymol-open-source/blob/d1359f125d/layer2/RepEllipsoid.cpp#L114
> >
> > To get sphere scaling equivalent of ellipsoid_probability=0.5, you can
> do:
> >
> > set sphere_scale, 1.53820
> >
> > I calculated this value with the following script:
> >
> > problevel = [ \
> >   0.4299, 0.5479, 0.6334, 0.7035, 0.7644, \
> >   0.8192, 0.8694, 0.9162, 0.9605, 1.0026, \
> >   1.0430, 1.0821, 1.1200, 1.1570, 1.1932, \
> >   1.2288, 1.2638, 1.2985, 1.3330, 1.3672, \
> >   1.4013, 1.4354, 1.4695, 1.5037, 1.5382, \
> >   1.5729, 1.6080, 1.6436, 1.6797, 1.7164, \
> >   1.7540, 1.7924, 1.8318, 1.8724, 1.9144, \
> >   1.9580, 2.0034, 2.0510, 2.1012, 2.1544, \
> >   2.2114, 2.2730, 2.3404, 2.4153, 2.5003, \
> >   2.5997, 2.7216, 2.8829, 3.1365, 6.0000 ]
> >
> > iprob = int((cmd.get_setting_float('ellipsoid_probability') + 0.01) * 50
> - 1)
> > pradius = problevel[iprob]
> >
> > cmd.set('sphere_scale', pradius *
> cmd.get_setting_float('ellipsoid_scale'))
> >
> > Hope this helps.
> >
> > Cheers,
> >   Thomas
> >
> >
> > > On Jun 24, 2019, at 7:21 AM, koji naka <pas...@gm...> wrote:
> > >
> > > Dear all,
> > >
> > > The size of isotropic atoms plotted by using "alter all, vdw =
> sqrt(b/8)/pi" and "show sphere" looks small compared with the size of
> anisotropic atoms displayed by "show ellipsoid" in PyMOL default setting
> with 50% probability.
> > >
> > > How can I plot the isotropic atoms with 50% probability?
> > >
> > > The data is a pdb file converted from a cif through Mercury software.
> > >
> > > Thank you very much for your help.
> > >
> > > Best regards,
> > > Koji
> > >
> > >
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > Archives:
> http://www.mail-archive.com/pym...@li...
> > > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Re: [PyMOL] Thermal ellipsoid plot

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

Hi Koji,

Yes it is my understanding that sphere_scale 1.1932 would correspond to 30% probability.

Cheers,
  Thomas

> On Jun 25, 2019, at 12:26 PM, koji naka <pas...@gm...> wrote:
> 
> Dear Mr. Thomas Holder,
> 
> Thank you very much for your kind reply.
> I am very happy to know the scale factor for the 50% probability, but I don't understand well.
> From the table, can I take a value the scale? For example, in case of 30% probability, is it ok to set " set sphere_scale,  1.1932"? or not?
> 
> I am sorry for bothering you again.
> 
> Best regards,
> Koji
> 
> 2019年6月25日(火) 18:49 Thomas Holder <tho...@sc...>:
> Hi Koji,
> 
> Interesting question, I wasn't aware of the ellipsoid_probability setting.
> 
> The probability to radius conversion is done with a lookup table, see:
> https://github.com/schrodinger/pymol-open-source/blob/d1359f125d/layer2/RepEllipsoid.cpp#L114
> 
> To get sphere scaling equivalent of ellipsoid_probability=0.5, you can do:
> 
> set sphere_scale, 1.53820
> 
> I calculated this value with the following script:
> 
> problevel = [ \
>   0.4299, 0.5479, 0.6334, 0.7035, 0.7644, \
>   0.8192, 0.8694, 0.9162, 0.9605, 1.0026, \
>   1.0430, 1.0821, 1.1200, 1.1570, 1.1932, \
>   1.2288, 1.2638, 1.2985, 1.3330, 1.3672, \
>   1.4013, 1.4354, 1.4695, 1.5037, 1.5382, \
>   1.5729, 1.6080, 1.6436, 1.6797, 1.7164, \
>   1.7540, 1.7924, 1.8318, 1.8724, 1.9144, \
>   1.9580, 2.0034, 2.0510, 2.1012, 2.1544, \
>   2.2114, 2.2730, 2.3404, 2.4153, 2.5003, \
>   2.5997, 2.7216, 2.8829, 3.1365, 6.0000 ]
> 
> iprob = int((cmd.get_setting_float('ellipsoid_probability') + 0.01) * 50 - 1)
> pradius = problevel[iprob]
> 
> cmd.set('sphere_scale', pradius * cmd.get_setting_float('ellipsoid_scale'))
> 
> Hope this helps.
> 
> Cheers,
>   Thomas
> 
> 
> > On Jun 24, 2019, at 7:21 AM, koji naka <pas...@gm...> wrote:
> > 
> > Dear all,
> > 
> > The size of isotropic atoms plotted by using "alter all, vdw = sqrt(b/8)/pi" and "show sphere" looks small compared with the size of anisotropic atoms displayed by "show ellipsoid" in PyMOL default setting with 50% probability.
> > 
> > How can I plot the isotropic atoms with 50% probability?
> > 
> > The data is a pdb file converted from a cif through Mercury software.
> > 
> > Thank you very much for your help.
> > 
> > Best regards,
> > Koji
> > 
> > 
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] set transparency for selected elements of secondary structure

[James S. <jms...@gm...>]

OK, with latest pymol

this works fine
set cartoon_transparency, 0.5, object

this does not work
set cartoon_transparency, 0.5, ss H+S

how I can select for example all of the objects in the current session
+ ss H+S ?

ср, 26 июн. 2019 г. в 11:13, Thomas Holder <tho...@sc...>:
>
> Hi James and Ali,
>
> Are you using PyMOL 2.3 yet?
>
> "As of PyMOL version 2.3, cartoon transparency is now an atom-level setting."
>
> https://pymolwiki.org/index.php/Cartoon_transparency
>
> Cheers,
>   Thomas
>
> > On Jun 26, 2019, at 10:26 AM, Ali Kusay <aku...@un...> wrote:
> >
> > Hi James,
> >
> > I am not sure what the exact cause of your issue is but I think if you make a selection first then apply the transparency to the selection that should work, i.e.:
> >
> > sele ss H+S
> > set cartoon_transparency, 0.5, sele
> >
> > Something to do with selection based transparency settings not enabling newer ones to be made
> >
> > Cheers,
> >
> > Ali
> >
> > On 26/6/19, 6:18 pm, "James Starlight" <jms...@gm...> wrote:
> >
> >    Dear pymol users!
> >
> >    I am trying to set transparency based on the secondary structure using
> >    pymol selection algebra
> >
> >    # set transparency to all helix and sheets but not loops
> >    set cartoon_transparency, 0.5, ss H+S
> >
> >    which produce the following output
> >    PyMOL>set cartoon_transparency, 0.5, ss H+S
> >     Setting: cartoon_transparency set for 144 atoms in object "0190_before_minim".
> >
> >    but actually do nothing in terms of visualization.
> >
> >    Could you suggest me how it would be possible to fix it?
> >
> >    Thanks in advance!
> >
> >
> >    _______________________________________________
> >    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
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>

Re: [PyMOL] set transparency for selected elements of secondary structure

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

Hi James and Ali,

Are you using PyMOL 2.3 yet?

"As of PyMOL version 2.3, cartoon transparency is now an atom-level setting."

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

Cheers,
  Thomas

> On Jun 26, 2019, at 10:26 AM, Ali Kusay <aku...@un...> wrote:
> 
> Hi James,
> 
> I am not sure what the exact cause of your issue is but I think if you make a selection first then apply the transparency to the selection that should work, i.e.:
> 
> sele ss H+S
> set cartoon_transparency, 0.5, sele
> 
> Something to do with selection based transparency settings not enabling newer ones to be made
> 
> Cheers,
> 
> Ali
> 
> On 26/6/19, 6:18 pm, "James Starlight" <jms...@gm...> wrote:
> 
>    Dear pymol users!
> 
>    I am trying to set transparency based on the secondary structure using
>    pymol selection algebra
> 
>    # set transparency to all helix and sheets but not loops
>    set cartoon_transparency, 0.5, ss H+S
> 
>    which produce the following output
>    PyMOL>set cartoon_transparency, 0.5, ss H+S
>     Setting: cartoon_transparency set for 144 atoms in object "0190_before_minim".
> 
>    but actually do nothing in terms of visualization.
> 
>    Could you suggest me how it would be possible to fix it?
> 
>    Thanks in advance!
> 
> 
>    _______________________________________________
>    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

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Export molecule does not keep changes

[Ali K. <aku...@un...>]

Hi Jesse,

I am not aware of a structure file (i.e. PDB) which can store information such as color and thus when you load a PDB file pymol applies the default colors to it.

You can however make it so that all proteins loaded into pymol are automatically assigned the grey colour, this is done by editing the pymolrc.

In the menu go:
File -> Edit -> pymolrc (will create file) -> type “set cartoon_color, grey80”

When you close and reopen pymol, this will ensure that all proteins loaded into pymol are given the grey80 colour, you can make any additional edits to the pymolrc file as you please i.e stick color is still default

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
Supervised by A/Prof Thomas Balle
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050

From: "Sarameri, Jesse" <jes...@he...>
Date: Wednesday, 26 June 2019 at 6:34 pm
To: "pym...@li..." <pym...@li...>
Subject: [PyMOL] Export molecule does not keep changes


Hello!

(English is not my native language; please excuse typing errors.)

Goal is to recolor molecule so it stays that way after the edit.



This is how I thought it would work:

Lets start by opening any molecule (like downloading 5jh0.cif from https://www.rcsb.org/structure/5jh0)

Changed the color of the molecule to grey, save as session (.pse file), open it and still grey, great!

But if I want to export to molecule (.pdb for example), open the molecule, no changes applied.

Tried to change Saved state settings and different formats but no effect.

No error messages either.



 I did RTFM and STFW not able to find answer.

(If I missed it, feel free to send pics with red circles and arrows to highlight it.)



Software and hardware used:

Open source PyMOL version 2.1.0.

Windows 10

Lenovo X280 Laptop



Many thanks for help incase someone else might encounter this problem.



Regards,

Jesse Sarameri

Re: [PyMOL] set transparency for selected elements of secondary structure

[Ali K. <aku...@un...>]

Hi James,

I am not sure what the exact cause of your issue is but I think if you make a selection first then apply the transparency to the selection that should work, i.e.:

sele ss H+S
set cartoon_transparency, 0.5, sele

Something to do with selection based transparency settings not enabling newer ones to be made

Cheers,

Ali

On 26/6/19, 6:18 pm, "James Starlight" <jms...@gm...> wrote:

    Dear pymol users!
    
    I am trying to set transparency based on the secondary structure using
    pymol selection algebra
    
    # set transparency to all helix and sheets but not loops
    set cartoon_transparency, 0.5, ss H+S
    
    which produce the following output
    PyMOL>set cartoon_transparency, 0.5, ss H+S
     Setting: cartoon_transparency set for 144 atoms in object "0190_before_minim".
    
    but actually do nothing in terms of visualization.
    
    Could you suggest me how it would be possible to fix it?
    
    Thanks in advance!
    
    
    _______________________________________________
    PyMOL-users mailing list
    Archives: http://www.mail-archive.com/pym...@li...
    Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
    

[PyMOL] set transparency for selected elements of secondary structure

[James S. <jms...@gm...>]

Dear pymol users!

I am trying to set transparency based on the secondary structure using
pymol selection algebra

# set transparency to all helix and sheets but not loops
set cartoon_transparency, 0.5, ss H+S

which produce the following output
PyMOL>set cartoon_transparency, 0.5, ss H+S
 Setting: cartoon_transparency set for 144 atoms in object "0190_before_minim".

but actually do nothing in terms of visualization.

Could you suggest me how it would be possible to fix it?

Thanks in advance!

Re: [PyMOL] PDB post-processing and TER records

[James S. <jms...@gm...>]

Awesome, thanks so much Jared for your usefull suggestions!

all the best

james

вт, 25 июн. 2019 г. в 22:00, Jared Sampson <jar...@co...>:
>
> Hi James - Glad you got it working.
>
> > chains_array = ["A", "B"]
>
> If you want a list of chains without having to hard-code them, try the `get_chains` command.
>
> ```
> chains_array = cmd.get_chains()
> ```
>
> > cmd.load('${pdb}')
> > cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
>
> Alternatively, if you want to remove all the chain IDs (which it appears you might), you don't need a list of chains at all, and can just do:
>
> ```
> alter all, chain=''
> ```
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On June 25, 2019 at 11:48:32 AM, James Starlight (jms...@gm...) wrote:
>
> I have got it, it works now!
> in my example the double quotes were not escaped in pymol script :-)
>
> the only (more python-oriented) question, would it be possible to
> indicate chains_array for all letters A-Z (e.g. using some python
> regex, rather just for A and B, chains_array = ["A", "B"], like in my
> example?
>
>
> вт, 25 июн. 2019 г. в 17:22, James Starlight <jms...@gm...>:
> >
> > I actually tried to do like that still defining chains_array = ["A",
> > "B"] inside of pymol script and use external bash loop to loop over
> > pdbs
> > but it does not works ;(
> >
> > #!/bin/bash
> > # this script rename chains in pdb to "empty" chain
> > home=$(pwd)
> > pdb_folder=$home/pdbs
> > output=$home/output
> > rm -r $output
> > mkdir $output
> >
> > #pymol -cQkd "
> > for pdb in "${pdb_folder}"/*.pdb ; do
> > pdb_name2=$(basename "${pdb}")
> > pdb_name="${pdb_name2/pdb}"
> > pymol -c -d "
> > from pymol import cmd
> > chains_array = ["A", "B"]
> > cmd.load('${pdb}')
> > cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
> > cmd.set('pdb_use_ter_records', 1)
> > cmd.set('retain_order', 1)
> > cmd.save('${output}/output_without'+"".join(chains_array) + '.pdb')
> > " > $output/pymol_${pdb_name}.log
> > done
> >
> > вт, 25 июн. 2019 г. в 16:58, James Starlight <jms...@gm...>:
> > >
> > > yes, actually it is better because we avoid looping!
> > > and how it would be possible to use array provided in the externall shell?
> > >
> > > #!/bin/bash
> > > pdb="final.pdb"
> > > output=$(pwd)
> > >
> > > # array given in bash
> > > chains_array=('A' 'B')
> > >
> > > # chains are cutted by pymol
> > > pymol -c -d "
> > > cmd.load('${pdb}')
> > > cmd.alter('chain ' + '+'.join($chains_array), 'chain=\"\"')
> > > cmd.set('pdb_use_ter_records', 1)
> > > cmd.set('retain_order', 1)
> > > cmd.save('output_without'+"".join($chains_array) + '.pdb')
> > > "
> > >
> > > вт, 25 июн. 2019 г. в 16:47, Thomas Holder <tho...@sc...>:
> > > >
> > > > If you want to rename multiple chains at once, make a selection like (chain A+B+C). This list selection syntax is documented here: https://pymolwiki.org/index.php/Property_Selectors
> > > >
> > > > cmd.load(pdb)
> > > > cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
> > > > cmd.save('output.pdb')
> > > >
> > > > Cheers,
> > > > Thomas
> > > >
> > > >
> > > > > On Jun 25, 2019, at 4:14 PM, James Starlight <jms...@gm...> wrote:
> > > > >
> > > > > thanks so much Thomas, for this example!
> > > > >
> > > > > Actually, your python script does exactly what my bash script -
> > > > > produces number of pdbs for each of the renamed chain.
> > > > > I would like rather to produce at the end ONE pdb with all chains
> > > > > renamed to empty chain...
> > > > > I guess I need to save the result outside of the loop something like this
> > > > >
> > > > > ################ hop hey lalaley #####
> > > > > from pymol import cmd
> > > > > pdb = "Ev_complex_model_final.pdb"
> > > > > chains_array = ["A", "B"] # add more chains in case of more complex pdb
> > > > >
> > > > > # loop over chains to rename it
> > > > > for chain in chains_array:
> > > > > cmd.load(pdb)
> > > > > cmd.alter('chain ' + chain, 'chain=""')
> > > > > cmd.delete('*')
> > > > > ######################################
> > > > >
> > > > > # save output as pdb
> > > > > # I need to add something in the name of output indicating how much
> > > > > chains have been renamed
> > > > > # like output_withoutAB.pdb
> > > > > cmd.save('output_' + '.pdb')
> > > > >
> > > > > thanks in advance for help!
> > > >
> > > > --
> > > > Thomas Holder
> > > > PyMOL Principal Developer
> > > > Schrödinger, Inc.
> > > >
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe