pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] How to inspect contents of 's' and 'p' for an atom?

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

Hi Mungo,

Introspecting the settings wrapper is a bit more tricky, but also possible:

from pymol import setting, stored
stored.s2dict = lambda s: dict((setting.name_dict[n], s[n]) for n in s)
iterate all, print(stored.s2dict(s))


I've updated the print() syntax in the documentation, thanks for the hint Blaine!

Cheers,
  Thomas


> On May 19, 2020, at 1:12 PM, Mungo Carstairs (Staff) <g.m...@du...> wrote:
> 
> Hi Blaine,
> 
> Thanks for that!
> 
> And is there an equivalent for the settings in 's'?
> So for example I can
> PyMOL> iterate 4zho//A/26/CA,print(s.transparency)
> PyMOL> 0.0
> but how to find all values in 's'?
> 
> Best regards,
> 
> Mungo
> 
> 
> 
>  
> 	 	 	
> Mungo Carstairs
> Jalview Computational Scientist
> The Barton Group
> Division of Computational Biology
> School of Life Sciences
> University of Dundee, Dundee, Scotland, UK
> www.jalview.org
> www.compbio.dundee.ac.uk 
> g.m...@du...
>       
> We're Scottish University of the Year again!
> The Times / Sunday Times Good University Guide 2016 and 2017
> From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
> Sent: 19 May 2020 11:47
> To: Mungo Carstairs (Staff) <g.m...@du...>; pym...@li...<pym...@li...>
> Subject: RE: How to inspect contents of 's' and 'p' for an atom?
>  
> Hi Mungo,
> 
> See https://pymol.org/dokuwiki/doku.php?id=properties.
> 
> This command will print the dictionary of properties for all of the atoms:
> 
> iterate /4zho//A/*/*, print(properties.all)
> 
> Note the Python3 print() function.
> The documentation needs to be updated.
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: Mungo Carstairs (Staff) [g.m...@du...]
> Sent: Tuesday, May 19, 2020 2:59 AM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] How to inspect contents of 's' and 'p' for an atom?
> 
> A PyMOL novice question here.
> 
> I can write custom atom properties to its 'p' dictionary, and print them:
> PyMOL>fetch 4zho
> 
> PyMOL>iterate 4zho//A/26/CA, p.metal_binding='Fe'
> 
> PyMOL>iterate 4zho//A/26/CA, print(p.metal_binding)
> 
> Fe
> 
> but how do I list the contents of the dictionary if I don't know what is in it?
> PyMOL>iterate 4zho//A/26/CA, print(p)
> <wrapper.PropertyWrapper object at 0x1140dcdb0>
> 
> Same question for 's':
> PyMOL>iterate 4zho//A/26/CA, print(s)
> <wrapper.SettingWrapper object at 0x1140dcdb0>
> 
> Better still, where would I find documentation for this?
> 
> Thanks,
> 
> Mungo
> 
> 
> Mungo Carstairs
> Jalview Computational Scientist
> 
> The Barton Group
> Division of Computational Biology
> 
> School of Life Sciences
> 
> University of Dundee, Dundee, Scotland, UK

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] How to inspect contents of 's' and 'p' for an atom?

[Mungo C. (Staff) <g.m...@du...>]

Hi Blaine,

Thanks for that!

And is there an equivalent for the settings in 's'?
So for example I can
PyMOL> iterate 4zho//A/26/CA,print(s.transparency)
PyMOL> 0.0
but how to find all values in 's'?

Best regards,

Mungo




[University of Dundee shield logo]<http://uod.ac.uk/sig-home>

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org<http://www.jalview.org>

www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>
g.m...@du...<mailto:g.m...@du...>

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________________________________
From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
Sent: 19 May 2020 11:47
To: Mungo Carstairs (Staff) <g.m...@du...>; pym...@li... <pym...@li...>
Subject: RE: How to inspect contents of 's' and 'p' for an atom?

Hi Mungo,

See https://pymol.org/dokuwiki/doku.php?id=properties.

This command will print the dictionary of properties for all of the atoms:

iterate /4zho//A/*/*, print(properties.all)

Note the Python3 print() function.
The documentation needs to be updated.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Mungo Carstairs (Staff) [g.m...@du...]
Sent: Tuesday, May 19, 2020 2:59 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] How to inspect contents of 's' and 'p' for an atom?

A PyMOL novice question here.

I can write custom atom properties to its 'p' dictionary, and print them:
PyMOL>fetch 4zho

PyMOL>iterate 4zho//A/26/CA, p.metal_binding='Fe'

PyMOL>iterate 4zho//A/26/CA, print(p.metal_binding)

Fe

but how do I list the contents of the dictionary if I don't know what is in it?
PyMOL>iterate 4zho//A/26/CA, print(p)
<wrapper.PropertyWrapper object at 0x1140dcdb0>

Same question for 's':
PyMOL>iterate 4zho//A/26/CA, print(s)
<wrapper.SettingWrapper object at 0x1140dcdb0>

Better still, where would I find documentation for this?

Thanks,

Mungo



[University of Dundee shield logo]<https://urldefense.proofpoint.com/v2/url?u=http-3A__uod.ac.uk_sig-2Dhome&d=DwMFAw&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HcZyTYAYwxaDM5jVRMvsUZT9bqmuiT6GegR62OpE3WY&s=pmTCDQ9ha-o3qwfjfSbuYLQz0XZbmOSqwVrXsZ_2fp0&e=>

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

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Re: [PyMOL] How to inspect contents of 's' and 'p' for an atom?

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

Hi Mungo,

See https://pymol.org/dokuwiki/doku.php?id=properties.

This command will print the dictionary of properties for all of the atoms:

iterate /4zho//A/*/*, print(properties.all)

Note the Python3 print() function.
The documentation needs to be updated.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Mungo Carstairs (Staff) [g.m...@du...]
Sent: Tuesday, May 19, 2020 2:59 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] How to inspect contents of 's' and 'p' for an atom?

A PyMOL novice question here.

I can write custom atom properties to its 'p' dictionary, and print them:
PyMOL>fetch 4zho

PyMOL>iterate 4zho//A/26/CA, p.metal_binding='Fe'

PyMOL>iterate 4zho//A/26/CA, print(p.metal_binding)

Fe

but how do I list the contents of the dictionary if I don't know what is in it?
PyMOL>iterate 4zho//A/26/CA, print(p)
<wrapper.PropertyWrapper object at 0x1140dcdb0>

Same question for 's':
PyMOL>iterate 4zho//A/26/CA, print(s)
<wrapper.SettingWrapper object at 0x1140dcdb0>

Better still, where would I find documentation for this?

Thanks,

Mungo



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Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

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[PyMOL] How to inspect contents of 's' and 'p' for an atom?

[Mungo C. (Staff) <g.m...@du...>]

A PyMOL novice question here.

I can write custom atom properties to its 'p' dictionary, and print them:
PyMOL>fetch 4zho

PyMOL>iterate 4zho//A/26/CA, p.metal_binding='Fe'

PyMOL>iterate 4zho//A/26/CA, print(p.metal_binding)

Fe

but how do I list the contents of the dictionary if I don't know what is in it?
PyMOL>iterate 4zho//A/26/CA, print(p)
<wrapper.PropertyWrapper object at 0x1140dcdb0>

Same question for 's':
PyMOL>iterate 4zho//A/26/CA, print(s)
<wrapper.SettingWrapper object at 0x1140dcdb0>

Better still, where would I find documentation for this?

Thanks,

Mungo



[University of Dundee shield logo]<http://uod.ac.uk/sig-home>

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org<http://www.jalview.org>

www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>
g.m...@du...<mailto:g.m...@du...>

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The Times / Sunday Times Good University Guide 2016 and 2017

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

Re: [PyMOL] Extract all phi and psi angles

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

Thank you Tamas, for suggesting that great MDanalysis tool, will try it
out!

Thank you Rob, yes that command worked (phi_psi obj), it gave a list of all
backbone dihedral angles!

On Sat, 9 May 2020 at 12:45, Tamas Hegedus <bio...@gm...> wrote:

> Hi,
>
> For this type of analysis I would use MDAnalysis (Python):
> https://www.mdanalysis.org/
>
> https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html
>
> Tamas
>
> On 5/9/20 5:08 PM, Neena Susan Eappen wrote:
>
> Hi Jarrett,
>
> Thank you for your reply. However, that command gives phi and psi angles
> for only one atom (when only one atom is selected). Is there one command we
> can use to extract all phi and psi angles?
>
> Thanks,
> Neena
>
>
>
> On Mon, 27 Apr 2020 at 22:01, Jarrett Johnson <
> jar...@sc...> wrote:
>
>> Hi Neena,
>>
>> Is this command sufficient?
>>
>> https://pymol.org/dokuwiki/doku.php?id=command:phi_psi
>>
>> Best,
>> Jarrett J
>>
>> On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen <
>> nee...@gm...> wrote:
>>
>>> Hello PyMOL users,
>>>
>>> How to extract all peptide dihedral angles (phi and psi) in PyMOL?
>>>
>>> Many thanks,
>>> Neena
>>> _______________________________________________
>>> 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
>> [image: Schrodinger Logo] <https://www.schrodinger.com/>
>>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
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> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] XML-RPC 'label' command format

[Mungo C. (Staff) <g.m...@du...>]

Any XML-RPC fans who can help me with this please?

This label command works in the PyMOL command line (after 'fetch 4zho'):

label 4zho//A/36/CA 4zho//B/36/CA, "hello world"

How do I format an equivalent XML-RPC request?
I've tried

<methodCall>
  <methodName>label</methodName>
  <params>
    <parameter>
      <value>4zho//A/36/CA  4zho//B/36/CA</value>
    </parameter>
    <parameter>
      <value>"hello world"</value>
    </parameter>
  </params>
</methodCall>

but get back a fault response XML message with

&lt;class 'SyntaxError'&gt;:invalid syntax (&lt;string&gt;, line 1)

I have also tried encoding the " as %22, or omitting the quotes, same result.

Any ideas please?

Thanks,

Mungo




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Jalview Computational Scientist

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Re: [PyMOL] Scenes

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

Hi Tim - 

One way to do this would be to duplicate the object before mutating and keep an "old" and "new" version as separate objects in the session.  Then you can enable one or the other as you like in your scenes.

Hope that helps,

Cheers,
Jared


From: Waybright, Timothy (NIH/NCI) [C] via PyMOL-users <pym...@li...>
Reply: Waybright, Timothy (NIH/NCI) [C] <way...@ma...>
Date: May 12, 2020 at 6:43:54 PM
To: pym...@li... <pym...@li...>
Subject:  [PyMOL] Scenes  

Hello,

 

I am looking at a protein with a nucleotide.  I want to see what happens when a residue close to the nucleotide (or far away) is changed via Mutagenesis to another residue.  When I store scenes from the initial views, they are fine – they have the ‘old’ residue in the positions I want the movie to show them as.  When I use Mutagenesis to change the residue, the previously-made scenes update to show the ‘new’ residue.  I don’t want this to happen, as I want the ‘old’ residue in the first few scenes, and then the ‘new’ residue in the later scenes.  I will then put them together to make a movie to show the effect of changing the residue.  Can someone assist me with how to keep the scenes as they are when I make them, and not update with the new residue?  Many thanks!

 

Cheers!

 

Tim

 

 

Timothy J Waybright (Contractor)

 

Research Associate III

Leidos Biomedical Research, Inc.

Frederick National Laboratory for Cancer Research

P.O. Box B, Frederick, MD 21702                                               

Phone: 301-846-7271                                     

way...@ma...                                                          

 

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[PyMOL] Scenes

[Waybright, T. (NIH/N. [C] <way...@ma...>]

Hello,

I am looking at a protein with a nucleotide.  I want to see what happens when a residue close to the nucleotide (or far away) is changed via Mutagenesis to another residue.  When I store scenes from the initial views, they are fine - they have the 'old' residue in the positions I want the movie to show them as.  When I use Mutagenesis to change the residue, the previously-made scenes update to show the 'new' residue.  I don't want this to happen, as I want the 'old' residue in the first few scenes, and then the 'new' residue in the later scenes.  I will then put them together to make a movie to show the effect of changing the residue.  Can someone assist me with how to keep the scenes as they are when I make them, and not update with the new residue?  Many thanks!

Cheers!

Tim



Timothy J Waybright (Contractor)

Research Associate III
Leidos Biomedical Research, Inc.
Frederick National Laboratory for Cancer Research
P.O. Box B, Frederick, MD 21702
Phone: 301-846-7271
way...@ma...<mailto:way...@ma...>

Re: [PyMOL] Extract all phi and psi angles

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

Hi Neena,

If you give a different selection, then phi_psi will give you a list of phi/psi angles for all residues in the selection.

For example if your protein object is called "obj_1", then typing

phi_psi obj_1

will provide a list of phi_psi values to the terminal:

PyMOL>phi_psi obj_1
 LYS-3:    (  -63.3,  -75.6 )
 GLY-4:    (  -62.6,  -32.9 )
 GLU-5:    (  -31.7,  -58.7 )
 GLU-6:    (  -57.3,  -23.4 )
 LEU-7:    (  -74.7,  -18.6 )
 PHE-8:    ( -106.0,    6.4 )
 THR-9:    (  -59.8,  -16.1 )
 GLY-10:   ( -140.4, -166.5 )

or you can assign the list to a dictionary variable with:

p = cmd.phi_psi('obj_1')

where p will be a dictionary with keys representing the residue numbers and pointing to a list of the phi/psi values for that residue.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
Queen's University, Kingston, ON K7L 3N6  Canada
<rob...@qu...>  http://pldserver1.biochem.queensu.ca/~rlc


On Sat, 2020-05-09 11:08  -0400,  Neena Susan Eappen <nee...@gm...> wrote:

> Hi Jarrett,
> 
> Thank you for your reply. However, that command gives phi and psi
> angles for only one atom (when only one atom is selected). Is there
> one command we can use to extract all phi and psi angles?
> 
> Thanks,
> Neena
> 
> 
> 
> On Mon, 27 Apr 2020 at 22:01, Jarrett Johnson <
> jar...@sc...> wrote:  
> 
> > Hi Neena,
> >
> > Is this command sufficient?
> >
> > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpymol.org%2Fdokuwiki%2Fdoku.php%3Fid%3Dcommand%3Aphi_psi&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438&amp;sdata=Y8U07iXlCYJ%2BE0GN2Oh04QSE7n68NPH5d2fc%2BaUhdSk%3D&amp;reserved=0
> >
> > Best,
> > Jarrett J
> >
> > On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen <  
> > nee...@gm...> wrote:  
> >  
> >> Hello PyMOL users,
> >>
> >> How to extract all peptide dihedral angles (phi and psi) in PyMOL?
> >>
> >> Many thanks,
> >> Neena
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> Archives:
> >> https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438&amp;sdata=%2F%2F%2BSyfR20FyqY2GFMhZVbBe0CHtQuoSLCIUMsBHgoLs%3D&amp;reserved=0
> >> Unsubscribe:
> >> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438&amp;sdata=gcqmQ9A%2BOEJMPVf3ubqWWGEh6DzZv95XVXXJULabe2w%3D&amp;reserved=0
> >>  
> >
> >
> >
> > --
> >
> > *Jarrett Johnson* | Senior Developer
> > [image: Schrodinger Logo]
> > <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.schrodinger.com%2F&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438&amp;sdata=QViEhtZ0MwQ2h0DLrVEcSdR%2FBW5DNGRF7kWbSDQIAaM%3D&amp;reserved=0> 

Re: [PyMOL] Extract all phi and psi angles

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

Hi,

For this type of analysis I would use MDAnalysis (Python):
https://www.mdanalysis.org/
https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html

Tamas

On 5/9/20 5:08 PM, Neena Susan Eappen wrote:
> Hi Jarrett,
>
> Thank you for your reply. However, that command gives phi and psi 
> angles for only one atom (when only one atom is selected). Is there 
> one command we can use to extract all phi and psi angles?
>
> Thanks,
> Neena
>
>
>
> On Mon, 27 Apr 2020 at 22:01, Jarrett Johnson 
> <jar...@sc... 
> <mailto:jar...@sc...>> wrote:
>
>     Hi Neena,
>
>     Is this command sufficient?
>
>     https://pymol.org/dokuwiki/doku.php?id=command:phi_psi
>
>     Best,
>     Jarrett J
>
>     On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen
>     <nee...@gm... <mailto:nee...@gm...>> wrote:
>
>         Hello PyMOL users,
>
>         How to extract all peptide dihedral angles (phi and psi) in PyMOL?
>
>         Many thanks,
>         Neena
>         _______________________________________________
>         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
>
>     Schrodinger Logo <https://www.schrodinger.com/>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Extract all phi and psi angles

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

Hi Jarrett,

Thank you for your reply. However, that command gives phi and psi angles
for only one atom (when only one atom is selected). Is there one command we
can use to extract all phi and psi angles?

Thanks,
Neena



On Mon, 27 Apr 2020 at 22:01, Jarrett Johnson <
jar...@sc...> wrote:

> Hi Neena,
>
> Is this command sufficient?
>
> https://pymol.org/dokuwiki/doku.php?id=command:phi_psi
>
> Best,
> Jarrett J
>
> On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen <
> nee...@gm...> wrote:
>
>> Hello PyMOL users,
>>
>> How to extract all peptide dihedral angles (phi and psi) in PyMOL?
>>
>> Many thanks,
>> Neena
>> _______________________________________________
>> 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
> [image: Schrodinger Logo] <https://www.schrodinger.com/>
>

Re: [PyMOL] Outlines thickness

[Gianluca T. <gia...@gm...>]

Hi Adam,

Thanks for your response.
As I imagined there isn't an easy way of doing this. I'll play around with
settings and try to find a good compromise.



On Thu, 7 May 2020, 17:02 h. adam steinberg, <h.a...@gm...>
wrote:

> I also use this feature for illustrations and would love to find a better
> way of controlling the outline thickness. Could anyone fill us in on the
> history of this feature?
>
> In Chimera black outline is just a simple slider and it’s super easy to
> use. You just move the slider up and down and it shows you the black
> outline thickness without even having to render the image.
>
> In PyMOL you can do a couple of things:
> 1. increasing the rendering size (more pixels in X and Y) will decrease
> the thickness of the black outline (and infilling).
> Decreasing the rendering size will make the black outline thicker.
> Note however that the detail/quality of the image is better with higher
> resolution and worse with lower resolution.
>
> 2. Change the ray_trace_gain. the default setting is 0.12.
> Setting this to 1 will give you more black, but it’s not great (black
> infill is worse in many areas) and it depends on the resolution you choose
> in X and Y.
> Setting this to 0 will give you less black, but it’s not great (infill
> will be removed but so will many of the black outlines) and it depends on
> the resolution you choose in X and Y.  0.06 works fairly good at 1500dpi
> for less black and less infill.
>
> 3. Setting the Ray_trace_slope_factor higher, will also reduce the infill
> black. 0.9 Ray_trace_slope_factor and ray_trace_gain of 0.2 at 1500dpi
> looks fairly good.
>
> It seems that PyMOL doesn’t have a way to easily control the ray traced
> black outline.
>
> > On May 6, 2020, at 10:47 AM, Gianluca Tomasello <gia...@gm...>
> wrote:
> >
> > Hi,
> > is there a proper way to increase outlines thickness in PyMol?
> >
> > I noticed that increasing ray_trace_gain setting outlines are drawn
> thicker but increasing this setting increases also the number of outlines.
> >
> > Is there a way to increase thickness without increasing the outlines
> number?
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Outlines thickness

[h. a. s. <h.a...@gm...>]

I also use this feature for illustrations and would love to find a better way of controlling the outline thickness. Could anyone fill us in on the history of this feature?

In Chimera black outline is just a simple slider and it’s super easy to use. You just move the slider up and down and it shows you the black outline thickness without even having to render the image.

In PyMOL you can do a couple of things:
1. increasing the rendering size (more pixels in X and Y) will decrease the thickness of the black outline (and infilling).
Decreasing the rendering size will make the black outline thicker.
Note however that the detail/quality of the image is better with higher resolution and worse with lower resolution.

2. Change the ray_trace_gain. the default setting is 0.12.
Setting this to 1 will give you more black, but it’s not great (black infill is worse in many areas) and it depends on the resolution you choose in X and Y. 
Setting this to 0 will give you less black, but it’s not great (infill will be removed but so will many of the black outlines) and it depends on the resolution you choose in X and Y.  0.06 works fairly good at 1500dpi for less black and less infill.

3. Setting the Ray_trace_slope_factor higher, will also reduce the infill black. 0.9 Ray_trace_slope_factor and ray_trace_gain of 0.2 at 1500dpi looks fairly good.

It seems that PyMOL doesn’t have a way to easily control the ray traced black outline.

> On May 6, 2020, at 10:47 AM, Gianluca Tomasello <gia...@gm...> wrote:
> 
> Hi, 
> is there a proper way to increase outlines thickness in PyMol? 
> 
> I noticed that increasing ray_trace_gain setting outlines are drawn thicker but increasing this setting increases also the number of outlines. 
> 
> Is there a way to increase thickness without increasing the outlines number? 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Capturing scene pixels without writing image to disk

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

Calling cmd.draw() will schedule a rendering event to be executed in the rending loop. This means the command will return before the image was rendered. The only way to access the result is with a callback, which will be asynchronous with the script you're executing.

Calling cmd.png() is related to that, but will not trigger the callback. It can enter a couple of different code paths, depending on the availability of the OpenGL context (on-screen display).

1) No OpenGL context (e.g. batch processing) -> Ray tracer will be used. Nothing asynchronous here, the PNG file will be available after the function call.
2) OpenGL context in different thread -> schedules an async task to be executed by the rendering thread. This means cmd.png() returns before the image was written (like cmd.draw)
3) Requesting width/height also triggers the async task

So the only option which is guaranteed to be synchronous is the ray tracing. Implementing direct numpy array or PNG buffer export would be possible, but the performance benefit for your script would probably not be significant.

Cheers,
  Thomas


> On May 6, 2020, at 5:42 PM, Antonio Serrano <ase...@uc...> wrote:
> 
> Thx for your quick response, Thomas. Please, could you elaborate the previous example a little bit further? I'm a little confused about what you can accomplish using the callback function you posted. Thx

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Outlines thickness

[Gianluca T. <gia...@gm...>]

Hi,
is there a proper way to increase outlines thickness in PyMol?

I noticed that increasing ray_trace_gain setting outlines are drawn thicker
but increasing this setting increases also the number of outlines.

Is there a way to increase thickness without increasing the outlines
number?

Re: [PyMOL] Capturing scene pixels without writing image to disk

[Antonio S. <ase...@uc...>]

Thx for your quick response, Thomas. Please, could you elaborate the
previous example a little bit further? I'm a little confused about what you
can accomplish using the callback function you posted. Thx

-- 

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distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y 
borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a 
la confidencialidad ni a ningún privilegio a causa de una transmisión 
errónea o por mal funcionamiento". 


"This message is private and 
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Re: [PyMOL] Capturing scene pixels without writing image to disk

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

Hi Antonio,

This is currently not possible for ray tracing or for capturing the displayed image.

It's possible for deferred on-screen rendering with a callback.

def mycallback(image):
    print("got image of dimension", image.shape)

cmd.raw_image_callback = mycallback
cmd.draw()


Cheers,
  Thomas

> On May 4, 2020, at 7:24 PM, Antonio Serrano <ase...@uc...> wrote:
> 
> So far, I've been able to capture the pixels from the scene in two steps using the png method along with imread:
> p1.cmd.png(image_path)
> img = plt.imread(image_path)
> 
> Since I have to do this quite often in my program, I'd to capture the pixels in a numpy ndarray avoiding writting the image to disk every time. Is that possible? Thx.
> 
> 
> 
> "Este mensaje es privado y confidencial y se dirige exclusivamente a su destinatario. Si usted recibe este mensaje por error, no debe revelar, distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a la confidencialidad ni a ningún privilegio a causa de una transmisión errónea o por mal funcionamiento". 
> 
> "This message is private and confidential and it is intended exclusively for the addressee. If your receive this message by mistake, you should not disseminate, distribute or copy this e-mail. Please inform the sender and delete the message and attachments from your system. No confidentiality or any privilege regarding the information is waived or lost by any mistransmission or malfunction".
> 
> No me imprimas si no es necesario.
> Don't print me unless it's necessary.
> 
> _______________________________________________
> 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] Coloring different carbons differently

[Chris F. <fa...@gm...>]

Hello again,

Here’s a simple command for selecting four specific atoms in the ligand
hemoglobin (HEM):
sele resn HEM & n. C1A+C3A+CHA+C4D

sele = select
resn = residue name
n. = atom name

Best,
Chris

On Tue, May 5, 2020 at 10:38 Chris Fage <fa...@gm...> wrote:

> Hello,
>
> You can always change the selection mode from residues to atoms (Mouse >
> Selection Mode > Atoms, at least in my version of Pymol). Then, select the
> appropriate atoms and change the color for that selection. I'm sure there
> are more sophisticated ways of doing this with the command line, but you'll
> need to know the PDB-formatted names of those atoms to do. That likely
> requires clicking on the atoms of interest anyway.
>
> Best,
> Chris
>
>
> <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virus-free.
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>
> On Tue, May 5, 2020 at 9:08 AM Полина Короткова <kor...@gm...>
> wrote:
>
>> Hello, I’m new to PyMOL and I need your help. I want to color different
>> carbons in molecule differently: 1 color - carbon at the beginning of a
>> chain, 2 color - carbon in the middle and 3 color - carbon at the end of
>> the chain. I need to do this for a few molecules. Is there a command to do
>> that? I tried to create different objects and color them in needed colors,
>> but maybe there is a simpler way.
>> Thank you in advance.
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Coloring different carbons differently

[Chris F. <fa...@gm...>]

Hello,

You can always change the selection mode from residues to atoms (Mouse >
Selection Mode > Atoms, at least in my version of Pymol). Then, select the
appropriate atoms and change the color for that selection. I'm sure there
are more sophisticated ways of doing this with the command line, but you'll
need to know the PDB-formatted names of those atoms to do. That likely
requires clicking on the atoms of interest anyway.

Best,
Chris

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On Tue, May 5, 2020 at 9:08 AM Полина Короткова <kor...@gm...>
wrote:

> Hello, I’m new to PyMOL and I need your help. I want to color different
> carbons in molecule differently: 1 color - carbon at the beginning of a
> chain, 2 color - carbon in the middle and 3 color - carbon at the end of
> the chain. I need to do this for a few molecules. Is there a command to do
> that? I tried to create different objects and color them in needed colors,
> but maybe there is a simpler way.
> Thank you 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] Coloring different carbons differently

[Полина К. <kor...@gm...>]

Hello, I’m new to PyMOL and I need your help. I want to color different carbons in molecule differently: 1 color - carbon at the beginning of a chain, 2 color - carbon in the middle and 3 color - carbon at the end of the chain. I need to do this for a few molecules. Is there a command to do that? I tried to create different objects and color them in needed colors, but maybe there is a simpler way. 
Thank you in advance. 

[PyMOL] Capturing scene pixels without writing image to disk

[Antonio S. <ase...@uc...>]

So far, I've been able to capture the pixels from the scene in two steps
using the png method along with imread:

p1.cmd.png(image_path)
img = plt.imread(image_path)

Since I have to do this quite often in my program, I'd to capture the
pixels in a numpy ndarray avoiding writting the image to disk every time.
Is that possible? Thx.

-- 

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Re: [PyMOL] [EXTERNAL] resn variable in label command

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

Hi Jianhao,

Any easy solution is to use cmd.do with lets you issue pml commands in Python:

cmd.do('label (n. CA and (resi 800-850 and chain A)), "%s%s"%(resn, resi)')

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: C.J. [bi...@gm...]
Sent: Saturday, May 02, 2020 4:23 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] resn variable in label command

Hi all,

I have some trouble in using label command.

The command below in "pymol>" box works
label (n. CA and (resi 800-850 and chain A)), "%s%s"%(resn, resi)

But the script below doesn't work.
cmd.label("(n. CA and (resi 800-850 and chain A))", "%s%s"%(resn, resi))

Do I have anything wrong with this? Thank you!

Jianhao

Re: [PyMOL] [EXTERNAL] resn variable in label command

[C.J. <bi...@gm...>]

Thank you, Blaine. It really works!

Mooers, Blaine H.M. (HSC) <Bla...@ou...> 于2020年5月2日周六 下午3:37写道：

> Hi Jianhao,
>
> Any easy solution is to use cmd.do with lets you issue pml commands in
> Python:
>
> cmd.do('label (n. CA and (resi 800-850 and chain A)), "%s%s"%(resn, resi)')
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> ________________________________________
> From: C.J. [bi...@gm...]
> Sent: Saturday, May 02, 2020 4:23 PM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] resn variable in label command
>
> Hi all,
>
> I have some trouble in using label command.
>
> The command below in "pymol>" box works
> label (n. CA and (resi 800-850 and chain A)), "%s%s"%(resn, resi)
>
> But the script below doesn't work.
> cmd.label("(n. CA and (resi 800-850 and chain A))", "%s%s"%(resn, resi))
>
> Do I have anything wrong with this? Thank you!
>
> Jianhao
>


-- 
Best regards!
C.J.

[PyMOL] resn variable in label command

[C.J. <bi...@gm...>]

Hi all,

I have some trouble in using label command.

The command below in "pymol>" box works
label (n. CA and (resi 800-850 and chain A)), "%s%s"%(resn, resi)

But the script below doesn't work.
cmd.label("(n. CA and (resi 800-850 and chain A))", "%s%s"%(resn, resi))

Do I have anything wrong with this? Thank you!

Jianhao

Re: [PyMOL] moving an object and keep others

[C.J. <bi...@gm...>]

Thank you!
But after choosing "drag", I find only rotation or moving forward or
backward is available. How can I translate the an object rather than all
object using mouse?

杨海滨 <yh...@16...> 于2020年4月29日周三 下午10:48写道：

> Firstly, select the one that u want to move, then click Action-drag
> coordinates, click shift without releasing when u move your target.
>
>
> 杨海滨
> 邮箱：yh...@16...
>
> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E6%9D%A8%E6%B5%B7%E6%BB%A8&uid=yhb4539%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=%5B%22%E9%82%AE%E7%AE%B1%EF%BC%9Ayhb4539%40163.com%22%5D>
>
> 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail88> 定制
> On 04/30/2020 13:35, C.J. <bi...@gm...> wrote:
>
>
> Hi,
>
> I'm new to pymol. My pymol version is "PyMOL 2.3.0 Open-Source". After
> opening two pdb files, how can I keep one object and move another one using
> mouse? Thank you!
>
> Jianhao
>
>

-- 
Best regards!
C.J.