pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] How to assign secondary structure as 3-10 helix in pymol?

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

Dear pymol user,

I wonder why sometimes the secondary structure of a protein can not be displayed incorrect in pymol. I have a structure, some residues are predicted to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only typing "dss" command in pymol doesn't work. I know by using the "alter" commad the secondary structures can be assigned. The following command:

alter 61-63/, ss='S' 

can assign residue 61-63 as sheet. However, what is the command to assign residues as 3-10 helix?

Thank you in advance.

Arthur

Re: [PyMOL] PyMOL-users Digest, Vol 157, Issue 2

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

Dear Hao

In PyMOL bonds are essentially drawn based on a distance cut-off: Two atoms are considered bonded if

distance <= connect_cutoff + (vdw1 + vdw2)/2

You can generally adjust the sensitivity of bond recognition by adjusting the connect_cutoff global variable ( https://pymolwiki.org/index.php/Connect_cutoff ),

eliminate a specific mis-assigned bond by using the unbond command

unbond atom1,atom2 ( https://pymolwiki.org/index.php/Unbond )

or add a missed bond  using the bond command:

bond [atom1, atom2 [,order]]  (https://pymolwiki.org/index.php/Bond)


best regards

Annemarie Honegger
____________________________________________________________

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     



> 
> Today's Topics:
> 
>   1. Unwanted bond formed in azetidine ring (Hao Li)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 3 Jun 2019 16:15:33 -0400
> From: Hao Li <hl...@um...>
> To: pym...@li...
> Subject: [PyMOL] Unwanted bond formed in azetidine ring
> Message-ID:
> 	<CAL...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear users,
> 
> I am working on a structure of a protein-ligand complex, and the ligand
> contains an azetidine group. Whenever I display this structure in pymol, an
> unwanted bond forms between 2 carbon atoms in the azetidine ring.
> 
> The pdb file of this ligand was generated by Chem3D and the restraint cif
> file was generated by eLBOW in Phenix. I tried to edit both pdb and cif
> files of the ligand but it did not work very well. I was able to remove
> certain atoms but not the bond.
> 
> I am kindly asking if there is a way to remove this unnecessary bond? Thank
> you.
> 
> Regards,
> Hao
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> 
> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> PyMOL-users mailing list
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> End of PyMOL-users Digest, Vol 157, Issue 2
> *******************************************

Re: [PyMOL] Unwanted bond formed in azetidine ring

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

The bonds are initially generated based on proximity between the atoms 
in the structure.

To remove the erroneously generated bonds use command Unbond:

unbond atom1,atom2

04.06.2019 3:46, pym...@li... пишет:
> Message: 1
> Date: Mon, 3 Jun 2019 16:15:33 -0400
> From: Hao Li<hl...@um...>
> To:pym...@li...
> Subject: [PyMOL] Unwanted bond formed in azetidine ring
> Message-ID:
> 	<CAL...@ma...>
> Content-Type: text/plain; charset="utf-8"
>
> Dear users,
>
> I am working on a structure of a protein-ligand complex, and the ligand
> contains an azetidine group. Whenever I display this structure in pymol, an
> unwanted bond forms between 2 carbon atoms in the azetidine ring.
>
> The pdb file of this ligand was generated by Chem3D and the restraint cif
> file was generated by eLBOW in Phenix. I tried to edit both pdb and cif
> files of the ligand but it did not work very well. I was able to remove
> certain atoms but not the bond.
>
> I am kindly asking if there is a way to remove this unnecessary bond? Thank
> you.

Re: [PyMOL] Unwanted bond formed in azetidine ring

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

Here is one way to do this:
change your mouse mode from “viewing” to “editing”.
left-click on the atoms at each end of the bond you wish to remove,
each atom will highlight with a gray ball around it,
In the command line type "unbond pkset” and hit the enter key,
your bond will be removed.

> On Jun 3, 2019, at 3:15 PM, Hao Li <hl...@um...> wrote:
> 
> Dear users,
> 
> I am working on a structure of a protein-ligand complex, and the ligand contains an azetidine group. Whenever I display this structure in pymol, an unwanted bond forms between 2 carbon atoms in the azetidine ring. 
> 
> The pdb file of this ligand was generated by Chem3D and the restraint cif file was generated by eLBOW in Phenix. I tried to edit both pdb and cif files of the ligand but it did not work very well. I was able to remove certain atoms but not the bond. 
> 
> I am kindly asking if there is a way to remove this unnecessary bond? Thank you.
> 
> Regards,
> Hao
> 
> 
> 
> <20190603160708.png>_______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Unwanted bond formed in azetidine ring

[Hao Li <hl...@um...>]

Dear users,

I am working on a structure of a protein-ligand complex, and the ligand
contains an azetidine group. Whenever I display this structure in pymol, an
unwanted bond forms between 2 carbon atoms in the azetidine ring.

The pdb file of this ligand was generated by Chem3D and the restraint cif
file was generated by eLBOW in Phenix. I tried to edit both pdb and cif
files of the ligand but it did not work very well. I was able to remove
certain atoms but not the bond.

I am kindly asking if there is a way to remove this unnecessary bond? Thank
you.

Regards,
Hao

[PyMOL] Regarding APBS tools in Pymol

[Dilraj L. <di...@bi...>]

Dear Pymol users,

                             I am trying to generate the electrostatic 
potential surface for my protein using the APBS plugin in Pymol. I 
installed "ver 1.8.4.0" through the per-compiled binary using "apt-get" 
in Ubuntu 18.04.2 LTS".

I am encountering the following error while trying to generate the 
potential surface.

*Could not find /tmp/pymol-generated.dx so searching for 
/tmp/pymol-generated-PE0.dx**
**ObjectMapLoadDXFile-Error: Unable to open file!**
**ObjectMapLoadDXFile: Does '/tmp/pymol-generated-PE0.dx' exist?*

I have looked through the mailing list and find that it has been 
encountered previously. However i am not able to resolve the issue at my 
end. Can anyone please shed some light on this issue?

I will be glad to get some suggestions.

Thank you,

Dilraj.

Re: [PyMOL] [EXTERNAL] Absymal performance when creating large numbers of bonds

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

Hi Lorenzo,

Looks like the cmd.bond() function is indeed very inefficient. I've found a "TO DO: optimize for performance" comment in the code - that speaks for itself.

https://github.com/schrodinger/pymol-open-source/blob/master/layer2/ObjectMolecule.cpp#L4492

Parallelization is not the solution. You are probably right that a new API function is needed which allows you to directly add a bond by atom indices instead of atom selections.

Cheers,
  Thomas

> On May 25, 2019, at 5:11 PM, Lorenzo Gaifas <br...@gm...> wrote:
> 
> Hi Blaine,
> 
> Thanks for your help.
> I don't think what you suggest is going to solve the problem. The loop itself is quite fast, and I don't need to perform anything else in the loop other than adding those bonds.
> I already have a list of tuples [(atom1, atom2), (atom3, atom4)] and all I need to do is create a bond between each pair. The bottleneck is the bond function, not the loop itself.
> 
> Also, I doubt simply the speed difference between C++ and Python could explain such a drastic difference (minutes against fractions of a second). There is clearly a difference in the way the `bond` command is implemented and the way bonds are generated at startup.
> 
> What I think is needed, is either a way for pymol to perform those actions in parallel (unlikely) or a way to get my hands on the way bonds are generated at startup and use those functions or at least the same approach.
> 
> Thank you,
> Lorenzo
> 
> Il giorno sab 25 mag 2019 alle ore 16:23 Mooers, Blaine H.M. (HSC) <Bla...@ou...> ha scritto:
> Hi Lorenzo,
> 
> You can import numpy  and replace your lists of coordinates with NumPy arrays. 
> Operations with numpy arrays can be >100 times faster than with lists in for loops. 
> See the last example the following blog post for inspiration: 
> 
> https://medium.freecodecamp.org/if-you-have-slow-loops-in-python-you-can-fix-it-until-you-cant-3a39e03b6f35.
> 
> Please recall that PyMOL is collection of C and C++ programs wrapped by Python. 
> The fast display of bonds inside the viewport is due to C or C++ programs. 
> 
> 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: Lorenzo Gaifas [br...@gm...]
> Sent: Saturday, May 25, 2019 5:48 AM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] Absymal performance when creating large numbers of bonds
> 
> Dear pymol users,
> 
> I'm working on a script, using the python API, that needs to add a very large number of bonds to the loaded structure.
> 
> I thought simply using cmd.bond() in a for loop would do the trick, but -even though it works- it is extremely slow. I figured something was fishy, since pymol at startup is almost istantaneous and there, too, it has to compute, draw and even guess equally large numbers of bonds.
> 
> I also tried to parallelise the command, but by now I *think* this can't be done due to the Global Intepreter Lock.
> 
> I feel like there must be something I'm missing (maybe a way to prevent pymol from updating the rendering between each cmd.bond call?) or at least an API function that better exposes the bond generation procedure. Does someone have suggestions on how to solve this problem?
> 
> Cheers,
> 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.

Re: [PyMOL] [EXTERNAL] Absymal performance when creating large numbers of bonds

[Lorenzo G. <br...@gm...>]

Hi Blaine,

Thanks for your help.
I don't think what you suggest is going to solve the problem. The loop
itself is quite fast, and I don't need to perform anything else in the loop
other than adding those bonds.
I already have a list of tuples [(atom1, atom2), (atom3, atom4)] and all I
need to do is create a bond between each pair. The bottleneck is the bond
function, not the loop itself.

Also, I doubt simply the speed difference between C++ and Python could
explain such a drastic difference (minutes against fractions of a second).
There is clearly a difference in the way the `bond` command is implemented
and the way bonds are generated at startup.

What I think is needed, is either a way for pymol to perform those actions
in parallel (unlikely) or a way to get my hands on the way bonds are
generated at startup and use those functions or at least the same approach.

Thank you,
Lorenzo

Il giorno sab 25 mag 2019 alle ore 16:23 Mooers, Blaine H.M. (HSC) <
Bla...@ou...> ha scritto:

> Hi Lorenzo,
>
> You can import numpy  and replace your lists of coordinates with NumPy
> arrays.
> Operations with numpy arrays can be >100 times faster than with lists in
> for loops.
> See the last example the following blog post for inspiration:
>
>
> https://medium.freecodecamp.org/if-you-have-slow-loops-in-python-you-can-fix-it-until-you-cant-3a39e03b6f35
> .
>
> Please recall that PyMOL is collection of C and C++ programs wrapped by
> Python.
> The fast display of bonds inside the viewport is due to C or C++ programs.
>
> 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: Lorenzo Gaifas [br...@gm...]
> Sent: Saturday, May 25, 2019 5:48 AM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] Absymal performance when creating large
> numbers of bonds
>
> Dear pymol users,
>
> I'm working on a script, using the python API, that needs to add a very
> large number of bonds to the loaded structure.
>
> I thought simply using cmd.bond() in a for loop would do the trick, but
> -even though it works- it is extremely slow. I figured something was fishy,
> since pymol at startup is almost istantaneous and there, too, it has to
> compute, draw and even guess equally large numbers of bonds.
>
> I also tried to parallelise the command, but by now I *think* this can't
> be done due to the Global Intepreter Lock.
>
> I feel like there must be something I'm missing (maybe a way to prevent
> pymol from updating the rendering between each cmd.bond call?) or at least
> an API function that better exposes the bond generation procedure. Does
> someone have suggestions on how to solve this problem?
>
> Cheers,
> Lorenzo
>

Re: [PyMOL] [EXTERNAL] Absymal performance when creating large numbers of bonds

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

Hi Lorenzo,

You can import numpy  and replace your lists of coordinates with NumPy arrays. 
Operations with numpy arrays can be >100 times faster than with lists in for loops. 
See the last example the following blog post for inspiration: 

https://medium.freecodecamp.org/if-you-have-slow-loops-in-python-you-can-fix-it-until-you-cant-3a39e03b6f35.

Please recall that PyMOL is collection of C and C++ programs wrapped by Python. 
The fast display of bonds inside the viewport is due to C or C++ programs. 

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: Lorenzo Gaifas [br...@gm...]
Sent: Saturday, May 25, 2019 5:48 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Absymal performance when creating large numbers of bonds

Dear pymol users,

I'm working on a script, using the python API, that needs to add a very large number of bonds to the loaded structure.

I thought simply using cmd.bond() in a for loop would do the trick, but -even though it works- it is extremely slow. I figured something was fishy, since pymol at startup is almost istantaneous and there, too, it has to compute, draw and even guess equally large numbers of bonds.

I also tried to parallelise the command, but by now I *think* this can't be done due to the Global Intepreter Lock.

I feel like there must be something I'm missing (maybe a way to prevent pymol from updating the rendering between each cmd.bond call?) or at least an API function that better exposes the bond generation procedure. Does someone have suggestions on how to solve this problem?

Cheers,
Lorenzo

[PyMOL] Absymal performance when creating large numbers of bonds

[Lorenzo G. <br...@gm...>]

Dear pymol users,

I'm working on a script, using the python API, that needs to add a very
large number of bonds to the loaded structure.

I thought simply using cmd.bond() in a for loop would do the trick, but
-even though it works- it is extremely slow. I figured something was fishy,
since pymol at startup is almost istantaneous and there, too, it has to
compute, draw and even guess equally large numbers of bonds.

I also tried to parallelise the command, but by now I *think* this can't be
done due to the Global Intepreter Lock.

I feel like there must be something I'm missing (maybe a way to prevent
pymol from updating the rendering between each cmd.bond call?) or at least
an API function that better exposes the bond generation procedure. Does
someone have suggestions on how to solve this problem?

Cheers,
Lorenzo

[PyMOL] cannot write text commands after pymol-open-source installation

[Thomas E. <te...@gm...>]

I am encountering a strange problem. After building the latest
pymol-open-source from github on Ubuntu 19.04 and Python 3.7.3 I am not
able to write text commands. It seems that PyMOL does not receive input
from the keyboard because neither the arrow buttons ->, <- work for moving
to the next and previous molecules in a multi-mol file. Does anyone
encounter a similar problem? Any idea how to fix this?

Thanks in advance.
Thomas

-- 

======================================================================

Dr. Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
  &
CEITEC - Central European Institute of Technology
<https://www.ceitec.eu/>, Brno,
Czech Republic

email: te...@gm..., Twitter: tevangelidis
<https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis
<https://www.linkedin.com/in/thomas-evangelidis-495b45125/>

website: https://sites.google.com/site/thomasevangelidishomepage/

[PyMOL] autodock python plugin bug

[Robi G. <ro...@ma...>]

<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>Hi:</div>

<div>&nbsp;</div>

<div>I can not get the autodock.py plugin for pymol to load.&nbsp; When I do :</div>

<div>&nbsp;</div>

<div>
<p>import&nbsp;pmg_tk.startup.autodock_plugin</p>

<p>&nbsp;</p>

<p>I get:&nbsp;&nbsp;</p>

<p>&nbsp;</p>

<p>ModuleNotFoundError:&nbsp;No&nbsp;module&nbsp;named&nbsp;&#39;pmg_tk.startup.autodock_plugin&#39;</p>

<p>invalid&nbsp;syntax&nbsp;(autodock.py,&nbsp;line&nbsp;75)<br/>
Unable&nbsp;to&nbsp;initialize&nbsp;plugin&nbsp;&#39;autodock&#39;&nbsp;(pmg_tk.startup.autodock).</p>

<p>&nbsp;</p>

<p>on pymol startup I get the same error</p>

<p>&nbsp;</p>

<p>invalid&nbsp;syntax&nbsp;(autodock.py,&nbsp;line&nbsp;75)<br/>
Unable&nbsp;to&nbsp;initialize&nbsp;plugin&nbsp;&#39;autodock&#39;&nbsp;(pmg_tk.startup.autodock)</p>

<p>I have seen this bug mentioned on other forums, but no solution seems to have been found.</p>

<p>&nbsp;</p>

<p>thank you, Amy</p>

<p>&nbsp;</p>

<p>&nbsp;</p>

<p>&nbsp;</p>

<p>&nbsp;</p>

<p>&nbsp;</p>

<p>&nbsp;</p>
</div></div></body></html>

Re: [PyMOL] STL export in PyMol

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

Hi Jan,

With Incentive PyMOL, just type on the command line:

PyMOL> save file.stl

We haven't released STL export with Open-Source PyMOL yet (I should update the release notes to make that clear).

Other geometry formats that PyMOL can export are COLLADA (.dae) and VRML (.wrl).

Cheers,
  Thomas


> On May 22, 2019, at 4:03 PM, Jan Gebauer <jan...@un...> wrote:
> 
> Dear all,
> 
> I found this in the 2.1 release note:
> 
> Release Date: March 13, 2018
> 
> Features
> 
> 	 .stl export (requires pycollada)
> However, I cannot find any hint how to use ist...
> 
> Thanks for any hints.
> 
> Best,
> 
> Jan
> 
> -- 
> Dr. Jan Gebauer
> AG Prof. Baumann
> Institut für Biochemie / Uni-Köln
> Zülpicher Str. 47 / 50674 Köln
> Fon: +49 (221) 470 3212	
> Fax: +49 (221) 470 5066
> 
> 
> http://px.uni-koeln.de/

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] STL export in PyMol

[Jan G. <jan...@un...>]

Dear all,

I found this in the 2.1 release note:

Release Date: March 13, 2018


    Features

  *
    ***.stl*export (requirespycollada
    <https://pypi.python.org/pypi/pycollada/>)

However, I cannot find any hint how to use ist...

Thanks for any hints.

Best,

Jan

-- 
Dr. Jan Gebauer
AG Prof. Baumann
Institut für Biochemie / Uni-Köln
Zülpicher Str. 47 / 50674 Köln
Fon: +49 (221) 470 3212	
Fax: +49 (221) 470 5066

http://px.uni-koeln.de/

Re: [PyMOL] Molecular surface area

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

Hi Andreas,

dot_solvent=0 is solvent excluded surface, also known as molecular surface or Connolly surface. PyMOL approximates it numerically by sampling points on the surface

See: https://pymolwiki.org/index.php/Get_Area#Settings

Cheers,
  Thomas

> On May 19, 2019, at 10:08 PM, Andreas Tosstorff <and...@cu...> wrote:
> 
> Hi all,
> 
> I am looking for the method by which the get_area command calculates the molecular surface area when dot_solvent=0.
> It is described for SASA in the mailing list but I could not find it for the default method.
> Thanks a lot for your help!
> Andreas
> 
> _______________________________________________
> 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] 3D viewing issue

[Jim R E. <ear...@uw...>]

I had an old PC that a person was using pyMol and displaying 3D.  I needed to replace the hard drive and now I can't seem to get pyMol to display 3D.

I have the following hardware (That of course used to work just fine)

APG6000 Active Glasses & IR Emitter System
NuVision 60GX-T50 60GX-G5  (IR emitter)
Quadro 3700 graphics card.
DepthQ WXGA projector

This was running XP.

So I installed XP, latest Nvidia drivers and the latest 32bit version of pyMol.  The refresh rate on the projector is 120Hz the IR emitter is hooked up to the little DIN connector on the video board.  I set Stereo Enable to on.

When I start pyMol in Quad Buffered 3D, it says "Yep, I see your card 3D is OK" and when I choose to display in Quad Buffered Stereo it looks to the naked eye that there are the two images.  I have checked the IR is emitting (via phone camera) and have tried multiple glasses to rule out dead battery in them.

I imagine that I'm missing some silly setting or something.  (I have also tried this with Windows 10 and the latest version of pyMol with same results). I know this is an old setup, but it was working just fine before the rebuild.  I have no idea what I must be missing.  Any suggestions are welcome.  Thanks.


Jim Earnshaw
Senior Computer Specialist
Department of Chemistry
University of Washington
206-616-4967

Re: [PyMOL] [EXTERNAL] Question about polymer selection criteria

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

Hi Ryan and Blaine,

In addition to the classification by residue identifiers, PyMOL looks for nucleic acid backbone atoms by name.

See:
https://github.com/schrodinger/pymol-open-source/blob/master/layer3/Selector.cpp#L1393
----------------------
        } else if (found_o3star && found_c3star && found_c4star && found_c5star
               && found_o5star && (found_o3_bond || found_p_bond)) {
          mask = cAtomFlag_polymer | cAtomFlag_nucleic;
----------------------

Hope that helps.

Cheers,
  Thomas


> On May 18, 2019, at 12:26 AM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:
> 
> Hi Ryan,
> 
> I think that the manual page for polymer will answer your question clearly
> 
> https://pymol.org/dokuwiki/doku.php?id=selection:polymer
> 
> 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: Kung, Ryan [rya...@ul...]
> Sent: Friday, May 17, 2019 4:46 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] Question about polymer selection criteria
> 
> Hello,
> 
> I have a question about how the pymol polymer.nucleic selection defines what is nucleic? Is there a list of atom names that are required? Does it have to actually be part of a polymer for the selection process to identify it? If someone can help me understand this, that would be great.
> 
> Thank you,
> Ryan Kung
> 
> _______________________________________________
> 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] Molecular surface area

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

Hi all,

I am looking for the method by which the get_area command calculates the molecular surface area when dot_solvent=0.
It is described for SASA in the mailing list but I could not find it for the default method.
Thanks a lot for your help!
Andreas

Re: [PyMOL] [EXTERNAL] Question about polymer selection criteria

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

Hi Ryan,

I think that the manual page for polymer will answer your question clearly

https://pymol.org/dokuwiki/doku.php?id=selection:polymer

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: Kung, Ryan [rya...@ul...]
Sent: Friday, May 17, 2019 4:46 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Question about polymer selection criteria

Hello,

I have a question about how the pymol polymer.nucleic selection defines what is nucleic? Is there a list of atom names that are required? Does it have to actually be part of a polymer for the selection process to identify it? If someone can help me understand this, that would be great.

Thank you,
Ryan Kung

[PyMOL] Question about polymer selection criteria

[Kung, R. <rya...@ul...>]

Hello,

I have a question about how the pymol polymer.nucleic selection defines
what is nucleic? Is there a list of atom names that are required? Does it
have to actually be part of a polymer for the selection process to identify
it? If someone can help me understand this, that would be great.

Thank you,
Ryan Kung

[PyMOL] How to show the boundary of each selected residues in surface presentation with pymol

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

Dear everyone,

It there a way to  show the boundary of each selected residues in surface presentation with pymol? 

Best regards

Arthur

Re: [PyMOL] How to make protein blur but keep ligand clear?

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

Hi Arthur,

The origin of rotation will become the focal point. So all you have to do is:

PyMOL> origin resn DUD

The blur will look better if you increase the sample size, e.g. samples=20.

Cheers,
  Thomas


> On May 15, 2019, at 9:50 AM, sunyeping via PyMOL-users <pym...@li...> wrote:
> 
> Dear all,
> 
> I have a protein-ligand complex and I wish to make the protein looks blur but keep the ligand clear and sharp with pymol. I find a "focalblur" script (https://pymolwiki.org/index.php/FocalBlur) which seems to be able to do this. However I can get the fancy effect illustrated in the examples of the wiki for this script. With the follow command:
> 
> FocalBlur aperture=2,samples=10,ray=1,width=1000,height=1000
> 
> 
> I just make the ligand rather the the protein become blur (Please see the image at https://drive.google.com/open?id=1qzXDLzVyxI85sJ8H6Zhv8pd8Cq7rA18U, and the pse file used to make this image is availabe at https://drive.google.com/open?id=1Gjrl5ePifadWEK8-AZYVXY7yX07kOLF7).
> 
> Could anyone help with this？ What does the argument "aperture" do? How to control which part become blur?   Is there better way to make the ligand blur?
> 
> Thank you very much!
> 
> Arthur
> _______________________________________________
> 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] How to make protein blur but keep ligand clear?

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

Dear all,

I have a protein-ligand complex and I wish to make the protein looks blur but keep the ligand clear and sharp with pymol. I find a "focalblur" script (https://pymolwiki.org/index.php/FocalBlur) which seems to be able to do this. However I can get the fancy effect illustrated in the examples of the wiki for this script. With the follow command:

FocalBlur aperture=2,samples=10,ray=1,width=1000,height=1000


I just make the ligand rather the the protein become blur (Please see the image at https://drive.google.com/open?id=1qzXDLzVyxI85sJ8H6Zhv8pd8Cq7rA18U, and the pse file used to make this image is availabe at https://drive.google.com/open?id=1Gjrl5ePifadWEK8-AZYVXY7yX07kOLF7).

 Could anyone help with this？ What does the argument "aperture" do? How to control which part become blur?   Is there better way to make the ligand blur?

Thank you very much!

Arthur

Re: [PyMOL] stereo in pymol 2

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

Hi Gary,

Stereo has not been dropped, it should work with PyMOL 2.x on Windows and Linux. Does PyMOL report "quad-buffer stereo 3D detected and enabled" on startup? Does it work if you run "pymol -S" (or "pymolwin +2 -S") from a command prompt?

Cheers,
  Thomas

> On May 10, 2019, at 1:55 PM, Gary Hunter <gar...@um...> wrote:
> 
> try as I might I cannot get quad buffered stereo to work in pymol since version 2 was released. Tried up to 2.3.
> My emitter does not even switch on.
> pymol 1.8.6 is still good to go in stereo mode, so whats happened? Has stereo been dropped in version 2?
> 
> using nvideo control panel and real D emitter with nuvision glasses on windows 7 and a CRT display - Quadro card with DIN plug.
> 
> Also tried using nvidia 3D vision with a TFT stereo display (USB controlled emitter). Thats also good with 1.8.6 but not 2.2 or 2.3
> 
> Any ideas what to try? Or let me know its no longer a feature please.
> 
> 
> 
> -- 
> Prof. Gary J. Hunter
> 
> Laboratory of Biochemistry and Protein Science
> 
> Department of Physiology and Biochemistry
> 
> University of Malta
> 
> Msida MSD 2080 
> 
> Malta
> 
> phone: +356 2340 2917
> 
> mobile: +356 7931 9138
> 
> phone: +356 21316655 (departmental secretary)  
> 
> Fax: +356 21310577
> 
> http://www.um.edu.mt/ms/physbiochem
> 
> There may be confidential information within the contents of this email meant only for the person addressed. This email must not be forwarded to third parties without the express consent of the sender. If you believe you have received this email in error please inform the sender and remove it from your system. 
> 
> _______________________________________________
> 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] stereo in pymol 2

[Gary H. <gar...@um...>]

try as I might I cannot get quad buffered stereo to work in pymol since
version 2 was released. Tried up to 2.3.
My emitter does not even switch on.
pymol 1.8.6 is still good to go in stereo mode, so whats happened? Has
stereo been dropped in version 2?

using nvideo control panel and real D emitter with nuvision glasses on
windows 7 and a CRT display - Quadro card with DIN plug.

Also tried using nvidia 3D vision with a TFT stereo display (USB controlled
emitter). Thats also good with 1.8.6 but not 2.2 or 2.3

Any ideas what to try? Or let me know its no longer a feature please.



-- 

Prof. Gary J. Hunter

Laboratory of Biochemistry and Protein Science

Department of Physiology and Biochemistry

University of Malta

Msida MSD 2080

Malta

phone: +356 2340 2917

mobile: +356 7931 9138

phone: +356 21316655 (departmental secretary)

Fax: +356 21310577

http://www.um.edu.mt/ms/physbiochem

There may be confidential information within the contents of this email
meant only for the person addressed. This email must not be forwarded to
third parties without the express consent of the sender. If you believe you
have received this email in error please inform the sender and remove it
from your system.