pymol-users Mailing List for PyMOL Molecular Graphics System

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.

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
>

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

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

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 <," rel="nofollow">https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
  &
CEITEC - Central European Institute of Technology
<," rel="nofollow">https://www.ceitec.eu/>, Brno,
Czech Republic

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

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

<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>

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.

Dear all,

I found this in the 2.1 release note:

Release Date: March 13, 2018


    Features

  *
    ***.stl*export (requirespycollada
    <)" rel="nofollow">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/

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.

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

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.

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

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

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

Dear everyone,

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

Best regards

Arthur

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.

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

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.

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.

Hi Julian,

I think the problem is that you format the radius as an integer:

# wrong (%d)
cmd.alter("helix%d" % i, expression="vdw=%d" % vdw_a)
# correct (%f)
cmd.alter("helix%d" % i, expression="vdw=%f" % vdw_a)
# also correct:
cmd.alter("helix%d" % i, "vdw=vdw_a", space={'vdw_a': vdw_a})

Hope that helps.

You didn't break any support-requesting rules, your problem was well described, just a bit tricky to understand. The only thing you should add next time is PyMOL version and operating system (wasn't relevant for this problem, but you never know).

Cheers,
  Thomas

On Tue, May 7, 2019 at 3:40 PM Julian Krumm <s2j...@un...> wrote:
> 
> Dear Pymol-Team,
> 
> very new in this forum i come along with a specific problem.
> I wrote a little pymol-script:
> 
> 
> load /work/jkrumm/edgelook/0.00M/cter/40-helix-edge/helix-40.pqr
> 
> hide lines
> show cartoon
> 
> radius = 2.7
> vdw_a = 2.7
> 
> for i in range(401,413,1):\
> print(i)\
> vdw_a = vdw_a + 2.7\
> print(vdw_a)\
> cmd.create("helix%d" % i, "/helix-40///PRT`%d/PRT" % i)\
> cmd.alter("helix%d" % i, expression="vdw=%d" % vdw_a)
> rebuild
> 
> disable all
> 
> 
> for i in range(401,413,1):\
> cmd.set(name="sphere_transparency", value=0.0, selection="helix%d" % i)\
> cmd.show(representation="sphere", selection="helix%d" % i)\
> cmd.enable(name="helix%d" % i)
> 
> enable helix-40
> 
> set_view (\
>     0.246392056,   -0.601405144,    0.760001123,\
>    -0.951444209,   -0.299392790,    0.071540825,\
>     0.184513614,   -0.740724683,   -0.645971537,\
>     0.000000000,    0.000000000, -270.700958252,\
>     0.528925896,    8.660091400,   -2.648437977,\
>   100.995597839,  440.406250000,  -20.000000000 )
> 
> bg_color white
> set reflect, 0
> png ./test.png, width=2400, height=1200, dpi=300, ray=0
> 
> 
> It is reading the PRT-entrys out of the input file to new objects and then
> adjusts the proper radius.
> The radius of the protein spheres is incremented by 2.7 Å. Moreover the
> sphere center is shifted away from the C-terminus towards the N-terminus
> by a distance equal to its radius (not done by pymol).
> This should lead to the situation, that the surfaces of all
> protein-spheres cut succinctly in one point at the C-Terminus, which they
> do not.
> It comes to slightly deviations when the spheres are getting visualized.
> 
> I already checked the sphere-centers. They are placed right. Also the
> radii are set right. After i showed this to my advisor he is the same
> opinion that the problem has to be pymol-based. I can't explain and i hope
> You are able to help me with this problem.
> 
> Attached to this mail You will find the pymol-session and the input PQR.
> 
> Sincerely,
> JuK
> 
> 
> P.S. If i broke any rule of support-requesting or if any information is
> missing please let me know._______________________________________________
> 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.

Dear Pymol-Team,

very new in this forum i come along with a specific problem.
I wrote a little pymol-script:


load /work/jkrumm/edgelook/0.00M/cter/40-helix-edge/helix-40.pqr

hide lines
show cartoon

radius = 2.7
vdw_a = 2.7

for i in range(401,413,1):\
 print(i)\
 vdw_a = vdw_a + 2.7\
 print(vdw_a)\
 cmd.create("helix%d" % i, "/helix-40///PRT`%d/PRT" % i)\
 cmd.alter("helix%d" % i, expression="vdw=%d" % vdw_a)
rebuild

disable all


for i in range(401,413,1):\
 cmd.set(name="sphere_transparency", value=0.0, selection="helix%d" % i)\
 cmd.show(representation="sphere", selection="helix%d" % i)\
 cmd.enable(name="helix%d" % i)

enable helix-40

set_view (\
     0.246392056,   -0.601405144,    0.760001123,\
    -0.951444209,   -0.299392790,    0.071540825,\
     0.184513614,   -0.740724683,   -0.645971537,\
     0.000000000,    0.000000000, -270.700958252,\
     0.528925896,    8.660091400,   -2.648437977,\
   100.995597839,  440.406250000,  -20.000000000 )

bg_color white
set reflect, 0
png ./test.png, width=2400, height=1200, dpi=300, ray=0


It is reading the PRT-entrys out of the input file to new objects and then
adjusts the proper radius.
The radius of the protein spheres is incremented by 2.7 Å. Moreover the
sphere center is shifted away from the C-terminus towards the N-terminus
by a distance equal to its radius (not done by pymol).
This should lead to the situation, that the surfaces of all
protein-spheres cut succinctly in one point at the C-Terminus, which they
do not.
It comes to slightly deviations when the spheres are getting visualized.

I already checked the sphere-centers. They are placed right. Also the
radii are set right. After i showed this to my advisor he is the same
opinion that the problem has to be pymol-based. I can't explain and i hope
You are able to help me with this problem.

Attached to this mail You will find the pymol-session and the input PQR.

Sincerely,
JuK


P.S. If i broke any rule of support-requesting or if any information is
missing please let me know.

Hi Vatsal,

The "min_mesh_spacing" setting only affects the "mesh" representation of molecules (molecular surface). To increase the mesh density of an isomesh, you need to upsample the map with the "map_double" command.

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

Hope that helps.

Cheers,
  Thomas

> On Apr 26, 2019, at 12:42 AM, Vatsal Purohit <vat...@gm...> wrote:
> 
> Hello,
> 
> I've been trying to use the minimum mesh spacing feature on pymol to make my meshes more defined and it doesn't seem to do anything. 
> 
> I use .map.ccp4 files that I generated on ccp4 using .mtz files I generated on phenix. Any suggestions on what I might be doing wrong and what I could do to fix this would be really appreciated!
> 
> Regards,
> Vatsal 
> 
> -- 
> Vatsal Purohit
> 
> PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University
> PULSe-Biophysics and Structural Biology training group
> vp...@pu... | 346-719-9409
> 
> _______________________________________________
> 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.

Hi Vatsal,

This is how you show positive and negative contour:

fetch 1ubq, diffmap, type=fofc, async=0
isomesh diffmesh, diffmap, 3.0
color green, diffmesh
set mesh_negative_color, red
set mesh_negative_visible

Example copied from:
https://pymolwiki.org/index.php/mesh_negative_visible

Cheers,
  Thomas


> On Apr 26, 2019, at 12:37 AM, Vatsal Purohit <vat...@gm...> wrote:
> 
> Hello,
> 
> I've been trying to color my Fo-Fc electron density maps in pymol with the positive Fo-Fc maps showing as green and negative Fo-Fc maps showing as red and having no luck with it. They either show up as red or green.
> 
> I generate my maps by converting .mtz from phenix to .ccp4 files on ccp4. Any suggestions about how I can try to color them individually this would be greatly appreciated!
> 
> Regards,
> Vatsal
> 
> -- 
> Vatsal Purohit
> 
> PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University
> PULSe-Biophysics and Structural Biology training group
> vp...@pu... | 346-719-9409
> 
> _______________________________________________
> 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.

Hi Yu and David,

I like to throw in one of the many ways to do this inside PyMOL :-)

from pymol import cmd
# load 3000 files into the "multi" object
for i in range(3000): cmd.load('file_{}.pdb'.format(i + 1), 'multi')
# if you want, fit to the first state
cmd.intra_fit('multi')

Morphing between each state is possible, but will take some time, and with the defaults you'll end up with 90000 states, which might be more than PyMOL can handle (also you'll have a 50 minute movie).

As a proof of concept, here is how you make a linear (faster than rigimol) morph with 3 interpolated states between each consecutive input state, for the first 100 of your files (yields 495 states):

from pymol import cmd
for i in range(100): cmd.load('file_{}.pdb'.format(i + 1), 'multi')
cmd.intra_fit('multi')
cmd.morph('morph', 'multi', state1=0, state2=0, refinement=0, steps=5, method='linear')

Hope that helps.

Cheers,
  Thomas


> On May 1, 2019, at 3:36 PM, David Gae <dd...@uc...> wrote:
> 
> Dear  Yu,
> 
> Try this  bash script and then run "pymol all.pdb” in your PDB directory. this might help you view your files as a trajectory. 
> 
> --------------------
> for i in {1..3000}
> do
> # change frame_$i.pdb to your file name. for example mine is frame_1.pdb
> [ -f "frame_$i.pdb" ] 
> z=frame_$i.pdb	
> sed  's/END/ENDMDL/g' $z > $z.r 
> { echo 'MODEL'; cat $z.r; } >$z.new
> 
> rm $z.r 
> done
> 
> cat *.new > all.pdb
> rm *.new
> ---------------------
> 
> I am sure there are many ways to do this inside pymol as well. you might want to look up https://pymolwiki.org/index.php/Main_Page
> 
> hope this helps,
> David
> 
>> On Apr 30, 2019, at 5:57 PM, Yu Qi <Yu...@du...> wrote:
>> 
>> Some background: I'm an undergraduate student and am doing research with my professor about modeling protein conformational changes. I am new to this field and and am actively learning how to use command lines, python and other relative tools. I have simulated how the protein will walk with CAMPARI and have gotten back 3000 trajectory (pdb) files, my question is: how do I use PyMOL to make a movie by using those trajectory files? Basically, I want to know how to visualize how the protein moved from the first pdb file to the second, then to the third, etc.
>> 
>> I tried morphing two pdb files with one step from file_1.pdb to file_2.pdb, I aligned them first, then morphed them. I'm not sure how to go from there because I had a result file with 2 states and 2 frames, then when I tried to morph the result file with file_3.pdb, it did not work as I expected.
>> 
>> please let me know if you have questions, and I really appreciate the help.
>> 
>> Thank you for the help,
>> Yu
>> 
>> _______________________________________________
>> 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.

Hi Ali,

I would typically use a temporary object for that, which is loaded into the work space but never rendered:

def intra_rms_tempobj(filename):
    from pymol import cmd
    tmpname = cmd.get_unused_name('_tmpobj')
    cmd.load(filename, tmpname, zoom=0)
    try:
        return cmd.intra_rms(tmpname)
    finally:
        cmd.delete(tmpname)

It's also possible to create a new instance of the PyMOL backend, this is probably closer to what you were looking for:

def intra_rms_tempinstance(filename):
    import pymol2
    with pymol2.PyMOL() as p:
        p.cmd.load(filename)
        return p.cmd.intra_rms('*')

See also:
https://pymolwiki.org/index.php/Launching_From_a_Script#Independent_PyMOL_Instances_.28Context_Manager.29

Cheers,
  Thomas


> On May 3, 2019, at 2:24 AM, Ali Kusay <aku...@un...> wrote:
> 
> I have noticed that PyMOL can be used to perform fast calculations by using it in command line or through something like Jupyter notebook since it doesn’t have to worry about the graphical geometries. I am curious if this can be performed within the PyMOL program itself. For example, loading the python interpreter in PyMOL and using it load a multistate object and calculate RMSD through intra_fit without actually loading the object in the work space. I would appreciate your help, this would be immensely time saving for larger proteins while providing the convince of not having to leave the program.
>  
> Kin regards,
>  
> Ali Kusay
> PhD student 
> _______________________________________________
> 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.