pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Crystal Operations from PyMOL

[Sumit K. <sum...@gm...>]

Hi all,

I have never used PyMOL before. I am trying to learn some few crystal
visualization softwares like VESTA, Avogardo. I need to perform some few
crystal operations such as translation and reflection. VESTA is good but I
wanted to know if there is any techniques on PyMOL for this operations?

Best,
Sumit Khadka

Re: [PyMOL] Calculate the angle between two domains

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

Hi Yikan -

Check out: https://pymolwiki.org/index.php/Angle_between_domains

Hope that helps.

Cheers,
Jared

On November 27, 2019 at 4:02:34 AM, Zhang Yikan via PyMOL-users (pym...@li...) wrote:

Hi all,
I am a beginner of the PyMol script. I have 200 pdbs(names, C_1, C_2, …..C_200), and all of them contain 2 domains(resi 1-80, or resi 92-160). I want to calculate the rotation angle between the two domains. I do this calculation with the orientation.py in batch mode.  Do someone know how to do that? Thank you!


Best,
Yikan
Ph. D
TsingHua University
School of life Sciences
Beijing, China
tel:010-62773783
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Re: [PyMOL] ModuleNotFoundError: No module named 'pymol._cmd'

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

Hi Markus,

You mention two directories, maybe you're running PyMOL from the wrong one?

/home/mheller/pymol-2.4/lib/python/pymol
/usr/local/Pymol-2.4/lib/python/Pymol


Cheers,
  Thomas


> On Nov 28, 2019, at 1:00 AM, Markus Heller <mh...@ad...> wrote:
> 
> Hi,
> 
> This is just an attempt to see if my issue has popped up before.
> 
> I have compiled open source Pymol 2.4, which I used for a few months now.  Today, the following error prevents launching Pymol:
> 
> <code>
> $ pymol
> Traceback (most recent call last):
>  File "/home/mheller/pymol-2.4/lib/python/pymol/__init__.py", line 64, in <module>
>    import pymol
>  File "/home/mheller/pymol-2.4/lib/python/pymol/__init__.py", line 564, in <module>
>    import pymol._cmd
> ModuleNotFoundError: No module named 'pymol._cmd'
> </code>
> 
> `/usr/local/Pymol-2.4/lib/python/Pymol` contains `cmd.py` and `_cmd.cpython-36m-x86_64-linux-gnu.so`
> 
> I'm baffled as to why Pymol fails to open, as I'm not aware of any changes made to my python setup or related.
> 
> I'd be very grateful for a slight nudge in the right direction ...
> 
> Thanks
> Markus
> 
> 
> 
> _______________________________________________
> 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] Autosave

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

It looks like strftime('%s') is not valid on Windows (it works fine for me on Linux and macOS). Here is an equivalent alternative that works on all platforms:

    filename = '~/pymol-auto-save-{}.pse'.format(int(time.time()))
    filename = os.path.expanduser(filename)

Binding a key is also easy. Here is an example which binds saving and rendering to the F1 key:

python
@cmd.set_key('F1')
def autosave_and_render():
    filename = os.path.expanduser('~/pymol-auto-save.pse')
    cmd.set('pse_binary_dump')
    cmd.save(filename, quiet=0)
    cmd.ray()
python end


Hope that helps.

Cheers,
  Thomas


> On Nov 22, 2019, at 11:48 PM, Junsu Park aka. Jason Mosier <par...@gm...> wrote:
> 
> Hello, I'm fairly new to pymol and python in general, but I honestly don't have to self control to save by myself very well and so I was trying to use the proof of concept code for autosaving. However, it was written for a way old version of pymol and so I was wondering if I could get some help with fixing this code up? If that would be too difficult, is there a way that I could bind a key to saving AND then rendering? Or even just clicking on the render button causes it to save before ray tracing? I keep rendering on a weak computer thinking it can handle it and then it crashes and I lose all my progress.
> 
> Link to code: https://pastebin.com/EJJQWc00  
> Link to output:  https://pastebin.com/TNSuA0fH
> 
> Thanks,
> -Jason
> _______________________________________________
> 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] Problem loading Amber trajectory

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

Hi Martin,

Would it be possible to share those files with me?

Thanks,
  Thomas

> On Nov 28, 2019, at 6:00 PM, Rosellen, Martin <mar...@uc...> wrote:
> 
> Dear all,
> 
> I have issues loading Amber trajectories. First, I load the the topology
> like this:
> 
> load WT.prmtop, WT, 1, top
> 
> output:
> 
>   ObjectMolecule: Attempting to read Amber7 topology file.
>   TOPStrToCoordSet: Warning: can't currently image a truncated octahedron...
> 
> 
> load_traj WT.trj, WT
> 
> output:
> 
> ObjMolLoadTRJFile-Error: Failed to read expected coordinate value.
>    This traj. does not match the loaded parameter/topology file.
>    Likely cause: either the atom count or the periodic box settings
>    are inconsistent between the two files.
> 
> 
> My guess is that pymol somehow changes the atom count because it cannot
> image the truncated box which causes the error with the trajectory.
> 
> I was thinking about putting the trajectory in a PDB but that would be a
> file of <20GB in the end.
> 
> Any comment, positive or negative, would be very much appreciated.
> 
> cheers
> 
> Martin
> 
> 
> _______________________________________________
> 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] ModuleNotFoundError: No module named 'pymol._cmd'

[Markus H. <mh...@ad...>]

I settled for a fresh start, i.e. recompiling PyMol.  This solved the issue.

> -----Original Message-----
> From: Markus Heller <mh...@ad...>
> Sent: Wednesday, November 27, 2019 4:01 PM
> To: pym...@li...
> Subject: [PyMOL] ModuleNotFoundError: No module named 'pymol._cmd'
> 
> Hi,
> 
> This is just an attempt to see if my issue has popped up before.
> 
> I have compiled open source Pymol 2.4, which I used for a few months now.
> Today, the following error prevents launching Pymol:
> 
> <code>
> $ pymol
> Traceback (most recent call last):
>   File "/home/mheller/pymol-2.4/lib/python/pymol/__init__.py", line 64, in
> <module>
>     import pymol
>   File "/home/mheller/pymol-2.4/lib/python/pymol/__init__.py", line 564, in
> <module>
>     import pymol._cmd
> ModuleNotFoundError: No module named 'pymol._cmd'
> </code>
> 
> `/usr/local/Pymol-2.4/lib/python/Pymol` contains `cmd.py` and `_cmd.cpython-
> 36m-x86_64-linux-gnu.so`
> 
> I'm baffled as to why Pymol fails to open, as I'm not aware of any changes made
> to my python setup or related.
> 
> I'd be very grateful for a slight nudge in the right direction ...
> 
> Thanks
> Markus
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-
> users/unsubscribe

[PyMOL] Problem loading Amber trajectory

[Rosellen, M. <mar...@uc...>]

Dear all,

I have issues loading Amber trajectories. First, I load the the topology
like this:

load WT.prmtop, WT, 1, top

output:

   ObjectMolecule: Attempting to read Amber7 topology file.
   TOPStrToCoordSet: Warning: can't currently image a truncated octahedron...


load_traj WT.trj, WT

output:

ObjMolLoadTRJFile-Error: Failed to read expected coordinate value.
    This traj. does not match the loaded parameter/topology file.
    Likely cause: either the atom count or the periodic box settings
    are inconsistent between the two files.


My guess is that pymol somehow changes the atom count because it cannot
image the truncated box which causes the error with the trajectory.

I was thinking about putting the trajectory in a PDB but that would be a
file of <20GB in the end.

Any comment, positive or negative, would be very much appreciated.

cheers

Martin

[PyMOL] ModuleNotFoundError: No module named 'pymol._cmd'

[Markus H. <mh...@ad...>]

Hi,

This is just an attempt to see if my issue has popped up before.

I have compiled open source Pymol 2.4, which I used for a few months now.  Today, the following error prevents launching Pymol:

<code>
$ pymol
Traceback (most recent call last):
  File "/home/mheller/pymol-2.4/lib/python/pymol/__init__.py", line 64, in <module>
    import pymol
  File "/home/mheller/pymol-2.4/lib/python/pymol/__init__.py", line 564, in <module>
    import pymol._cmd
ModuleNotFoundError: No module named 'pymol._cmd'
</code>

`/usr/local/Pymol-2.4/lib/python/Pymol` contains `cmd.py` and `_cmd.cpython-36m-x86_64-linux-gnu.so`

I'm baffled as to why Pymol fails to open, as I'm not aware of any changes made to my python setup or related.

I'd be very grateful for a slight nudge in the right direction ...

Thanks
Markus

[PyMOL] Calculate the angle between two domains

[Zhang Y. <yik...@ic...>]

Hi all,
I am a beginner of the PyMol script. I have 200 pdbs(names, C_1, C_2, …..C_200), and all of them contain 2 domains(resi 1-80, or resi 92-160). I want to calculate the rotation angle between the two domains. I do this calculation with the orientation.py in batch mode.  Do someone know how to do that? Thank you!


Best,
Yikan
Ph. D 
TsingHua University
School of life Sciences 
Beijing, China
tel:010-62773783

Re: [PyMOL] Autosave

[Pedro L. <psl...@gm...>]

I would rather create a QTimer to autosave and autorender. It would report
correct CPU usage.

After then you may of course create a plugin:
https://pymolwiki.org/index.php/Plugins_Tutorial.

Em sex, 22 de nov de 2019 22:41, Pedro Lacerda <psl...@gm...>
escreveu:

> Only now I see your code. I'm not very versed with PyMOL code but maybe
> you want to wait for the pymol lock. Grep for the lock and wait for it. Can
> you imagine the last auto rendering be a wrong image after a long and hard
> session.
>
> Em sex, 22 de nov de 2019 22:36, Pedro Lacerda <psl...@gm...>
> escreveu:
>
>> Hi Jason,
>>
>> You can save with Ctrl-S, as you might know. Auto rendering would be
>> complicated because there is a lot of options. For instance, you may have
>> to choose low DPI for quick inspection or high for final rendering.
>>
>> Best regards,
>> Pedro Lacerda
>>
>> Em sex, 22 de nov de 2019 19:49, Junsu Park aka. Jason Mosier <
>> par...@gm...> escreveu:
>>
>>> Hello, I'm fairly new to pymol and python in general, but I honestly
>>> don't have to self control to save by myself very well and so I was trying
>>> to use the proof of concept code for autosaving. However, it was written
>>> for a way old version of pymol and so I was wondering if I could get some
>>> help with fixing this code up? If that would be too difficult, is there a
>>> way that I could bind a key to saving AND then rendering? Or even just
>>> clicking on the render button causes it to save before ray tracing? I keep
>>> rendering on a weak computer thinking it can handle it and then it crashes
>>> and I lose all my progress.
>>>
>>> Link to code: https://pastebin.com/EJJQWc00
>>> <https://gnldr.online/tracker/click?redirect=https%3A%2F%2Fpastebin.com%2FEJJQWc00&dID=1574462896168&linkName=https://pastebin.com/EJJQWc00>
>>>
>>> Link to output:  https://pastebin.com/TNSuA0fH
>>> <https://gnldr.online/tracker/click?redirect=https%3A%2F%2Fpastebin.com%2FTNSuA0fH&dID=1574462896168&linkName=https://pastebin.com/TNSuA0fH>
>>>
>>> Thanks,
>>> -Jason
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>

Re: [PyMOL] Autosave

[Pedro L. <psl...@gm...>]

Only now I see your code. I'm not very versed with PyMOL code but maybe you
want to wait for the pymol lock. Grep for the lock and wait for it. Can you
imagine the last auto rendering be a wrong image after a long and hard
session.

Em sex, 22 de nov de 2019 22:36, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi Jason,
>
> You can save with Ctrl-S, as you might know. Auto rendering would be
> complicated because there is a lot of options. For instance, you may have
> to choose low DPI for quick inspection or high for final rendering.
>
> Best regards,
> Pedro Lacerda
>
> Em sex, 22 de nov de 2019 19:49, Junsu Park aka. Jason Mosier <
> par...@gm...> escreveu:
>
>> Hello, I'm fairly new to pymol and python in general, but I honestly
>> don't have to self control to save by myself very well and so I was trying
>> to use the proof of concept code for autosaving. However, it was written
>> for a way old version of pymol and so I was wondering if I could get some
>> help with fixing this code up? If that would be too difficult, is there a
>> way that I could bind a key to saving AND then rendering? Or even just
>> clicking on the render button causes it to save before ray tracing? I keep
>> rendering on a weak computer thinking it can handle it and then it crashes
>> and I lose all my progress.
>>
>> Link to code: https://pastebin.com/EJJQWc00
>> <https://gnldr.online/tracker/click?redirect=https%3A%2F%2Fpastebin.com%2FEJJQWc00&dID=1574462896168&linkName=https://pastebin.com/EJJQWc00>
>>
>> Link to output:  https://pastebin.com/TNSuA0fH
>> <https://gnldr.online/tracker/click?redirect=https%3A%2F%2Fpastebin.com%2FTNSuA0fH&dID=1574462896168&linkName=https://pastebin.com/TNSuA0fH>
>>
>> Thanks,
>> -Jason
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Autosave

[Pedro L. <psl...@gm...>]

Hi Jason,

You can save with Ctrl-S, as you might know. Auto rendering would be
complicated because there is a lot of options. For instance, you may have
to choose low DPI for quick inspection or high for final rendering.

Best regards,
Pedro Lacerda

Em sex, 22 de nov de 2019 19:49, Junsu Park aka. Jason Mosier <
par...@gm...> escreveu:

> Hello, I'm fairly new to pymol and python in general, but I honestly don't
> have to self control to save by myself very well and so I was trying to use
> the proof of concept code for autosaving. However, it was written for a way
> old version of pymol and so I was wondering if I could get some help with
> fixing this code up? If that would be too difficult, is there a way that I
> could bind a key to saving AND then rendering? Or even just clicking on the
> render button causes it to save before ray tracing? I keep rendering on a
> weak computer thinking it can handle it and then it crashes and I lose all
> my progress.
>
> Link to code: https://pastebin.com/EJJQWc00
> <https://gnldr.online/tracker/click?redirect=https%3A%2F%2Fpastebin.com%2FEJJQWc00&dID=1574462896168&linkName=https://pastebin.com/EJJQWc00>
>
> Link to output:  https://pastebin.com/TNSuA0fH
> <https://gnldr.online/tracker/click?redirect=https%3A%2F%2Fpastebin.com%2FTNSuA0fH&dID=1574462896168&linkName=https://pastebin.com/TNSuA0fH>
>
> Thanks,
> -Jason
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Autosave

[Junsu P. a. J. M. <par...@gm...>]

Hello, I'm fairly new to pymol and python in general, but I honestly don't
have to self control to save by myself very well and so I was trying to use
the proof of concept code for autosaving. However, it was written for a way
old version of pymol and so I was wondering if I could get some help with
fixing this code up? If that would be too difficult, is there a way that I
could bind a key to saving AND then rendering? Or even just clicking on the
render button causes it to save before ray tracing? I keep rendering on a
weak computer thinking it can handle it and then it crashes and I lose all
my progress.

Link to code: https://pastebin.com/EJJQWc00
<https://gnldr.online/tracker/click?redirect=https%3A%2F%2Fpastebin.com%2FEJJQWc00&dID=1574462896168&linkName=https://pastebin.com/EJJQWc00>

Link to output:  https://pastebin.com/TNSuA0fH
<https://gnldr.online/tracker/click?redirect=https%3A%2F%2Fpastebin.com%2FTNSuA0fH&dID=1574462896168&linkName=https://pastebin.com/TNSuA0fH>

Thanks,
-Jason

[PyMOL] How to display electronic density for nucleic acid pymol

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

Dear Pymol users,

I wish to prepare a image which looks like the picture at the follow link:

   https://drive.google.com/file/d/1HPwTCNqD7hlTPX9QDHif00YW5ZIv8PCa/view?usp=sharing

I have ckecked the pymolwiki for different mode for drawing nucleic acid ladder and ring, but cannot find any thing that can produce an image like what I want. I don't know how to change the phosphoric acid backbond to stick from what looks like putty. Could you help me what this?

I will be very grateful if you can help.

Best regards.

[PyMOL] Admins for Pymol-script-repo needed

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

Hi PyMOL User -

Are you proficient with Python and Git? Then we could need your help with the Pymol-script-repo! The project currently has 6 admins, but it seems that most of them have moved on and are no longer available to help out.

What's needed? Code review on pull requests, giving feedback to the author if needed, and merging the pull request when it looks good. Also any sort of maintenance on the code base you feel is necessary and appropriate.

https://github.com/Pymol-Scripts/Pymol-script-repo

The Pymol-script-repo is not owned or managed by Schrödinger, it's a community project (which doesn't stop Schrödinger from contributing, we're part of the community as well :-)). The repository hosts most of the scripts and (single file) plugins from the PyMOLWiki.

There is currently one open pull request from Pedro:
https://github.com/Pymol-Scripts/Pymol-script-repo/pull/105

So if you want to become a Pymol-script-repo admin, please send me an email.

Thanks,
  Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Re. Pymol Ray problem

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

Hi Changdev - 

Try the following command, which will save a ray-traced PNG image with transparent background (which is what is represented by the checkerboard pattern):

    png myfigure.png, ray=1

Alternatively, you can adjust the ray background setting:

    set ray_opaque_background, 1

Hope that helps.

Cheers,
Jared

On November 13, 2019 at 7:08:16 AM, Gadhe Changdev Gorakshnath (cha...@1s...) wrote:

Hello there,

When I do ray, it shows brown and white square in the background.

I want to capture image directly from screen but squares also get copied.

Is there any way to remove these squares and capture image directly from the screen.

 

Regards,

Changdev

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[PyMOL] Re. Pymol Ray problem

[Gadhe C. G. <cha...@1s...>]

Hello there,
When I do ray, it shows brown and white square in the background.
I want to capture image directly from screen but squares also get copied.
Is there any way to remove these squares and capture image directly from the screen.

Regards,
Changdev

Re: [PyMOL] Pymol Qt Wayland

[RDirective <rdi...@gm...>]

Hi Thomas,

Yes that appears to work wiith qt5-wayland package installed.  I run pymol
in a container so the command is

#!/bin/bash -e
export LC_LANG="en_US.utf8"
toolbox -v run --container pymol bash -exec 'QT_QPA_PLATFORM=xcb
~/Pymol/install/bin/pymol'

Best,
Quyen

On Tue, Nov 5, 2019 at 10:12 AM Thomas Holder <tho...@sc...>
wrote:

> Hi Quyen,
>
> This works for me:
>
>   export QT_QPA_PLATFORM=xcb
>   pymol
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
>
>
> On Sun, Nov 3, 2019 at 6:15 AM RDirective <rdi...@gm...> wrote:
> >
> > Dear all,
> >
> > I have a slight problem with Pymol on Fedora 31. The vanilla
> distribution runs Gnome on Wayland.  Pymol complains that [qt.qpa.plugin:
> Could not find the Qt platform plugin "wayland" in ""]. The GUI and 3D
> render will still work but if I were to install qt5-qtwayland-devel to
> provide the plugin, then the GUI will load but the 3D render no longer
> shows anything. It is just a blank frame.  What can be done about this?
> >
> > Best,
> > Quyen
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Re: [PyMOL] Get surface coordinates

[Pedro L. <psl...@gm...>]

Hi Jared,

May I reopen the ticket?

I got the `get_volume_field` idea. It returns the grid. My grid was trimmed
or was justified to have only the observations and because of this my
shapes seemed incoherent.

I jumped in the code yesterday to add the `quiet` flag on `dump`. This is
code is like the `get_volume_field` but return points instead of the grid
itself. Seems that there is no way on the PyMOL API to handle a grid
dislocated from origin (except dump level by level until fill a volume and
then parse each file). Some notes: (1) my build has no numpy and no idea
why; (2) and I'm not sure if I got the offset alright; (3) didn't handled
other typeofs, only float.

Can you review this code for me?


void ObjectMapDump(ObjectMap* om, const char* fname, int state, int quiet)
{
  auto file = fopen(fname, "wb");
  if (!file) {
    ErrMessage(om->G, "ObjectMapDump", "can't open file for writing");
  }

  ObjectMapState* oms = om->State + 0;

  int zd = oms->Field->dimensions[2];
  int yd = oms->Field->dimensions[1];
  int xd = oms->Field->dimensions[0];

  float zs = (oms->ExtentMax[2] - oms->ExtentMin[2]) /
(oms->Field->dimensions[2]);
  float ys = (oms->ExtentMax[1] - oms->ExtentMin[1]) /
(oms->Field->dimensions[1]);
  float xs = (oms->ExtentMax[0] - oms->ExtentMin[0]) /
(oms->Field->dimensions[0]);

  int offset = 0;
  for (int zi = 0; zi < oms->Field->dimensions[2]; zi++) {
    for (int yi = 0; yi < oms->Field->dimensions[1]; yi++) {
      for (int xi = 0; xi < oms->Field->dimensions[0]; xi++) {

        float z = oms->ExtentMin[2] + zs * zi;
        float y = oms->ExtentMin[1] + ys * yi;
        float x = oms->ExtentMin[0] + xs * xi;

        float* data = (float*) oms->Field->data->data;
        float value = data[offset];
        offset += 1;

        fprintf(file, "%10.4f%10.4f%10.4f%10.4f\n", x, y, z, value);
      }
    }
  }
  fclose(file);
  if (!quiet) {
    PRINTFB(om->G, FB_ObjectMap, FB_Actions)
      " ObjectMapDump: %s written to %s\n", om->Name, fname ENDFB(om->G);
  }
}

Em qui., 7 de nov. de 2019 às 11:41, Jared Sampson <
jar...@co...> escreveu:

> Hi Pedro - Glad you have something working for your use case.
>
> Best,
> Jared
>
>
> On November 5, 2019 at 9:32:51 AM, Pedro Lacerda (psl...@gm...)
> wrote:
>
> Update:
>
> worked the same for me, but may have impact in other cases:
>
> MIN_LEVEL = 0
> MAX_LEVEL = 20
> LEVEL_RANGE = np.arange(MIN_LEVEL, MAX_LEVEL+0.5, 0.5)
>
> def _get_map(map_name):
>     dump_fhandle, dump_fname = tempfile.mkstemp()
>     open(dump_fhandle).close()
>
>     try:
>         levels = {}
>         for level in LEVEL_RANGE:
>             # dump level
>             cmd.isodot('_i', map_name, level)
>             cmd.dump(dump_fname, '_i')
>             cmd.delete('_i')
>
>             # load level
>             with warnings.catch_warnings():
>                 xyz = np.loadtxt(dump_fname)
>                 warnings.simplefilter("ignore")
>
>             # handle empty maps
>             if len(xyz) == 0:
>                 xyz = np.ndarray((0, 3))
>
>             xyz = xyz[:, :3]
>             levels[level] = xyz
>
>         return levels
>     finally:
>         os.unlink(dump_fname)
>
> Em ter., 5 de nov. de 2019 às 11:13, Pedro Lacerda <psl...@gm...>
> escreveu:
>
>> For the sake of completeness here is some working code.
>>
>> `dump` exports the surface of map representations. They are all surfaces.
>>
>> So I had to dump the map at each level (0.5 by 0.5 increment) in order to
>> get a filled volume. If you concatenate all xyz arrays you get the filled
>> volume of the level 20 surface.
>>
>> Thank you for the support.
>>
>>
>> MIN_LEVEL = 0
>> MAX_LEVEL = 20
>> LEVEL_RANGE = np.arange(MIN_LEVEL, MAX_LEVEL+0.5, 0.5)
>>
>>
>> def _get_map(map_name):
>>     dump_fhandle, dump_fname = tempfile.mkstemp()
>>     open(dump_fhandle).close()
>>
>>     try:
>>         levels = {}
>>         skip = False
>>         for level in LEVEL_RANGE:
>>             if not skip:
>>                 # dump level
>>                 cmd.isodot('_i', map_name, level)
>>                 cmd.dump(dump_fname, '_i')
>>                 cmd.delete('_i')
>>
>>                 # load level
>>                 with warnings.catch_warnings():
>>                     xyz = np.loadtxt(dump_fname)
>>                     warnings.simplefilter("ignore")
>>
>>             # handle empty maps
>>             if skip or len(xyz) == 0:
>>                 xyz = np.ndarray((0, 3))
>>                 skip = True
>>
>>             xyz = xyz[:, :3]
>>             levels[level] = xyz
>>
>>         return levels
>>     finally:
>>         os.unlink(dump_fname)
>>
>> Em seg., 4 de nov. de 2019 às 01:38, Pedro Lacerda <psl...@gm...>
>> escreveu:
>>
>>> Hi Jared,
>>>
>>> So COLLADA exports some kind of already rendered 3D image.
>>>
>>> Took me some time to figure out if dump exports the map points or
>>> something specific to the surface representation. In fact, it is yet to be
>>> figured out.
>>>
>>> Dump can export at least map and surface objects.
>>>
>>> When I export two different overlapping surfaces of the same map there
>>> is points of the outer surface that aren't in the inner. I expected all
>>> points of the inner to be present in both dumps.
>>>
>>> So I guess that when I dump surface objects it exports newly created
>>> points of the enclosed volume of that surface. Is it correct?
>>>
>>> To export the map directly would preserve the original points? (Which I
>>> hope to be the original grid count of the server's method)
>>>
>>> Is overlap is defined for map objects?
>>>
>>>
>>> Sorry maybe I'm not saying very clear.
>>>
>>> And about the get_volume_field(), if I remember correctly it returned on
>>> a call an ndarray of shape (28, 26, 15) and on other call an ndarray of
>>> shape (28, 28, 16). Something like that.
>>>
>>>
>>> Cheers,
>>>
>>>
>>> Em sex, 1 de nov de 2019 10:33, Jared Sampson <
>>> jar...@co...> escreveu:
>>>
>>>> Hi Pedro -
>>>>
>>>> The COLLADA option exports unlabeled mesh objects so I couldn't figure
>>>> out which one is acceptor or donor.
>>>>
>>>> Yes, you're correct about that.  This is due to the fact that COLLADA
>>>> export uses geometry after it is prepared for ray tracing, which doesn't
>>>> know about object names (see the primary function call
>>>> <https://github.com/schrodinger/pymol-open-source/blob/master/layer1/COLLADA.cpp#L667>).
>>>> It might be interesting/useful to export things in a more granular way
>>>> using pre-ray-tracing information as it is stored in the PyMOL session, but
>>>> that would involve substantial effort, and wasn't included when we planned
>>>> this export feature.
>>>>
>>>> If you wanted to know which mesh is which, you could export objects
>>>> one-at-a-time by disabling all the others, although to me, the dump command
>>>> output looks more helpful as it can be more easily parsed.
>>>>
>>>> Just one more question, what are these normal values?
>>>>
>>>>
>>>> The normal values Thomas refers to are the 3 components of the vector
>>>> indicating the direction toward the "outside" of the object, which is
>>>> normal to the surface the triangle mesh attempts to approximate.  This is
>>>> used in shading.
>>>>
>>>> https://en.wikipedia.org/wiki/Vertex_normal
>>>>
>>>> The cmd.get_volume_field() returns a sparse ndarray with unknow layout
>>>> and all dimensions variables depending of the object. How to interpret such
>>>> array?
>>>> On PyMOL 1.x it returned -1 but in 2.x returned the array.
>>>>
>>>> The dump command worked (almost) like a charm.
>>>> I expect to extract the "dump" array from get_volume_field() so don't
>>>> need to write the file just to be read and deleted afterwards. Is it
>>>> possible?
>>>>
>>>>
>>>> I'm not familiar with `cmd.get_volume_field()`, so I'll defer to others
>>>> on those questions.
>>>>
>>>> Hope that helps.
>>>>
>>>> Cheers,
>>>> Jared
>>>>
>>>
>>
>> --
>> Pedro Sousa Lacerda
>>
>>
>> *Laboratório de Bioinformática e Modelagem Molecular*
>> *Faculdade de Farmácia / UFBA*
>>
>> *@pslacerda*
>>
>> *+55 71 9 9981-1856*
>>
>
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>
>

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] View manger (and how to store arbitrary data on the session?)

[Pedro L. <psl...@gm...>]

Jared,

I did a pull request with the plugin and asked a account on pymolwiki.org.

I thought the account email was a bot so I was a bit lame. First I sent an
email titled "New Account" with no more text.

https://github.com/Pymol-Scripts/Pymol-script-repo/pull/105



Em qua., 30 de out. de 2019 às 20:13, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi Jared,
>
> Glad you liked and thank you for the patch and incentive. I'll pull it on
> the repo and create a wiki page.
>
> Best regards,
> Pedro Lacerda
>
>
> Em qua, 30 de out de 2019 14:16, Jared Sampson <jar...@co...>
> escreveu:
>
>> Hi Pedro -
>>
>> I just took a look at the plugin, and it seems quite convenient.  I
>> imagine using this as a tool to complement PyMOL's default scenes, as a way
>> of looking at different representations or objects from the same viewpoint.
>>
>> Looking at the code, I was curious about all the Q* global variable
>> assignments near the top, and thought they might be cleaner and easier to
>> maintain as imports.  (Plus many of them were unused in the plugin code.)
>>  Apparently due to the way pymol.Qt is a wrapper for PyQt5, we can't do
>> `from pymol.Qt.QtWidgets import *`, but the following does work:
>>
>> ```
>> from pymol.Qt import QtWidgets, QtCore, QtGui
>> ```
>>
>> then use e.g. `QtWidgets.QWidget()` in the body of the code; see the
>> attached patch (I hope you don't mind my sending it!).  As a side note,
>> this appears to be—at least unofficially—a preferred way to do it,
>> according to an example plugin
>> <https://github.com/Pymol-Scripts/pymol2-demo-plugin/blob/master/__init__.py#L51> by
>> PyMOL lead developer Thomas Holder (speleo3).
>>
>> Also, I would encourage you to add your plugin to the PyMOL scripts repo
>> <https://github.com/Pymol-Scripts/Pymol-script-repo> on Github, and to
>> create a PyMOL Wiki page for it.
>>
>> Thanks for sharing!
>>
>> Cheers,
>> Jared
>>
>> On October 26, 2019 at 12:39:35 PM, Pedro Lacerda (psl...@gm...)
>> wrote:
>>
>> And the plugin, of course!
>>
>> Em sáb, 26 de out de 2019 às 13:37, Pedro Lacerda <psl...@gm...>
>> escreveu:
>>
>>> Hi,
>>>
>>> I just made a graphical plugin to set and get views. It uses the
>>> set_view and get_view functions.
>>>
>>> It is available in the last option ("Show views") on the "Scene" menu.
>>> Double-click to rename a view. Erase it's name to delete it.
>>>
>>> In order to persist data in the PSE session it stores data into the
>>> mesh_clear_selection setting. It was the only way I found.
>>>
>>> How to store arbitrary data on the session? Some "ostate" string
>>> settings are preserved on the PSE session. But not all support set
>>> arbitrary data (eg, bg_image_filename). It is very hackish and not a
>>> definite solution.
>>>
>>> Just wondering, maybe a hidden "setting" (not visible to can be be used
>>> as a key-value store. It would hold serialized data (eg json or pickle) and
>>> have a pair of functions set_key(key, obj) and get(key) that read and write
>>> the setting.
>>>
>>> Another great addition would be able to set arbitrary strings to objects
>>> and atoms. But in case of implementing a key-value store would be some
>>> overlap.
>>>
>>> Best regards,
>>>
>>>
>>> [image: image.png]
>>>
>>> --
>>> Pedro Sousa Lacerda
>>>
>>>
>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>> *Faculdade de Farmácia / UFBA*
>>>
>>> *@pslacerda*
>>>
>>> *+55 71 9 9981-1856*
>>>
>>
>>
>> --
>> Pedro Sousa Lacerda
>>
>>
>> *Laboratório de Bioinformática e Modelagem Molecular*
>> *Faculdade de Farmácia / UFBA*
>>
>> *@pslacerda*
>>
>> *+55 71 9 9981-1856*
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubsc
>> <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
>>
>>

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

[PyMOL] Show lone pairs

[Pedro L. <psl...@gm...>]

Hi,

According to this page seems that GOLD software craft pseudoatoms to
represent lone pairs.

https://chemistryandcomputers.wordpress.com/2012/05/31/pymol-tip/

I would expect some `lone_pairs` setting (like `valence` and `RepValence`)
would represent it.

Is there any way to show lone eletron pairs?


-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] Pymol Qt Wayland

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

Hi Quyen,

This works for me:

  export QT_QPA_PLATFORM=xcb
  pymol

Hope that helps.

Cheers,
  Thomas



On Sun, Nov 3, 2019 at 6:15 AM RDirective <rdi...@gm...> wrote:
>
> Dear all,
>
> I have a slight problem with Pymol on Fedora 31. The vanilla distribution runs Gnome on Wayland.  Pymol complains that [qt.qpa.plugin: Could not find the Qt platform plugin "wayland" in ""]. The GUI and 3D render will still work but if I were to install qt5-qtwayland-devel to provide the plugin, then the GUI will load but the 3D render no longer shows anything. It is just a blank frame.  What can be done about this?
>
> Best,
> Quyen
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Get surface coordinates

[Pedro L. <psl...@gm...>]

Update:

worked the same for me, but may have impact in other cases:

MIN_LEVEL = 0
MAX_LEVEL = 20
LEVEL_RANGE = np.arange(MIN_LEVEL, MAX_LEVEL+0.5, 0.5)

def _get_map(map_name):
    dump_fhandle, dump_fname = tempfile.mkstemp()
    open(dump_fhandle).close()

    try:
        levels = {}
        for level in LEVEL_RANGE:
            # dump level
            cmd.isodot('_i', map_name, level)
            cmd.dump(dump_fname, '_i')
            cmd.delete('_i')

            # load level
            with warnings.catch_warnings():
                xyz = np.loadtxt(dump_fname)
                warnings.simplefilter("ignore")

            # handle empty maps
            if len(xyz) == 0:
                xyz = np.ndarray((0, 3))

            xyz = xyz[:, :3]
            levels[level] = xyz

        return levels
    finally:
        os.unlink(dump_fname)

Em ter., 5 de nov. de 2019 às 11:13, Pedro Lacerda <psl...@gm...>
escreveu:

> For the sake of completeness here is some working code.
>
> `dump` exports the surface of map representations. They are all surfaces.
>
> So I had to dump the map at each level (0.5 by 0.5 increment) in order to
> get a filled volume. If you concatenate all xyz arrays you get the filled
> volume of the level 20 surface.
>
> Thank you for the support.
>
>
> MIN_LEVEL = 0
> MAX_LEVEL = 20
> LEVEL_RANGE = np.arange(MIN_LEVEL, MAX_LEVEL+0.5, 0.5)
>
>
> def _get_map(map_name):
>     dump_fhandle, dump_fname = tempfile.mkstemp()
>     open(dump_fhandle).close()
>
>     try:
>         levels = {}
>         skip = False
>         for level in LEVEL_RANGE:
>             if not skip:
>                 # dump level
>                 cmd.isodot('_i', map_name, level)
>                 cmd.dump(dump_fname, '_i')
>                 cmd.delete('_i')
>
>                 # load level
>                 with warnings.catch_warnings():
>                     xyz = np.loadtxt(dump_fname)
>                     warnings.simplefilter("ignore")
>
>             # handle empty maps
>             if skip or len(xyz) == 0:
>                 xyz = np.ndarray((0, 3))
>                 skip = True
>
>             xyz = xyz[:, :3]
>             levels[level] = xyz
>
>         return levels
>     finally:
>         os.unlink(dump_fname)
>
> Em seg., 4 de nov. de 2019 às 01:38, Pedro Lacerda <psl...@gm...>
> escreveu:
>
>> Hi Jared,
>>
>> So COLLADA exports some kind of already rendered 3D image.
>>
>> Took me some time to figure out if dump exports the map points or
>> something specific to the surface representation. In fact, it is yet to be
>> figured out.
>>
>> Dump can export at least map and surface objects.
>>
>> When I export two different overlapping surfaces of the same map there is
>> points of the outer surface that aren't in the inner. I expected all points
>> of the inner to be present in both dumps.
>>
>> So I guess that when I dump surface objects it exports newly created
>> points of the enclosed volume of that surface. Is it correct?
>>
>> To export the map directly would preserve the original points? (Which I
>> hope to be the original grid count of the server's method)
>>
>> Is overlap is defined for map objects?
>>
>>
>> Sorry maybe I'm not saying very clear.
>>
>> And about the get_volume_field(), if I remember correctly it returned on
>> a call an ndarray of shape (28, 26, 15) and on other call an ndarray of
>> shape (28, 28, 16). Something like that.
>>
>>
>> Cheers,
>>
>>
>> Em sex, 1 de nov de 2019 10:33, Jared Sampson <jar...@co...>
>> escreveu:
>>
>>> Hi Pedro -
>>>
>>> The COLLADA option exports unlabeled mesh objects so I couldn't figure
>>> out which one is acceptor or donor.
>>>
>>> Yes, you're correct about that.  This is due to the fact that COLLADA
>>> export uses geometry after it is prepared for ray tracing, which doesn't
>>> know about object names (see the primary function call
>>> <https://github.com/schrodinger/pymol-open-source/blob/master/layer1/COLLADA.cpp#L667>).
>>> It might be interesting/useful to export things in a more granular way
>>> using pre-ray-tracing information as it is stored in the PyMOL session, but
>>> that would involve substantial effort, and wasn't included when we planned
>>> this export feature.
>>>
>>> If you wanted to know which mesh is which, you could export objects
>>> one-at-a-time by disabling all the others, although to me, the dump command
>>> output looks more helpful as it can be more easily parsed.
>>>
>>> Just one more question, what are these normal values?
>>>
>>>
>>> The normal values Thomas refers to are the 3 components of the vector
>>> indicating the direction toward the "outside" of the object, which is
>>> normal to the surface the triangle mesh attempts to approximate.  This is
>>> used in shading.
>>>
>>> https://en.wikipedia.org/wiki/Vertex_normal
>>>
>>> The cmd.get_volume_field() returns a sparse ndarray with unknow layout
>>> and all dimensions variables depending of the object. How to interpret such
>>> array?
>>> On PyMOL 1.x it returned -1 but in 2.x returned the array.
>>>
>>> The dump command worked (almost) like a charm.
>>> I expect to extract the "dump" array from get_volume_field() so don't
>>> need to write the file just to be read and deleted afterwards. Is it
>>> possible?
>>>
>>>
>>> I'm not familiar with `cmd.get_volume_field()`, so I'll defer to others
>>> on those questions.
>>>
>>> Hope that helps.
>>>
>>> Cheers,
>>> Jared
>>>
>>
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>


-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] Get surface coordinates

[Pedro L. <psl...@gm...>]

For the sake of completeness here is some working code.

`dump` exports the surface of map representations. They are all surfaces.

So I had to dump the map at each level (0.5 by 0.5 increment) in order to
get a filled volume. If you concatenate all xyz arrays you get the filled
volume of the level 20 surface.

Thank you for the support.


MIN_LEVEL = 0
MAX_LEVEL = 20
LEVEL_RANGE = np.arange(MIN_LEVEL, MAX_LEVEL+0.5, 0.5)


def _get_map(map_name):
    dump_fhandle, dump_fname = tempfile.mkstemp()
    open(dump_fhandle).close()

    try:
        levels = {}
        skip = False
        for level in LEVEL_RANGE:
            if not skip:
                # dump level
                cmd.isodot('_i', map_name, level)
                cmd.dump(dump_fname, '_i')
                cmd.delete('_i')

                # load level
                with warnings.catch_warnings():
                    xyz = np.loadtxt(dump_fname)
                    warnings.simplefilter("ignore")

            # handle empty maps
            if skip or len(xyz) == 0:
                xyz = np.ndarray((0, 3))
                skip = True

            xyz = xyz[:, :3]
            levels[level] = xyz

        return levels
    finally:
        os.unlink(dump_fname)

Em seg., 4 de nov. de 2019 às 01:38, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi Jared,
>
> So COLLADA exports some kind of already rendered 3D image.
>
> Took me some time to figure out if dump exports the map points or
> something specific to the surface representation. In fact, it is yet to be
> figured out.
>
> Dump can export at least map and surface objects.
>
> When I export two different overlapping surfaces of the same map there is
> points of the outer surface that aren't in the inner. I expected all points
> of the inner to be present in both dumps.
>
> So I guess that when I dump surface objects it exports newly created
> points of the enclosed volume of that surface. Is it correct?
>
> To export the map directly would preserve the original points? (Which I
> hope to be the original grid count of the server's method)
>
> Is overlap is defined for map objects?
>
>
> Sorry maybe I'm not saying very clear.
>
> And about the get_volume_field(), if I remember correctly it returned on a
> call an ndarray of shape (28, 26, 15) and on other call an ndarray of shape
> (28, 28, 16). Something like that.
>
>
> Cheers,
>
>
> Em sex, 1 de nov de 2019 10:33, Jared Sampson <jar...@co...>
> escreveu:
>
>> Hi Pedro -
>>
>> The COLLADA option exports unlabeled mesh objects so I couldn't figure
>> out which one is acceptor or donor.
>>
>> Yes, you're correct about that.  This is due to the fact that COLLADA
>> export uses geometry after it is prepared for ray tracing, which doesn't
>> know about object names (see the primary function call
>> <https://github.com/schrodinger/pymol-open-source/blob/master/layer1/COLLADA.cpp#L667>).
>> It might be interesting/useful to export things in a more granular way
>> using pre-ray-tracing information as it is stored in the PyMOL session, but
>> that would involve substantial effort, and wasn't included when we planned
>> this export feature.
>>
>> If you wanted to know which mesh is which, you could export objects
>> one-at-a-time by disabling all the others, although to me, the dump command
>> output looks more helpful as it can be more easily parsed.
>>
>> Just one more question, what are these normal values?
>>
>>
>> The normal values Thomas refers to are the 3 components of the vector
>> indicating the direction toward the "outside" of the object, which is
>> normal to the surface the triangle mesh attempts to approximate.  This is
>> used in shading.
>>
>> https://en.wikipedia.org/wiki/Vertex_normal
>>
>> The cmd.get_volume_field() returns a sparse ndarray with unknow layout
>> and all dimensions variables depending of the object. How to interpret such
>> array?
>> On PyMOL 1.x it returned -1 but in 2.x returned the array.
>>
>> The dump command worked (almost) like a charm.
>> I expect to extract the "dump" array from get_volume_field() so don't
>> need to write the file just to be read and deleted afterwards. Is it
>> possible?
>>
>>
>> I'm not familiar with `cmd.get_volume_field()`, so I'll defer to others
>> on those questions.
>>
>> Hope that helps.
>>
>> Cheers,
>> Jared
>>
>

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*

Re: [PyMOL] Get surface coordinates

[Pedro L. <psl...@gm...>]

Hi Jared,

So COLLADA exports some kind of already rendered 3D image.

Took me some time to figure out if dump exports the map points or something
specific to the surface representation. In fact, it is yet to be figured
out.

Dump can export at least map and surface objects.

When I export two different overlapping surfaces of the same map there is
points of the outer surface that aren't in the inner. I expected all points
of the inner to be present in both dumps.

So I guess that when I dump surface objects it exports newly created points
of the enclosed volume of that surface. Is it correct?

To export the map directly would preserve the original points? (Which I
hope to be the original grid count of the server's method)

Is overlap is defined for map objects?


Sorry maybe I'm not saying very clear.

And about the get_volume_field(), if I remember correctly it returned on a
call an ndarray of shape (28, 26, 15) and on other call an ndarray of shape
(28, 28, 16). Something like that.


Cheers,


Em sex, 1 de nov de 2019 10:33, Jared Sampson <jar...@co...>
escreveu:

> Hi Pedro -
>
> The COLLADA option exports unlabeled mesh objects so I couldn't figure out
> which one is acceptor or donor.
>
> Yes, you're correct about that.  This is due to the fact that COLLADA
> export uses geometry after it is prepared for ray tracing, which doesn't
> know about object names (see the primary function call
> <https://github.com/schrodinger/pymol-open-source/blob/master/layer1/COLLADA.cpp#L667>).
> It might be interesting/useful to export things in a more granular way
> using pre-ray-tracing information as it is stored in the PyMOL session, but
> that would involve substantial effort, and wasn't included when we planned
> this export feature.
>
> If you wanted to know which mesh is which, you could export objects
> one-at-a-time by disabling all the others, although to me, the dump command
> output looks more helpful as it can be more easily parsed.
>
> Just one more question, what are these normal values?
>
>
> The normal values Thomas refers to are the 3 components of the vector
> indicating the direction toward the "outside" of the object, which is
> normal to the surface the triangle mesh attempts to approximate.  This is
> used in shading.
>
> https://en.wikipedia.org/wiki/Vertex_normal
>
> The cmd.get_volume_field() returns a sparse ndarray with unknow layout and
> all dimensions variables depending of the object. How to interpret such
> array?
> On PyMOL 1.x it returned -1 but in 2.x returned the array.
>
> The dump command worked (almost) like a charm.
> I expect to extract the "dump" array from get_volume_field() so don't need
> to write the file just to be read and deleted afterwards. Is it possible?
>
>
> I'm not familiar with `cmd.get_volume_field()`, so I'll defer to others on
> those questions.
>
> Hope that helps.
>
> Cheers,
> Jared
>