pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] pref_get() on library mode

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

It worked like a charm, thank you.

Em seg., 26 de out. de 2020 às 04:37, Thomas Holder <
tho...@sc...> escreveu:

> Hi Pedro,
>
> If you call `plugin_load` that will trigger initialization.
>
> pymol.plugins.plugin_load('yourplugin')
> value = pymol.plugins.pref_get('YOUPLUGIN_SOME_KEY')
>
>
> I feel like this plugin API is due for an overhaul, there are no great
> answers to your various questions :-/
>
> Cheers,
>   Thomas
>
>
> > On Oct 26, 2020, at 5:40 AM, Pedro Lacerda <psl...@gm...> wrote:
> >
> > Hi,
> >
> > How to use pref_get() on library mode.
> >
> > Or even better, how to use pref_get() even before library mode?
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular / UFBA
> > Mestrando em Ciências Farmácias / UEFS
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
> > _______________________________________________
> > 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.
>
>

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

[PyMOL] Generating list of polar contacts

[Marcelo D. <mar...@gm...>]

Hi,

I have a set of protein structures and I want to quantify the amount of
internal H-bond, salt-bridges and non-polar interactions in each of them.

I was wondering if there is a way to use Pymol to provide a list of
internal H-bond and salt-bridges. Maybe with polar contacts?

Best regards,
--
Marcelo Depólo Polêto
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464

Re: [PyMOL] pref_get() on library mode

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

Hi Pedro,

If you call `plugin_load` that will trigger initialization.

pymol.plugins.plugin_load('yourplugin')
value = pymol.plugins.pref_get('YOUPLUGIN_SOME_KEY')


I feel like this plugin API is due for an overhaul, there are no great answers to your various questions :-/

Cheers,
  Thomas


> On Oct 26, 2020, at 5:40 AM, Pedro Lacerda <psl...@gm...> wrote:
> 
> Hi,
> 
> How to use pref_get() on library mode.
> 
> Or even better, how to use pref_get() even before library mode?
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
> _______________________________________________
> 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] Formatted output

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

Hi Pedro,

The Incentive PyMOL Qt GUI is able to handle a small subset of ANSI color codes.

pymol.colorprinting.error("Text in red")
pymol.colorprinting.warning("Text in magenta")
print("\033[31mRed \033[32mGreen \033[33mYellow\033[m Default")

https://en.wikipedia.org/wiki/ANSI_escape_code

Open-Source PyMOL will simply strip the color codes.

Cheers,
  Thomas


> On Oct 26, 2020, at 3:10 AM, Pedro Lacerda <psl...@gm...> wrote:
> 
> I see that probably you are using HTML for this.
> https://github.com/schrodinger/pymol-open-source/blob/69b1f0b53b4109c34604adcea3983e4d3886069e/modules/pymol/colorprinting.py
> 
> But printing HTML directly into the console didn't worked.
> 
> Em dom., 25 de out. de 2020 às 23:06, Pedro Lacerda <psl...@gm...> escreveu:
> Hi,
> 
> How can I print formatted output into the PyMOL console?
> 
> I see that on the incentive version the output is coloured (eg errors are red).
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
> _______________________________________________
> 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 In using Pymol 2.4 through IDLE -Python 3

[Dr. V. M. <vij...@gm...>]

Thank you, Dr. Christopher Gohlke
I downloaded and installed Microsoft Visual C++ Redistributable for
Visual Studio 2015, 2017 and 2019. This solved the problem. Now, PyMOL is
running without any problem. In fact, I just successfully ran PyMOL from
Portable Python 3.8 and also from IDLE.
Cheers

With Warm Regards
*Dr. Vijay H. Masand*
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/



On Sat, Oct 24, 2020 at 9:17 AM Christoph Gohlke <cg...@uc...> wrote:

> Try installing the Microsoft Visual C++ Redistributable for Visual
> Studio 2015, 2017 and 2019
> <
> https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads
> >
>
> Christoph
>
>
> On 10/23/2020 8:11 PM, Dr. Vijay Masand wrote:
> > Hello PyMOL users
> > I installed open source PyMOL 2.4 (Python 3.7) on Windows 10 (64 bit).
> > It strated without any problem when the icon was double clicked.But when
> > I tried to use it from IDLE (PYTHON 3.7- 64bit), it showed following
> error:
> > "ImportError: DLL load failed: The specified module could not be found."
> >
> > To find a solution, I installed Pymol 2.4 with Python 3.8, but Pymol did
> > not start at all. Then, I tried Pymol 2.4 with Python 3.9 also, again
> > PyMOL 2.4 did not start at all.
> > Finally, I tried Python 2.7 (using PyMOL 2.0), it worked perfectly and
> > was running from IDLE, as well.
> >
> > I need help to remove the error
> > "ImportError: DLL load failed: The specified module could not be found."
> > to run PyMOL 2.4 with Python 3 using IDLE?
> >
> > Thanks in advance.
> >
> > With Warm Regards
> > *Dr. Vijay H. Masand*
> > Department of Chemistry,
> > Vidya Bharati College, Amravati, 444 602
> > Maharashtra, India.
> > Phone number- +91-9403312628
> > https://sites.google.com/site/vijaymasand/
> > <https://sites.google.com/site/vijaymasand/>
> >
> >
> >
> > _______________________________________________
> > 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
>

[PyMOL] pref_get() on library mode

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

Hi,

How to use pref_get() on library mode.

Or even better, how to use pref_get() even before library mode?

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

Re: [PyMOL] Formatted output

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

I see that probably you are using HTML for this.
https://github.com/schrodinger/pymol-open-source/blob/69b1f0b53b4109c34604adcea3983e4d3886069e/modules/pymol/colorprinting.py

But printing HTML directly into the console didn't worked.

Em dom., 25 de out. de 2020 às 23:06, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi,
>
> How can I print formatted output into the PyMOL console?
>
> I see that on the incentive version the output is coloured (eg errors are
> red).
>
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
>


-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

[PyMOL] Formatted output

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

Hi,

How can I print formatted output into the PyMOL console?

I see that on the incentive version the output is coloured (eg errors are
red).


-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

Re: [PyMOL] Problem In using Pymol 2.4 through IDLE -Python 3

[Christoph G. <cg...@uc...>]

Try installing the Microsoft Visual C++ Redistributable for Visual 
Studio 2015, 2017 and 2019 
<https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads>

Christoph


On 10/23/2020 8:11 PM, Dr. Vijay Masand wrote:
> Hello PyMOL users
> I installed open source PyMOL 2.4 (Python 3.7) on Windows 10 (64 bit).
> It strated without any problem when the icon was double clicked.But when 
> I tried to use it from IDLE (PYTHON 3.7- 64bit), it showed following error:
> "ImportError: DLL load failed: The specified module could not be found."
> 
> To find a solution, I installed Pymol 2.4 with Python 3.8, but Pymol did 
> not start at all. Then, I tried Pymol 2.4 with Python 3.9 also, again 
> PyMOL 2.4 did not start at all.
> Finally, I tried Python 2.7 (using PyMOL 2.0), it worked perfectly and 
> was running from IDLE, as well.
> 
> I need help to remove the error
> "ImportError: DLL load failed: The specified module could not be found."
> to run PyMOL 2.4 with Python 3 using IDLE?
> 
> Thanks in advance.
> 
> With Warm Regards
> *Dr. Vijay H. Masand*
> Department of Chemistry,
> Vidya Bharati College, Amravati, 444 602
> Maharashtra, India.
> Phone number- +91-9403312628
> https://sites.google.com/site/vijaymasand/ 
> <https://sites.google.com/site/vijaymasand/>
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 

[PyMOL] Problem In using Pymol 2.4 through IDLE -Python 3

[Dr. V. M. <vij...@gm...>]

 Hello PyMOL users
I installed open source PyMOL 2.4 (Python 3.7) on Windows 10 (64 bit).
It strated without any problem when the icon was double clicked.But when I
tried to use it from IDLE (PYTHON 3.7- 64bit), it showed following error:
"ImportError: DLL load failed: The specified module could not be found."

To find a solution, I installed Pymol 2.4 with Python 3.8, but Pymol did
not start at all. Then, I tried Pymol 2.4 with Python 3.9 also, again PyMOL
2.4 did not start at all.
Finally, I tried Python 2.7 (using PyMOL 2.0), it worked perfectly and was
running from IDLE, as well.

I need help to remove the error
"ImportError: DLL load failed: The specified module could not be found."
to run PyMOL 2.4 with Python 3 using IDLE?

Thanks in advance.

With Warm Regards
*Dr. Vijay H. Masand*
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

Re: [PyMOL] [EXTERNAL] Generation of images using png

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

just left my Mac during the night to generate images:
new benchmark record:

PyMOL>  cmd.draw(800,800);cmd.png('/img/cne_998.png',width=800,height=800,dpi=50,ray=1)

 Ray: render time: 18259.74 sec. = 0.2 frames/hour (18259.74 sec. accum.).

:-)

ср, 21 окт. 2020 г. в 15:31, Jeff Saxon <jms...@gm...>:
>
> Here are some benchmarks
> 1)This is an example for rendering of the image based on a multi-model
> pdb of 240 frames (all states splitted into the same model)
>  Ray: render time: 698.52 sec. = 5.2 frames/hour (698.52 sec. accum.).
> 2) This is the same for 20 model pdb
>
> Ray: render time: 19.26 sec. = 186.9 frames/hour (19.26 sec. accum.).
>
> My hardware is iMAC 3.4 ghz Core i7, 16Go 13000 DDR3
> I am using pymol 2.4.1 (full version)
>
> ср, 21 окт. 2020 г. в 14:59, Jeff Saxon <jms...@gm...>:
> >
> > thank you, Blaine!
> > actually this problem only exists for the saving image of the system
> > consisted of many models loaded into save pymol session after its
> > splitting
> > I've already tried with dpi=50 (keeping the same resolution) but It
> > did not produce any differences :-)
> > Cheers,
> > J.
> >
> > ср, 21 окт. 2020 г. в 13:18, Mooers, Blaine H.M. (HSC)
> > <Bla...@ou...>:
> > >
> > > Hi Jeff,
> > >
> > > 10 minutes is a long time for a 800 by 800 pixel image.
> > > Maybe you need to use a computer with more memory.
> > >
> > > You can set the dpi in the argument to the png command to a lower value like 300 or 200 to speed up writing the png file.
> > > You can also turn off the casting of shadows:  cmd.do("set ray_shadows,off"), which might save a few seconds.
> > >
> > > 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: Jeff Saxon [jms...@gm...]
> > > Sent: Wednesday, October 21, 2020 4:03 AM
> > > To: pymol-users
> > > Subject: [EXTERNAL] [PyMOL] Generation of images using png
> > >
> > > Dear PyMol users,
> > > I am generating png images of protein-ligand complex using png command
> > > of pymol. This is the syntax that I am using from my bash script:
> > >
> > > image=800
> > > pdb='my.pdb'
> > > # load pdb, split states, make image
> > >   MacPyMOL -c -d "
> > >   from pymol import cmd
> > >   cmd.load('${pdb}')
> > >   cmd.split_states('complex*')
> > >   cmd.bg_color('white')
> > >  cmd.draw(${image},${image});cmd.png('test.png',width=${image},height=${image},ray=1)
> > >   "
> > >
> > > Briefly, it works well but the time of the production of each image is
> > > up to 10 minutes (in the case if I have many models in my.pdb). Is it
> > > possible to speed PNG, while keeping the same resolution of image
> > > (800x800)?
> > >
> > > Cheers,
> > > J.
> > >
> > >
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=6yGrvyC36T9_kcNYvKJuml1-crRw2Sxuz4rvhpoS8ac&e=
> > > Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=1dpWe_laCFcfkMNzKcE1bNSXz6dvC6fkVX1QqUEUdjc&e=

Re: [PyMOL] [EXTERNAL] Generation of images using png

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

Here are some benchmarks
1)This is an example for rendering of the image based on a multi-model
pdb of 240 frames (all states splitted into the same model)
 Ray: render time: 698.52 sec. = 5.2 frames/hour (698.52 sec. accum.).
2) This is the same for 20 model pdb

Ray: render time: 19.26 sec. = 186.9 frames/hour (19.26 sec. accum.).

My hardware is iMAC 3.4 ghz Core i7, 16Go 13000 DDR3
I am using pymol 2.4.1 (full version)

ср, 21 окт. 2020 г. в 14:59, Jeff Saxon <jms...@gm...>:
>
> thank you, Blaine!
> actually this problem only exists for the saving image of the system
> consisted of many models loaded into save pymol session after its
> splitting
> I've already tried with dpi=50 (keeping the same resolution) but It
> did not produce any differences :-)
> Cheers,
> J.
>
> ср, 21 окт. 2020 г. в 13:18, Mooers, Blaine H.M. (HSC)
> <Bla...@ou...>:
> >
> > Hi Jeff,
> >
> > 10 minutes is a long time for a 800 by 800 pixel image.
> > Maybe you need to use a computer with more memory.
> >
> > You can set the dpi in the argument to the png command to a lower value like 300 or 200 to speed up writing the png file.
> > You can also turn off the casting of shadows:  cmd.do("set ray_shadows,off"), which might save a few seconds.
> >
> > 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: Jeff Saxon [jms...@gm...]
> > Sent: Wednesday, October 21, 2020 4:03 AM
> > To: pymol-users
> > Subject: [EXTERNAL] [PyMOL] Generation of images using png
> >
> > Dear PyMol users,
> > I am generating png images of protein-ligand complex using png command
> > of pymol. This is the syntax that I am using from my bash script:
> >
> > image=800
> > pdb='my.pdb'
> > # load pdb, split states, make image
> >   MacPyMOL -c -d "
> >   from pymol import cmd
> >   cmd.load('${pdb}')
> >   cmd.split_states('complex*')
> >   cmd.bg_color('white')
> >  cmd.draw(${image},${image});cmd.png('test.png',width=${image},height=${image},ray=1)
> >   "
> >
> > Briefly, it works well but the time of the production of each image is
> > up to 10 minutes (in the case if I have many models in my.pdb). Is it
> > possible to speed PNG, while keeping the same resolution of image
> > (800x800)?
> >
> > Cheers,
> > J.
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=6yGrvyC36T9_kcNYvKJuml1-crRw2Sxuz4rvhpoS8ac&e=
> > Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=1dpWe_laCFcfkMNzKcE1bNSXz6dvC6fkVX1QqUEUdjc&e=

Re: [PyMOL] [EXTERNAL] Generation of images using png

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

thank you, Blaine!
actually this problem only exists for the saving image of the system
consisted of many models loaded into save pymol session after its
splitting
I've already tried with dpi=50 (keeping the same resolution) but It
did not produce any differences :-)
Cheers,
J.

ср, 21 окт. 2020 г. в 13:18, Mooers, Blaine H.M. (HSC)
<Bla...@ou...>:
>
> Hi Jeff,
>
> 10 minutes is a long time for a 800 by 800 pixel image.
> Maybe you need to use a computer with more memory.
>
> You can set the dpi in the argument to the png command to a lower value like 300 or 200 to speed up writing the png file.
> You can also turn off the casting of shadows:  cmd.do("set ray_shadows,off"), which might save a few seconds.
>
> 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: Jeff Saxon [jms...@gm...]
> Sent: Wednesday, October 21, 2020 4:03 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] Generation of images using png
>
> Dear PyMol users,
> I am generating png images of protein-ligand complex using png command
> of pymol. This is the syntax that I am using from my bash script:
>
> image=800
> pdb='my.pdb'
> # load pdb, split states, make image
>   MacPyMOL -c -d "
>   from pymol import cmd
>   cmd.load('${pdb}')
>   cmd.split_states('complex*')
>   cmd.bg_color('white')
>  cmd.draw(${image},${image});cmd.png('test.png',width=${image},height=${image},ray=1)
>   "
>
> Briefly, it works well but the time of the production of each image is
> up to 10 minutes (in the case if I have many models in my.pdb). Is it
> possible to speed PNG, while keeping the same resolution of image
> (800x800)?
>
> Cheers,
> J.
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=6yGrvyC36T9_kcNYvKJuml1-crRw2Sxuz4rvhpoS8ac&e=
> Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=1dpWe_laCFcfkMNzKcE1bNSXz6dvC6fkVX1QqUEUdjc&e=

Re: [PyMOL] [EXTERNAL] Generation of images using png

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

Hi Jeff,

10 minutes is a long time for a 800 by 800 pixel image.
Maybe you need to use a computer with more memory.

You can set the dpi in the argument to the png command to a lower value like 300 or 200 to speed up writing the png file.
You can also turn off the casting of shadows:  cmd.do("set ray_shadows,off"), which might save a few seconds.

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: Jeff Saxon [jms...@gm...]
Sent: Wednesday, October 21, 2020 4:03 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] Generation of images using png

Dear PyMol users,
I am generating png images of protein-ligand complex using png command
of pymol. This is the syntax that I am using from my bash script:

image=800
pdb='my.pdb'
# load pdb, split states, make image
  MacPyMOL -c -d "
  from pymol import cmd
  cmd.load('${pdb}')
  cmd.split_states('complex*')
  cmd.bg_color('white')
 cmd.draw(${image},${image});cmd.png('test.png',width=${image},height=${image},ray=1)
  "

Briefly, it works well but the time of the production of each image is
up to 10 minutes (in the case if I have many models in my.pdb). Is it
possible to speed PNG, while keeping the same resolution of image
(800x800)?

Cheers,
J.


_______________________________________________
PyMOL-users mailing list
Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=6yGrvyC36T9_kcNYvKJuml1-crRw2Sxuz4rvhpoS8ac&e=
Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=dR6VXes1u9h9KRDTJ3O_4buil9-Nbow2k7Zm5Q3PKQM&s=1dpWe_laCFcfkMNzKcE1bNSXz6dvC6fkVX1QqUEUdjc&e=

Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

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

Hi Jeff,

Yes, there are many ways to add customized labels in PyMOL.
The labels will be saved to your png file.
As Saurabh suggested, Please see the examples here https://pymolwiki.org/index.php/Label.

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: Saurabh Gayali [sau...@gm...]
Sent: Wednesday, October 21, 2020 5:54 AM
To: Jeff Saxon
Cc: pymol-users
Subject: Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

I think you can superimpose the name externally after the image is produced using GD libraries of python.
Also I am not sure that Pymol labels could help,
https://pymolwiki.org/index.php/Label<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Label&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=DrgJ6lV_1gdnhXA-GZQcnykt60-aQBIrBqPr9Irv6Pg&e=>

-------

I also have a question.
I am also trying to achieve something similar, but with docking output files where models are saved as frames and I want a particular frame. I dont know the question should be in the same thread or I should start a new one.

________________________________
[https://i.imgur.com/KatpbrU.jpg]

Saurabh Gayali / Post Doctoral Fellow
sau...@gm...<mailto:sau...@gm...> / +91 8800412916

CSIR-IGIB
<https://urldefense.proofpoint.com/v2/url?u=http-3A__example.com_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=uWtW0pw2aLchvAV3eOX1UFjoMNMC1QnC8twXa7EFP7k&e=>New Delhi, India


On Tue, Oct 20, 2020 at 9:17 PM Jeff Saxon <jms...@gm...<mailto:jms...@gm...>> wrote:
Right, thank you! just tested it with the recent Pymol version.
one question - is there any way to plot the name of the loaded pdb on
the image (produced by PNG command) in some automatic fashion (it
could be useful when I use it directly from terminal, without GUI)?

вт, 20 окт. 2020 г. в 14:46, Thomas Holder <tho...@sc...<mailto:tho...@sc...>>:
>
> See last question here ("Ray tracing does not work"):
> https://pymol.org/edu/faq.php<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_edu_faq.php&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=UQ4HfX4kGVvTsIoXylaT19Or6Xzlk6UjUJUkVvAKKws&e=>
>
> Cheers,
>   Thomas
>
> On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC)
> <Bla...@ou...<mailto:Bla...@ou...>> wrote:
> >
> > Hi Jeff,
> >
> > I have the incentive version of PyMOL.
> > It too is saving draw images with ray tracing when using the batch mode and also when using the pymol api in Jupyter.
> > As you report, saving a draw image from inside PyMOL works.
> >
> > This is a very annoying bug.
> > You should report it as an issue on the PyMOL github site.
> >
> > Perhaps this is not an issue with an order version of PyMOL.
> > Try one from before the switch from lines to cartoon as the default molecular representation (say version 2.1).
> >
> > 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: Jeff Saxon [jms...@gm...<mailto:jms...@gm...>]
> > Sent: Tuesday, October 20, 2020 5:48 AM
> > To: Mooers, Blaine H.M.  (HSC); pymol-users
> > Subject: Re: [EXTERNAL] [PyMOL] png command in Educational Pymol
> >
> > Hi Blaine,
> > I've just checked on trial 26 day version of Pymol it use always RAY=1
> > while I run pymol from script regardless of ray flag (tested with
> > ray=1, ray=0, without ray as in you case etc :-)
> > I am going to try open source pymol!
> > Cheers,
> > J
> >
> > вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
> > <Bla...@ou...<mailto:Bla...@ou...>>:
> > >
> > > Hi Jeff,
> > >
> > > I do not know the answer to your question. This is a work around.
> > > Try dropping ray=0 and adding the draw command with the dimensions in pixels (width, height).
> > >
> > > cmd.draw(1600,1600);cmd.png('test1600.png')
> > >
> > > I would not use the Educational PyMOL for the kind of serious work that you are trying to do.
> > > The PyMOL Wiki has several pages about open source versions of PyMOL.
> > > Use one of those instead.
> > >
> > > 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: Jeff Saxon [jms...@gm...<mailto:jms...@gm...>]
> > > Sent: Tuesday, October 20, 2020 5:24 AM
> > > To: pymol-users
> > > Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
> > >
> > > hello,
> > > I am using educational version of Pymol to generate png image of
> > > protein-ligand complex
> > >
> > > First, there are no problems in the case of PNG command from pymol's
> > > GUI. However if I run the same from script from terminal:
> > >
> > >   MacPyMOL -c -d "
> > >   from pymol import cmd
> > >   cmd.load('${pdb}')
> > >   cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
> > >   "
> > > it  does not produce an image with the following message:
> > >
> > >  ! Ray tracing is not supported in Educational-Use-Only PyMOL. This version
> > >
> > >  ! has a reduced set of features compared to the full Incentive PyMOL version.
> > >
> > >  ! Please visit https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_edu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=wc9BhPQsimg9JTvkDK5bNL1mUeSQplkvyIKIvNtXP5A&e=  for details. If you want to generate
> > >
> > >  ! figures for publication, then please obtain an academic license,
> > >
> > >  ! see https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_academic&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=AyyjBPHDzcks30uu67ZXdfPu0lx4oJroZwNpS2_J1Yc&e=
> > >
> > > note that ray is disabled in my command (since I do not need a HQ
> > > image) and as I've mentioned there were no problems to create an image
> > > from gui session using the same command. Could it be fixed for my case
> > > or I need another version of Pymol ?
> > >
> > > Thank you !
> > >
> > >
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=-1_AqsLVgFJuceEfbluv4cGyYN2K2-202Lt95lZ68pE&e=
> > > Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=lOpzpCHVKu9bGPvhNAelWdeyEfwzTmXG7Z3ZFgOimQs&e=
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=qDvoQ4fQobq5o0Gm3kNL2jSFxG737Q4K-WS-Bw2wxrM&e=>
> > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=w7XKWcijJ9qnOQ2CmbqcwsN-n66FY3bJz9lgvVRg8WI&e=>


_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=qDvoQ4fQobq5o0Gm3kNL2jSFxG737Q4K-WS-Bw2wxrM&e=>
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=w7XKWcijJ9qnOQ2CmbqcwsN-n66FY3bJz9lgvVRg8WI&e=>

Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

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

Hi Saurabh,

I recommend that you start a new thread because your goal is not identical to Jeff's.

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: Saurabh Gayali [sau...@gm...]
Sent: Wednesday, October 21, 2020 5:54 AM
To: Jeff Saxon
Cc: pymol-users
Subject: Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

I think you can superimpose the name externally after the image is produced using GD libraries of python.
Also I am not sure that Pymol labels could help,
https://pymolwiki.org/index.php/Label<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Label&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=DrgJ6lV_1gdnhXA-GZQcnykt60-aQBIrBqPr9Irv6Pg&e=>

-------

I also have a question.
I am also trying to achieve something similar, but with docking output files where models are saved as frames and I want a particular frame. I dont know the question should be in the same thread or I should start a new one.

________________________________
[https://i.imgur.com/KatpbrU.jpg]

Saurabh Gayali / Post Doctoral Fellow
sau...@gm...<mailto:sau...@gm...> / +91 8800412916

CSIR-IGIB
<https://urldefense.proofpoint.com/v2/url?u=http-3A__example.com_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=uWtW0pw2aLchvAV3eOX1UFjoMNMC1QnC8twXa7EFP7k&e=>New Delhi, India


On Tue, Oct 20, 2020 at 9:17 PM Jeff Saxon <jms...@gm...<mailto:jms...@gm...>> wrote:
Right, thank you! just tested it with the recent Pymol version.
one question - is there any way to plot the name of the loaded pdb on
the image (produced by PNG command) in some automatic fashion (it
could be useful when I use it directly from terminal, without GUI)?

вт, 20 окт. 2020 г. в 14:46, Thomas Holder <tho...@sc...<mailto:tho...@sc...>>:
>
> See last question here ("Ray tracing does not work"):
> https://pymol.org/edu/faq.php<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymol.org_edu_faq.php&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=UQ4HfX4kGVvTsIoXylaT19Or6Xzlk6UjUJUkVvAKKws&e=>
>
> Cheers,
>   Thomas
>
> On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC)
> <Bla...@ou...<mailto:Bla...@ou...>> wrote:
> >
> > Hi Jeff,
> >
> > I have the incentive version of PyMOL.
> > It too is saving draw images with ray tracing when using the batch mode and also when using the pymol api in Jupyter.
> > As you report, saving a draw image from inside PyMOL works.
> >
> > This is a very annoying bug.
> > You should report it as an issue on the PyMOL github site.
> >
> > Perhaps this is not an issue with an order version of PyMOL.
> > Try one from before the switch from lines to cartoon as the default molecular representation (say version 2.1).
> >
> > 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: Jeff Saxon [jms...@gm...<mailto:jms...@gm...>]
> > Sent: Tuesday, October 20, 2020 5:48 AM
> > To: Mooers, Blaine H.M.  (HSC); pymol-users
> > Subject: Re: [EXTERNAL] [PyMOL] png command in Educational Pymol
> >
> > Hi Blaine,
> > I've just checked on trial 26 day version of Pymol it use always RAY=1
> > while I run pymol from script regardless of ray flag (tested with
> > ray=1, ray=0, without ray as in you case etc :-)
> > I am going to try open source pymol!
> > Cheers,
> > J
> >
> > вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
> > <Bla...@ou...<mailto:Bla...@ou...>>:
> > >
> > > Hi Jeff,
> > >
> > > I do not know the answer to your question. This is a work around.
> > > Try dropping ray=0 and adding the draw command with the dimensions in pixels (width, height).
> > >
> > > cmd.draw(1600,1600);cmd.png('test1600.png')
> > >
> > > I would not use the Educational PyMOL for the kind of serious work that you are trying to do.
> > > The PyMOL Wiki has several pages about open source versions of PyMOL.
> > > Use one of those instead.
> > >
> > > 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: Jeff Saxon [jms...@gm...<mailto:jms...@gm...>]
> > > Sent: Tuesday, October 20, 2020 5:24 AM
> > > To: pymol-users
> > > Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
> > >
> > > hello,
> > > I am using educational version of Pymol to generate png image of
> > > protein-ligand complex
> > >
> > > First, there are no problems in the case of PNG command from pymol's
> > > GUI. However if I run the same from script from terminal:
> > >
> > >   MacPyMOL -c -d "
> > >   from pymol import cmd
> > >   cmd.load('${pdb}')
> > >   cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
> > >   "
> > > it  does not produce an image with the following message:
> > >
> > >  ! Ray tracing is not supported in Educational-Use-Only PyMOL. This version
> > >
> > >  ! has a reduced set of features compared to the full Incentive PyMOL version.
> > >
> > >  ! Please visit https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_edu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=wc9BhPQsimg9JTvkDK5bNL1mUeSQplkvyIKIvNtXP5A&e=  for details. If you want to generate
> > >
> > >  ! figures for publication, then please obtain an academic license,
> > >
> > >  ! see https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_academic&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=AyyjBPHDzcks30uu67ZXdfPu0lx4oJroZwNpS2_J1Yc&e=
> > >
> > > note that ray is disabled in my command (since I do not need a HQ
> > > image) and as I've mentioned there were no problems to create an image
> > > from gui session using the same command. Could it be fixed for my case
> > > or I need another version of Pymol ?
> > >
> > > Thank you !
> > >
> > >
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=-1_AqsLVgFJuceEfbluv4cGyYN2K2-202Lt95lZ68pE&e=
> > > Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=lOpzpCHVKu9bGPvhNAelWdeyEfwzTmXG7Z3ZFgOimQs&e=
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=qDvoQ4fQobq5o0Gm3kNL2jSFxG737Q4K-WS-Bw2wxrM&e=>
> > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=w7XKWcijJ9qnOQ2CmbqcwsN-n66FY3bJz9lgvVRg8WI&e=>


_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=qDvoQ4fQobq5o0Gm3kNL2jSFxG737Q4K-WS-Bw2wxrM&e=>
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=H3QkLbCmhos8V00vJyuUau1ptNGcudWdH4VGKdTaHbU&s=w7XKWcijJ9qnOQ2CmbqcwsN-n66FY3bJz9lgvVRg8WI&e=>

Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

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

I think you can superimpose the name externally after the image is produced
using GD libraries of python.
Also I am not sure that Pymol labels could help,
https://pymolwiki.org/index.php/Label

-------

I also have a question.
I am also trying to achieve something similar, but with docking output
files where models are saved as frames and I want a particular frame. I
dont know the question should be in the same thread or I should start a new
one.

------------------------------

*Saurabh Gayali* / Post Doctoral Fellow
sau...@gm... / +91 8800412916

*CSIR-IGIB*
<http://example.com/>New Delhi, India


On Tue, Oct 20, 2020 at 9:17 PM Jeff Saxon <jms...@gm...> wrote:

> Right, thank you! just tested it with the recent Pymol version.
> one question - is there any way to plot the name of the loaded pdb on
> the image (produced by PNG command) in some automatic fashion (it
> could be useful when I use it directly from terminal, without GUI)?
>
> вт, 20 окт. 2020 г. в 14:46, Thomas Holder <tho...@sc...
> >:
> >
> > See last question here ("Ray tracing does not work"):
> > https://pymol.org/edu/faq.php
> >
> > Cheers,
> >   Thomas
> >
> > On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC)
> > <Bla...@ou...> wrote:
> > >
> > > Hi Jeff,
> > >
> > > I have the incentive version of PyMOL.
> > > It too is saving draw images with ray tracing when using the batch
> mode and also when using the pymol api in Jupyter.
> > > As you report, saving a draw image from inside PyMOL works.
> > >
> > > This is a very annoying bug.
> > > You should report it as an issue on the PyMOL github site.
> > >
> > > Perhaps this is not an issue with an order version of PyMOL.
> > > Try one from before the switch from lines to cartoon as the default
> molecular representation (say version 2.1).
> > >
> > > 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: Jeff Saxon [jms...@gm...]
> > > Sent: Tuesday, October 20, 2020 5:48 AM
> > > To: Mooers, Blaine H.M.  (HSC); pymol-users
> > > Subject: Re: [EXTERNAL] [PyMOL] png command in Educational Pymol
> > >
> > > Hi Blaine,
> > > I've just checked on trial 26 day version of Pymol it use always RAY=1
> > > while I run pymol from script regardless of ray flag (tested with
> > > ray=1, ray=0, without ray as in you case etc :-)
> > > I am going to try open source pymol!
> > > Cheers,
> > > J
> > >
> > > вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
> > > <Bla...@ou...>:
> > > >
> > > > Hi Jeff,
> > > >
> > > > I do not know the answer to your question. This is a work around.
> > > > Try dropping ray=0 and adding the draw command with the dimensions
> in pixels (width, height).
> > > >
> > > > cmd.draw(1600,1600);cmd.png('test1600.png')
> > > >
> > > > I would not use the Educational PyMOL for the kind of serious work
> that you are trying to do.
> > > > The PyMOL Wiki has several pages about open source versions of PyMOL.
> > > > Use one of those instead.
> > > >
> > > > 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: Jeff Saxon [jms...@gm...]
> > > > Sent: Tuesday, October 20, 2020 5:24 AM
> > > > To: pymol-users
> > > > Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
> > > >
> > > > hello,
> > > > I am using educational version of Pymol to generate png image of
> > > > protein-ligand complex
> > > >
> > > > First, there are no problems in the case of PNG command from pymol's
> > > > GUI. However if I run the same from script from terminal:
> > > >
> > > >   MacPyMOL -c -d "
> > > >   from pymol import cmd
> > > >   cmd.load('${pdb}')
> > > >   cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
> > > >   "
> > > > it  does not produce an image with the following message:
> > > >
> > > >  ! Ray tracing is not supported in Educational-Use-Only PyMOL. This
> version
> > > >
> > > >  ! has a reduced set of features compared to the full Incentive
> PyMOL version.
> > > >
> > > >  ! Please visit
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_edu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=wc9BhPQsimg9JTvkDK5bNL1mUeSQplkvyIKIvNtXP5A&e=
> for details. If you want to generate
> > > >
> > > >  ! figures for publication, then please obtain an academic license,
> > > >
> > > >  ! see
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_academic&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=AyyjBPHDzcks30uu67ZXdfPu0lx4oJroZwNpS2_J1Yc&e=
> > > >
> > > > note that ray is disabled in my command (since I do not need a HQ
> > > > image) and as I've mentioned there were no problems to create an
> image
> > > > from gui session using the same command. Could it be fixed for my
> case
> > > > or I need another version of Pymol ?
> > > >
> > > > Thank you !
> > > >
> > > >
> > > > _______________________________________________
> > > > PyMOL-users mailing list
> > > > Archives:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=-1_AqsLVgFJuceEfbluv4cGyYN2K2-202Lt95lZ68pE&e=
> > > > Unsubscribe:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=lOpzpCHVKu9bGPvhNAelWdeyEfwzTmXG7Z3ZFgOimQs&e=
> > >
> > >
> > > _______________________________________________
> > > 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

[PyMOL] Generation of images using png

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

Dear PyMol users,
I am generating png images of protein-ligand complex using png command
of pymol. This is the syntax that I am using from my bash script:

image=800
pdb='my.pdb'
# load pdb, split states, make image
  MacPyMOL -c -d "
  from pymol import cmd
  cmd.load('${pdb}')
  cmd.split_states('complex*')
  cmd.bg_color('white')
 cmd.draw(${image},${image});cmd.png('test.png',width=${image},height=${image},ray=1)
  "

Briefly, it works well but the time of the production of each image is
up to 10 minutes (in the case if I have many models in my.pdb). Is it
possible to speed PNG, while keeping the same resolution of image
(800x800)?

Cheers,
J.

Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

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

Right, thank you! just tested it with the recent Pymol version.
one question - is there any way to plot the name of the loaded pdb on
the image (produced by PNG command) in some automatic fashion (it
could be useful when I use it directly from terminal, without GUI)?

вт, 20 окт. 2020 г. в 14:46, Thomas Holder <tho...@sc...>:
>
> See last question here ("Ray tracing does not work"):
> https://pymol.org/edu/faq.php
>
> Cheers,
>   Thomas
>
> On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC)
> <Bla...@ou...> wrote:
> >
> > Hi Jeff,
> >
> > I have the incentive version of PyMOL.
> > It too is saving draw images with ray tracing when using the batch mode and also when using the pymol api in Jupyter.
> > As you report, saving a draw image from inside PyMOL works.
> >
> > This is a very annoying bug.
> > You should report it as an issue on the PyMOL github site.
> >
> > Perhaps this is not an issue with an order version of PyMOL.
> > Try one from before the switch from lines to cartoon as the default molecular representation (say version 2.1).
> >
> > 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: Jeff Saxon [jms...@gm...]
> > Sent: Tuesday, October 20, 2020 5:48 AM
> > To: Mooers, Blaine H.M.  (HSC); pymol-users
> > Subject: Re: [EXTERNAL] [PyMOL] png command in Educational Pymol
> >
> > Hi Blaine,
> > I've just checked on trial 26 day version of Pymol it use always RAY=1
> > while I run pymol from script regardless of ray flag (tested with
> > ray=1, ray=0, without ray as in you case etc :-)
> > I am going to try open source pymol!
> > Cheers,
> > J
> >
> > вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
> > <Bla...@ou...>:
> > >
> > > Hi Jeff,
> > >
> > > I do not know the answer to your question. This is a work around.
> > > Try dropping ray=0 and adding the draw command with the dimensions in pixels (width, height).
> > >
> > > cmd.draw(1600,1600);cmd.png('test1600.png')
> > >
> > > I would not use the Educational PyMOL for the kind of serious work that you are trying to do.
> > > The PyMOL Wiki has several pages about open source versions of PyMOL.
> > > Use one of those instead.
> > >
> > > 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: Jeff Saxon [jms...@gm...]
> > > Sent: Tuesday, October 20, 2020 5:24 AM
> > > To: pymol-users
> > > Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
> > >
> > > hello,
> > > I am using educational version of Pymol to generate png image of
> > > protein-ligand complex
> > >
> > > First, there are no problems in the case of PNG command from pymol's
> > > GUI. However if I run the same from script from terminal:
> > >
> > >   MacPyMOL -c -d "
> > >   from pymol import cmd
> > >   cmd.load('${pdb}')
> > >   cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
> > >   "
> > > it  does not produce an image with the following message:
> > >
> > >  ! Ray tracing is not supported in Educational-Use-Only PyMOL. This version
> > >
> > >  ! has a reduced set of features compared to the full Incentive PyMOL version.
> > >
> > >  ! Please visit https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_edu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=wc9BhPQsimg9JTvkDK5bNL1mUeSQplkvyIKIvNtXP5A&e=  for details. If you want to generate
> > >
> > >  ! figures for publication, then please obtain an academic license,
> > >
> > >  ! see https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_academic&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=AyyjBPHDzcks30uu67ZXdfPu0lx4oJroZwNpS2_J1Yc&e=
> > >
> > > note that ray is disabled in my command (since I do not need a HQ
> > > image) and as I've mentioned there were no problems to create an image
> > > from gui session using the same command. Could it be fixed for my case
> > > or I need another version of Pymol ?
> > >
> > > Thank you !
> > >
> > >
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=-1_AqsLVgFJuceEfbluv4cGyYN2K2-202Lt95lZ68pE&e=
> > > Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=lOpzpCHVKu9bGPvhNAelWdeyEfwzTmXG7Z3ZFgOimQs&e=
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Visualisation of ligand clusters

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

Dear Pymol Users,

I am dealing with the analysis of protein-ligand binding predicted by
Auto-Dock, mainly focusing on the visualization of ligand clusters on
the surface of the receptor.

Assuming that I have in current pymol session several distinct
clusters of ligand, would it be possible to color each of the cluster
automatically using some dynamical selection to discriminate between
structures within each of the cluster (e.g. based on the distances) ?
For example having 3 distinct clusters (on the distance of 5A between
each other) composed on 10, 5 and 5 structures I would like to colour
them in blue, red in yellow.
Looking forward to hearing your ideas!
Cheers,
J

Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

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

See last question here ("Ray tracing does not work"):
https://pymol.org/edu/faq.php

Cheers,
  Thomas

On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC)
<Bla...@ou...> wrote:
>
> Hi Jeff,
>
> I have the incentive version of PyMOL.
> It too is saving draw images with ray tracing when using the batch mode and also when using the pymol api in Jupyter.
> As you report, saving a draw image from inside PyMOL works.
>
> This is a very annoying bug.
> You should report it as an issue on the PyMOL github site.
>
> Perhaps this is not an issue with an order version of PyMOL.
> Try one from before the switch from lines to cartoon as the default molecular representation (say version 2.1).
>
> 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: Jeff Saxon [jms...@gm...]
> Sent: Tuesday, October 20, 2020 5:48 AM
> To: Mooers, Blaine H.M.  (HSC); pymol-users
> Subject: Re: [EXTERNAL] [PyMOL] png command in Educational Pymol
>
> Hi Blaine,
> I've just checked on trial 26 day version of Pymol it use always RAY=1
> while I run pymol from script regardless of ray flag (tested with
> ray=1, ray=0, without ray as in you case etc :-)
> I am going to try open source pymol!
> Cheers,
> J
>
> вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
> <Bla...@ou...>:
> >
> > Hi Jeff,
> >
> > I do not know the answer to your question. This is a work around.
> > Try dropping ray=0 and adding the draw command with the dimensions in pixels (width, height).
> >
> > cmd.draw(1600,1600);cmd.png('test1600.png')
> >
> > I would not use the Educational PyMOL for the kind of serious work that you are trying to do.
> > The PyMOL Wiki has several pages about open source versions of PyMOL.
> > Use one of those instead.
> >
> > 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: Jeff Saxon [jms...@gm...]
> > Sent: Tuesday, October 20, 2020 5:24 AM
> > To: pymol-users
> > Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
> >
> > hello,
> > I am using educational version of Pymol to generate png image of
> > protein-ligand complex
> >
> > First, there are no problems in the case of PNG command from pymol's
> > GUI. However if I run the same from script from terminal:
> >
> >   MacPyMOL -c -d "
> >   from pymol import cmd
> >   cmd.load('${pdb}')
> >   cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
> >   "
> > it  does not produce an image with the following message:
> >
> >  ! Ray tracing is not supported in Educational-Use-Only PyMOL. This version
> >
> >  ! has a reduced set of features compared to the full Incentive PyMOL version.
> >
> >  ! Please visit https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_edu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=wc9BhPQsimg9JTvkDK5bNL1mUeSQplkvyIKIvNtXP5A&e=  for details. If you want to generate
> >
> >  ! figures for publication, then please obtain an academic license,
> >
> >  ! see https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_academic&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=AyyjBPHDzcks30uu67ZXdfPu0lx4oJroZwNpS2_J1Yc&e=
> >
> > note that ray is disabled in my command (since I do not need a HQ
> > image) and as I've mentioned there were no problems to create an image
> > from gui session using the same command. Could it be fixed for my case
> > or I need another version of Pymol ?
> >
> > Thank you !
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=-1_AqsLVgFJuceEfbluv4cGyYN2K2-202Lt95lZ68pE&e=
> > Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=lOpzpCHVKu9bGPvhNAelWdeyEfwzTmXG7Z3ZFgOimQs&e=
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] [EXTERNAL] Re: Open source Pymol for MAC

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

PyMOL from macports has been rock solid for several years.

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: Jeff Saxon [jms...@gm...]
Sent: Tuesday, October 20, 2020 6:01 AM
To: Michel Rickhaus; pymol-users
Subject: [EXTERNAL] Re: [PyMOL] Open source Pymol for MAC

hey Michel,

I always use homebrew without sudo, since

Error: Running Homebrew as root is extremely dangerous and no longer supported.

As Homebrew does not drop privileges on installation you would be giving all

build scripts full access to your system.

вт, 20 окт. 2020 г. в 12:55, Michel Rickhaus <mic...@gm...>:
>
> Have you tried running it with sudo?
>
> Cheers
> Michel
>
> On Tue, 20 Oct 2020 at 12:53, Jeff Saxon <jms...@gm...> wrote:
>>
>> Hello,
>>
>> I am trying to install Open source version of Pymol on my mac using
>> recommended method. Although I've never had problems with brew, here I
>> got the following error message:
>>
>>  brew install brewsci/bio/pymol
>>
>> touch: /usr/local/Homebrew/.git/FETCH_HEAD: Permission denied
>>
>> touch: /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/.git/FETCH_HEAD:
>> Permission denied
>>
>> fatal: Unable to create '/usr/local/Homebrew/.git/index.lock': Permission denied
>>
>> fatal: Unable to create '/usr/local/Homebrew/.git/index.lock': Permission denied
>>
>> error: could not lock config file .git/config: Permission denied
>>
>> ==> Tapping brewsci/bio
>>
>> fatal: could not create leading directories of
>> '/usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio': Permission
>> denied
>>
>> Error: Failure while executing; `git clone
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_brewsci_homebrew-2Dbio&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=nwRA7SQtfnpsl0MGmxQ3Q5hdWE5Ma6DXH_iA8L5SSj8&s=qUwOx0avPN9QggLWYC9Tygzn05NqDQ6vzrR9M8ruBWs&e=
>> /usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio` exited with
>> 128.
>>
>> Could you suggest me another solution?
>> Cheers,
>> J
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=nwRA7SQtfnpsl0MGmxQ3Q5hdWE5Ma6DXH_iA8L5SSj8&s=6QikLJh-F0382M3vFKG773RyijDvNl87MAys2O_nNR4&e=
>> Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=nwRA7SQtfnpsl0MGmxQ3Q5hdWE5Ma6DXH_iA8L5SSj8&s=bGeV5mP_nWGRfH693DOtYhMGjHgz9OOdrjhVIMLCnxc&e=


_______________________________________________
PyMOL-users mailing list
Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=nwRA7SQtfnpsl0MGmxQ3Q5hdWE5Ma6DXH_iA8L5SSj8&s=6QikLJh-F0382M3vFKG773RyijDvNl87MAys2O_nNR4&e=
Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=nwRA7SQtfnpsl0MGmxQ3Q5hdWE5Ma6DXH_iA8L5SSj8&s=bGeV5mP_nWGRfH693DOtYhMGjHgz9OOdrjhVIMLCnxc&e=

Re: [PyMOL] [EXTERNAL] png command in Educational Pymol

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

Hi Jeff,

I have the incentive version of PyMOL.
It too is saving draw images with ray tracing when using the batch mode and also when using the pymol api in Jupyter.
As you report, saving a draw image from inside PyMOL works.

This is a very annoying bug.
You should report it as an issue on the PyMOL github site.

Perhaps this is not an issue with an order version of PyMOL.
Try one from before the switch from lines to cartoon as the default molecular representation (say version 2.1).

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: Jeff Saxon [jms...@gm...]
Sent: Tuesday, October 20, 2020 5:48 AM
To: Mooers, Blaine H.M.  (HSC); pymol-users
Subject: Re: [EXTERNAL] [PyMOL] png command in Educational Pymol

Hi Blaine,
I've just checked on trial 26 day version of Pymol it use always RAY=1
while I run pymol from script regardless of ray flag (tested with
ray=1, ray=0, without ray as in you case etc :-)
I am going to try open source pymol!
Cheers,
J

вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
<Bla...@ou...>:
>
> Hi Jeff,
>
> I do not know the answer to your question. This is a work around.
> Try dropping ray=0 and adding the draw command with the dimensions in pixels (width, height).
>
> cmd.draw(1600,1600);cmd.png('test1600.png')
>
> I would not use the Educational PyMOL for the kind of serious work that you are trying to do.
> The PyMOL Wiki has several pages about open source versions of PyMOL.
> Use one of those instead.
>
> 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: Jeff Saxon [jms...@gm...]
> Sent: Tuesday, October 20, 2020 5:24 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] png command in Educational Pymol
>
> hello,
> I am using educational version of Pymol to generate png image of
> protein-ligand complex
>
> First, there are no problems in the case of PNG command from pymol's
> GUI. However if I run the same from script from terminal:
>
>   MacPyMOL -c -d "
>   from pymol import cmd
>   cmd.load('${pdb}')
>   cmd.png('${storage}/${experiment}/${pdb_name}.png',ray=0)
>   "
> it  does not produce an image with the following message:
>
>  ! Ray tracing is not supported in Educational-Use-Only PyMOL. This version
>
>  ! has a reduced set of features compared to the full Incentive PyMOL version.
>
>  ! Please visit https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_edu&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=wc9BhPQsimg9JTvkDK5bNL1mUeSQplkvyIKIvNtXP5A&e=  for details. If you want to generate
>
>  ! figures for publication, then please obtain an academic license,
>
>  ! see https://urldefense.proofpoint.com/v2/url?u=http-3A__pymol.org_academic&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=AyyjBPHDzcks30uu67ZXdfPu0lx4oJroZwNpS2_J1Yc&e=
>
> note that ray is disabled in my command (since I do not need a HQ
> image) and as I've mentioned there were no problems to create an image
> from gui session using the same command. Could it be fixed for my case
> or I need another version of Pymol ?
>
> Thank you !
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=-1_AqsLVgFJuceEfbluv4cGyYN2K2-202Lt95lZ68pE&e=
> Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ekV4vGVtZ_Ip0bd5oppJvQFpcvZkMLPz2SnRpDwdiT0&s=lOpzpCHVKu9bGPvhNAelWdeyEfwzTmXG7Z3ZFgOimQs&e=

Re: [PyMOL] Open source Pymol for MAC

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

hey Michel,

I always use homebrew without sudo, since

Error: Running Homebrew as root is extremely dangerous and no longer supported.

As Homebrew does not drop privileges on installation you would be giving all

build scripts full access to your system.

вт, 20 окт. 2020 г. в 12:55, Michel Rickhaus <mic...@gm...>:
>
> Have you tried running it with sudo?
>
> Cheers
> Michel
>
> On Tue, 20 Oct 2020 at 12:53, Jeff Saxon <jms...@gm...> wrote:
>>
>> Hello,
>>
>> I am trying to install Open source version of Pymol on my mac using
>> recommended method. Although I've never had problems with brew, here I
>> got the following error message:
>>
>>  brew install brewsci/bio/pymol
>>
>> touch: /usr/local/Homebrew/.git/FETCH_HEAD: Permission denied
>>
>> touch: /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/.git/FETCH_HEAD:
>> Permission denied
>>
>> fatal: Unable to create '/usr/local/Homebrew/.git/index.lock': Permission denied
>>
>> fatal: Unable to create '/usr/local/Homebrew/.git/index.lock': Permission denied
>>
>> error: could not lock config file .git/config: Permission denied
>>
>> ==> Tapping brewsci/bio
>>
>> fatal: could not create leading directories of
>> '/usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio': Permission
>> denied
>>
>> Error: Failure while executing; `git clone
>> https://github.com/brewsci/homebrew-bio
>> /usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio` exited with
>> 128.
>>
>> Could you suggest me another solution?
>> Cheers,
>> J
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Open source Pymol for MAC

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

Hello,

I am trying to install Open source version of Pymol on my mac using
recommended method. Although I've never had problems with brew, here I
got the following error message:

 brew install brewsci/bio/pymol

touch: /usr/local/Homebrew/.git/FETCH_HEAD: Permission denied

touch: /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/.git/FETCH_HEAD:
Permission denied

fatal: Unable to create '/usr/local/Homebrew/.git/index.lock': Permission denied

fatal: Unable to create '/usr/local/Homebrew/.git/index.lock': Permission denied

error: could not lock config file .git/config: Permission denied

==> Tapping brewsci/bio

fatal: could not create leading directories of
'/usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio': Permission
denied

Error: Failure while executing; `git clone
https://github.com/brewsci/homebrew-bio
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio` exited with
128.

Could you suggest me another solution?
Cheers,
J