Re: [PyMOL] how to convert .pse to html?

2017-01-25 Thread Robert Hanson 
Albert, I just note that JSmol reads PyMOL PSE files directly - fully
JavaScript/HTML5 - and allows interactive viewing of them in JavaScript as
well as all the functionality of Jmol; nothing to change in terms of the
PyMOL file. Just load it.

Of course, not every capability of PyMOL is reproduced. It's a moving
target.
​
Bob Hanson
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] how to convert .pse to html?

2017-01-25 Thread Thomas Holder 
Hi Albert,

For batch processing (no GUI), run PyMOL with -c. See also 
https://pymolwiki.org/index.php/Command_Line_Options

I fixed the script, it was written for an old PyMOL version.

Cheers,
  Thomas

On 25 Jan 2017, at 17:01, Albert  wrote:

> BTW, I try to run the example command line, but it always failed with 
> messages:
> 
> 
> PyMOL>pymol2glmol 1tqn
> Traceback (most recent call last):
>  File "/usr/lib64/python2.7/site-packages/pymol/parser.py", line 256, in parse
>self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>  File "/home/albert/install/pymol/Pymol-script-repo/pymol2glmol.py", line 
> 152, in dump_rep
>int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))
> IndexError: tuple index out of range
> 
> 
> Do you have any idea what's the problem?
> 
> THX again.
> 
> 
> On 01/25/2017 10:46 PM, Thomas Holder wrote:
>> Hi Albert,
>> 
>> What kind of HTML content do you expect? A page with a PNG image? Or an 
>> interactive 3D model? Check out 
>> this:https://pymolwiki.org/index.php/Pymol2glmol
>> 
>> Cheers,
>>   Thomas

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] how to convert .pse to html?

2017-01-25 Thread Albert 
BTW, I try to run the example command line, but it always failed with 
messages:


PyMOL>pymol2glmol 1tqn
Traceback (most recent call last):
   File "/usr/lib64/python2.7/site-packages/pymol/parser.py", line 256, 
in parse
 self.result=apply(layer.kw[0],layer.args,layer.kw_args)
   File "/home/albert/install/pymol/Pymol-script-repo/pymol2glmol.py", 
line 152, in dump_rep
 int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2])))
IndexError: tuple index out of range


Do you have any idea what's the problem?

THX again.


On 01/25/2017 10:46 PM, Thomas Holder wrote:
> Hi Albert,
>
> What kind of HTML content do you expect? A page with a PNG image? Or an 
> interactive 3D model? Check out 
> this:https://pymolwiki.org/index.php/Pymol2glmol
>
> Cheers,
>Thomas


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] how to convert .pse to html?

2017-01-25 Thread Albert 
Hi Thomas,

Thanks a lot for your information. I know this command and that's what I 
needed.

However, I don't what to open the PyMOL GUI. Is it possible that we run 
PyMOL with a text mode and convert the .pse file directly to a .html file?

Thanks again.

Albert



On 01/25/2017 10:46 PM, Thomas Holder wrote:
> Hi Albert,
>
> What kind of HTML content do you expect? A page with a PNG image? Or an 
> interactive 3D model? Check out 
> this:https://pymolwiki.org/index.php/Pymol2glmol
>
> Cheers,
>Thomas


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] unable to initialize pymol plugin

2017-01-25 Thread Thomas Holder 
Hi Hena,

You're probably missing additional module requirements for these plugins. To 
get a meaningful stacktrace, import the plugin modules on the PyMOL command 
line. E.g.:

import pmg_tk.startup.mtsslDockGui

For 3D stereo: Have you tried "Display > Stereo" from the menu?

Cheers,
  Thomas

On 21 Jan 2017, at 18:09, Hena Dutta  wrote:

> Dear Users,
> Could someone help to solve the following initializing problem? I am using a 
> Toshiba Qosmio laptop. Also how can I see 3d here? 
> Thank you in advance.
> Hena
> 
>  PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
>  Copyright (c) Schrodinger, LLC.
>  All Rights Reserved.
>  
> Created by Warren L. DeLano, Ph.D. 
>  
> PyMOL is user-supported open-source software.  Although some versions
> are freely available, PyMOL is not in the public domain.
>  
> If PyMOL is helpful in your work or study, then please volunteer 
> support for our ongoing efforts to create open and affordable scientific
> software by purchasing a PyMOL Maintenance and/or Support subscription.
>  
> More information can be found at "http://www.pymol.org;.
>  
> Enter "help" for a list of commands.
> Enter "help " for information on a specific command.
>  
>  Hit ESC anytime to toggle between text and graphics.
>  
>  Detected OpenGL version 2.0 or greater. Shaders available.
>  Detected GLSL version 4.50.
>  OpenGL graphics engine:
>   GL_VENDOR:   NVIDIA Corporation
>   GL_RENDERER: GeForce GTX 670M/PCIe/SSE2
>   GL_VERSION:  4.5.0 NVIDIA 369.09
>  Detected 8 CPU cores.  Enabled multithreaded rendering.
>  OpenGL quad-buffer stereo 3D detected and enabled.
>  Executive: Loading version 1.600 session...
> Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui).
> Unable to initialize plugin 'mtsslWizard' (pmg_tk.startup.mtsslWizard).
> Unable to initialize plugin 'mtsslPlotter' (pmg_tk.startup.mtsslPlotter).
> Unable to initialize plugin 'mtsslTrilaterate' 
> (pmg_tk.startup.mtsslTrilaterate).

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] how to convert .pse to html?

2017-01-25 Thread Thomas Holder 
Hi Albert,

What kind of HTML content do you expect? A page with a PNG image? Or an 
interactive 3D model? Check out this: 
https://pymolwiki.org/index.php/Pymol2glmol

Cheers,
  Thomas

On 23 Jan 2017, at 16:11, Albert  wrote:

> Hello,
> 
> I've got a pymol .pse file and I am just wondering how can we convert it 
> with a Linux command line directly to a .html file without opening pymol 
> GUI?
> 
> Thank you very much.
> 
> Albert

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] How to convert .mae files to .PDB

2017-01-25 Thread Thomas Holder 
Hi Himesh,

On the PyMOL command line, this should do the trick:

# load desmond trajectory
load  sample-out.cms, mytraj
load_traj sample_trj/clickme.dtr, mytraj

# save multi-model PDB file
save multi.pdb, mytraj, state=0

See also:
https://pymolwiki.org/index.php/Load_Traj#Examples
https://pymolwiki.org/index.php/Save

Cheers,
  Thomas

On 25 Jan 2017, at 03:46, Himesh Makala  wrote:

> Hello, 
> 
> I would like to convert the simulation output [which was performed by using 
> Desmond (maestro)] into .PDB format. It will be very helpful if anyone help 
> me out with the same.
> 
> Thanks a lot,
> 
> Himesh
> 
> -- 
> 
> Thanks & Regards,
> 
> Himesh Makala

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] How to convert .mae files to .PDB

2017-01-25 Thread Himesh Makala 
Hello,

I would like to convert the simulation output [which was performed by using
Desmond (maestro)] into .PDB format. It will be very helpful if anyone help
me out with the same.

Thanks a lot,

Himesh

-- 

Thanks & Regards,

Himesh Makala
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net