pymol-users Mailing List for PyMOL Molecular Graphics System

Dear Stephen,

an alternative to get help is to either use the Help forum<" rel="nofollow">http://insilab.org/help.php> or write to the author whose email is also available on the Help forum.

I am not a user of Lisica specifically so I cannot help you directly.

Kind regards,
Matic


On 26. 01. 2017 15:35, S. P. Molnar wrote:

Linux PyMol v-1.8.4.0

I have installed the LISICA module with no warning or error messages.

Unfortunately qwhen I try to use the plugin I get a 'No module named
License' error.

Here is the entire error message:

Error: 2
<type 'exceptions.ImportError'> Exception in Tk callback
   Function: <function <lambda> at 0x7f9b800706e0> (type: <type 'function'>)
   Args: ()
Traceback (innermost last):
   File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
     return apply(self.func, args)
   File "/home/comp/.pymol/startup/lisica.py", line 202, in <lambda>
     self.menuBar.addmenuitem('Plugin', 'command', 'LiSiCA', label =
'LiSiCA', command=lambda s=self: main())
   File "/home/comp/.pymol/startup/lisica.py", line 198, in main
     run()
   File "/home/comp/.pymol/startup/lisica.py", line 176, in run
     import License
<type 'exceptions.ImportError'>: No module named License

Comments and/or solutions?

Thanks in advance.

Hi Cris
Please include the ray=1 option in your png test.png, dpi=300 command or
use the set opaque_background, off instead of the set
ray_opaque_background, off command.

Commands to create a PNG file with a transparent background:

set opaque_background, off

png test.png, dpi=300, ray=1

*PNG file creation*
https://pymolwiki.org/index.php/Png

*Opaque background*

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

Emilio
​

On Fri, Jan 27, 2017 at 12:27 PM, cristopher garduno <gar...@gm...
> wrote:

> Hello, my name is Cris and I am attempting to save a version of my protein
> with a transparent background. I have tried using the commands
>
>
> set ray_opaque_background, off
>
> png test.png, dpi=300
>
>
> but this doesn't seem to work. I have the educational version of PyMol, is
> this the reason that I'm unable to use the option for a transparent
> background?
>
> Thank you,
> Cris
>
> --
> Cristopher D. Garduno Luna
> Neuroscience, B.S.
> Class of 2017
> University of California, Los Angeles
> gar...@gm...
> Curriculum Vitae <" rel="nofollow">https://sites.google.com/site/1992cgarduno/cv>
>
> ------------------------------------------------------------
> ------------------
> 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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Laurie,

The list of bonds is accessible with cmd.get_model(), see
https://pymolwiki.org/index.php/Get_Model

PyMOL> m = cmd.get_model()
PyMOL> print m.bond[0].index
[0, 1]
PyMOL> print m.bond[0].order
1

Cheers,
  Thomas

On 26 Jan 2017, at 13:50, Laurence Williams <Wil...@ca...> wrote:

> Dear pymol users,
> 
> I understand that pymol does not explicitly need connectivity data to visualise molecules as bonds are drawn when two atoms are within in a given distance. However, once those bonds are drawn for the molecule, is connectivity data stored somewhere whilst the file is in use? I ask with the aim to extract that data into a python object.
> 
> Thanks
> Laurie

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello, my name is Cris and I am attempting to save a version of my protein
with a transparent background. I have tried using the commands


set ray_opaque_background, off

png test.png, dpi=300


but this doesn't seem to work. I have the educational version of PyMol, is
this the reason that I'm unable to use the option for a transparent
background?

Thank you,
Cris

-- 
Cristopher D. Garduno Luna
Neuroscience, B.S.
Class of 2017
University of California, Los Angeles
gar...@gm...
Curriculum Vitae <" rel="nofollow">https://sites.google.com/site/1992cgarduno/cv>

​Hey Tsjerk!
So good to connect again here!
​I will look up Mole plugin for possible channels, come back and write here
again and a script would of course be very nice to have.

Thanks for the help.
Kanika

On Thu, Jan 26, 2017 at 10:39 PM, Tsjerk Wassenaar <ts...@gm...>
wrote:

> Hi Kanika,
>
> That's been quite a while! Nice to see you again and to see you're still
> your determined self, still a bit impatient, reposting a message within a
> day :)
>
> The issue with the second question is not about center_of_mass, but about
> center_of_no_mass, which is a bit harder (and I don't think there's an
> import for that). You can have a look at hollow.sourceforge.net or so. If
> they're channels, connected to the surface of the protein, you can also
> have a look at the Mole plugin on the Pymol wiki. Alternatively, I have
> some bits of code that could be forged together to get something similar
> and which would allow for getting a center_of_no_mass, but I probably won't
> be able to do the forging before next week.
>
> Hope it helps,
>
> Tsjerk
>
> On Thu, Jan 26, 2017 at 10:14 PM, Hitesh Patel <hit...@gm...>
> wrote:
>
>> Hi,
>>
>> For your 2nd question:
>> You can make pseudoatom at Center of mass or center of geometry (for an
>> object or probably selection too) using the following script:
>> https://pymolwiki.org/index.php/Center_of_mass
>>
>> In your case you mat try:
>>
>> import center_of_mass
>>
>> com SelectionObjectName, state=1#Create a pseudoatom representing the Object COG and store it as "SelectionObjectName_COM"
>>
>>
>>
>> On Thu, Jan 26, 2017 at 4:52 AM kanika sharma <ksh...@gm...>
>> wrote:
>>
>>> Dear PyMol Users,
>>>
>>> I am struggling here two things.
>>> 1). I want to place a pseudoatom in the charge centre of a non aromatic
>>> residue, like arginine.
>>> 2). Is it possible to place another pseudoatom in the centre of a cavity
>>> in the protein? I am thinking how can I define the co ordinates of the
>>> position where I wan t to place the pseudoatom?
>>>
>>> ​Thanks ​
>>>
>>> --
>>> *Best,*
>>>
>>> *Kanika*
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> 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 (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>
>> --
>> Regards,
>>
>> Dr. Hitesh Patel
>> Post-Doctoral Fellow,
>> CADD Group,
>> Building 376, Room: 205A
>> Chemical Biology laboratory,
>> Center for Cancer Research,
>> National Cancer Institute,
>> Frederick, MD-21702
>>
>> Work: +1 301 846 5993 <(301)%20846-5993>
>> Mob.: +1 240 367 5208 <(240)%20367-5208>
>> Website: http://www.hiteshpatel379.com/
>> Email: hit...@ni...
>>
>> ------------------------------------------------------------
>> ------------------
>> 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 (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>


-- 
*Best,*

*Kanika Sharma*

Is there a way to calculate COM for a tunnel?

On Thu, Jan 26, 2017 at 10:14 PM, Hitesh Patel <hit...@gm...>
wrote:

> Hi,
>
> For your 2nd question:
> You can make pseudoatom at Center of mass or center of geometry (for an
> object or probably selection too) using the following script:
> https://pymolwiki.org/index.php/Center_of_mass
>
> In your case you mat try:
>
> import center_of_mass
>
> com SelectionObjectName, state=1#Create a pseudoatom representing the Object COG and store it as "SelectionObjectName_COM"
>
>
>
> On Thu, Jan 26, 2017 at 4:52 AM kanika sharma <ksh...@gm...>
> wrote:
>
>> Dear PyMol Users,
>>
>> I am struggling here two things.
>> 1). I want to place a pseudoatom in the charge centre of a non aromatic
>> residue, like arginine.
>> 2). Is it possible to place another pseudoatom in the centre of a cavity
>> in the protein? I am thinking how can I define the co ordinates of the
>> position where I wan t to place the pseudoatom?
>>
>> ​Thanks ​
>>
>> --
>> *Best,*
>>
>> *Kanika*
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> 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 (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
> --
> Regards,
>
> Dr. Hitesh Patel
> Post-Doctoral Fellow,
> CADD Group,
> Building 376, Room: 205A
> Chemical Biology laboratory,
> Center for Cancer Research,
> National Cancer Institute,
> Frederick, MD-21702
>
> Work: +1 301 846 5993 <+1%20301-846-5993>
> Mob.: +1 240 367 5208 <+1%20240-367-5208>
> Website: http://www.hiteshpatel379.com/
> Email: hit...@ni...
>



-- 
*Best,*

*Kanika Sharma*

Thanks Jared.

First part, is perfect. So pseudo atom lies between nitrogen atoms.
Second part, I don't have specific xyz coordinates because it is centre of
a tunnel in the protein and that's the struggle.

On Thu, Jan 26, 2017 at 10:01 PM, Sampson, Jared M. <
jm...@cu...> wrote:

> Hi Kanika -
>
> You can get more information on the wiki: https://pymolwiki.org/
> index.php/Pseudoatom.
>
> To answer your specific questions, to make a pseudoatom between the two
> terminal Ns of Arg 100 on chain A of myobj:
>
> ```
> pseudoatom my_ps1, myobj and chain A and resi 100 and name NH1+NH2
> ```
>
> and to place a pseudoatom at a specific XYZ coordinate, pass the `pos`
> parameter with a 3-tuple of floats:
>
> ```
> pseudoatom my_ps2, pos=[1.0, 2.0, 3.0]
> ```
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Jan 26, 2017, at 8:58 AM, kanika sharma <ksh...@gm...> wrote:
>
>
>
> Dear PyMol Users,
>
> ​I asked this question but no body replied so I am trying again. ​
>
> I am struggling here two things.
> 1). I want to place a pseudo
> ​ ​
> atom in the charge centre of a non aromatic residue, like arginine.
> 2). Is it possible to place
> ​a
>  pseudo
> ​ ​
> atom in the centre of a cavity in the protein? I am thinking how can I
> define the co ordinates of the position where I wan t to place the pseudo
> ​ ​
> atom?
>
> ​Thanks ​
>
> --
> *Best,*
>
> *Kanika*
> ------------------------------------------------------------
> ------------------
> 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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>


-- 
*Best,*

*Kanika Sharma*

Hi Kanika,

That's been quite a while! Nice to see you again and to see you're still
your determined self, still a bit impatient, reposting a message within a
day :)

The issue with the second question is not about center_of_mass, but about
center_of_no_mass, which is a bit harder (and I don't think there's an
import for that). You can have a look at hollow.sourceforge.net or so. If
they're channels, connected to the surface of the protein, you can also
have a look at the Mole plugin on the Pymol wiki. Alternatively, I have
some bits of code that could be forged together to get something similar
and which would allow for getting a center_of_no_mass, but I probably won't
be able to do the forging before next week.

Hope it helps,

Tsjerk

On Thu, Jan 26, 2017 at 10:14 PM, Hitesh Patel <hit...@gm...>
wrote:

> Hi,
>
> For your 2nd question:
> You can make pseudoatom at Center of mass or center of geometry (for an
> object or probably selection too) using the following script:
> https://pymolwiki.org/index.php/Center_of_mass
>
> In your case you mat try:
>
> import center_of_mass
>
> com SelectionObjectName, state=1#Create a pseudoatom representing the Object COG and store it as "SelectionObjectName_COM"
>
>
>
> On Thu, Jan 26, 2017 at 4:52 AM kanika sharma <ksh...@gm...>
> wrote:
>
>> Dear PyMol Users,
>>
>> I am struggling here two things.
>> 1). I want to place a pseudoatom in the charge centre of a non aromatic
>> residue, like arginine.
>> 2). Is it possible to place another pseudoatom in the centre of a cavity
>> in the protein? I am thinking how can I define the co ordinates of the
>> position where I wan t to place the pseudoatom?
>>
>> ​Thanks ​
>>
>> --
>> *Best,*
>>
>> *Kanika*
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> 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 (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
> --
> Regards,
>
> Dr. Hitesh Patel
> Post-Doctoral Fellow,
> CADD Group,
> Building 376, Room: 205A
> Chemical Biology laboratory,
> Center for Cancer Research,
> National Cancer Institute,
> Frederick, MD-21702
>
> Work: +1 301 846 5993 <(301)%20846-5993>
> Mob.: +1 240 367 5208 <(240)%20367-5208>
> Website: http://www.hiteshpatel379.com/
> Email: hit...@ni...
>
> ------------------------------------------------------------
> ------------------
> 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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Hi,

For your 2nd question:
You can make pseudoatom at Center of mass or center of geometry (for an
object or probably selection too) using the following script:
https://pymolwiki.org/index.php/Center_of_mass

In your case you mat try:

import center_of_mass

com SelectionObjectName, state=1#Create a pseudoatom representing the
Object COG and store it as "SelectionObjectName_COM"



On Thu, Jan 26, 2017 at 4:52 AM kanika sharma <ksh...@gm...> wrote:

> Dear PyMol Users,
>
> I am struggling here two things.
> 1). I want to place a pseudoatom in the charge centre of a non aromatic
> residue, like arginine.
> 2). Is it possible to place another pseudoatom in the centre of a cavity
> in the protein? I am thinking how can I define the co ordinates of the
> position where I wan t to place the pseudoatom?
>
> ​Thanks ​
>
> --
> *Best,*
>
> *Kanika*
>
>
>
> ------------------------------------------------------------------------------
> 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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

-- 
Regards,

Dr. Hitesh Patel
Post-Doctoral Fellow,
CADD Group,
Building 376, Room: 205A
Chemical Biology laboratory,
Center for Cancer Research,
National Cancer Institute,
Frederick, MD-21702

Work: +1 301 846 5993
Mob.: +1 240 367 5208
Website: http://www.hiteshpatel379.com/
Email: hit...@ni...

Hi Kanika -

You can get more information on the wiki: https://pymolwiki.org/index.php/Pseudoatom.

To answer your specific questions, to make a pseudoatom between the two terminal Ns of Arg 100 on chain A of myobj:

```
pseudoatom my_ps1, myobj and chain A and resi 100 and name NH1+NH2
```

and to place a pseudoatom at a specific XYZ coordinate, pass the `pos` parameter with a 3-tuple of floats:

```
pseudoatom my_ps2, pos=[1.0, 2.0, 3.0]
```

Hope that helps.

Cheers,
Jared


On Jan 26, 2017, at 8:58 AM, kanika sharma <ksh...@gm...<mailto:ksh...@gm...>> wrote:



Dear PyMol Users,

​I asked this question but no body replied so I am trying again. ​

I am struggling here two things.
1). I want to place a pseudo
​ ​
atom in the charge centre of a non aromatic residue, like arginine.
2). Is it possible to place
​a
 pseudo
​ ​
atom in the centre of a cavity in the protein? I am thinking how can I define the co ordinates of the position where I wan t to place the pseudo
​ ​
atom?

​Thanks ​

--
Best,

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

Dear pymol users,

I understand that pymol does not explicitly need connectivity data to visualise molecules as bonds are drawn when two atoms are within in a given distance. However, once those bonds are drawn for the molecule, is connectivity data stored somewhere whilst the file is in use? I ask with the aim to extract that data into a python object.

Thanks
Laurie

Sent from my iPad

Linux PyMol v-1.8.4.0

I have installed the LISICA module with no warning or error messages.

Unfortunately qwhen I try to use the plugin I get a 'No module named 
License' error.

Here is the entire error message:

Error: 2
<type 'exceptions.ImportError'> Exception in Tk callback
   Function: <function <lambda> at 0x7f9b800706e0> (type: <type 'function'>)
   Args: ()
Traceback (innermost last):
   File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", 
line 1747, in __call__
     return apply(self.func, args)
   File "/home/comp/.pymol/startup/lisica.py", line 202, in <lambda>
     self.menuBar.addmenuitem('Plugin', 'command', 'LiSiCA', label = 
'LiSiCA', command=lambda s=self: main())
   File "/home/comp/.pymol/startup/lisica.py", line 198, in main
     run()
   File "/home/comp/.pymol/startup/lisica.py", line 176, in run
     import License
<type 'exceptions.ImportError'>: No module named License

Comments and/or solutions?

Thanks in advance.

-- 
Stephen P. Molnar, Ph.D.	Life is a fuzzy set
www.Molecular-Modeling.net	Stochastic and multivariate
(614)312-7528 (c)
Skype:  smolnar1

Dear PyMol Users,

​I asked this question but no body replied so I am trying again. ​

I am struggling here two things.
1). I want to place a pseudo
​ ​
atom in the charge centre of a non aromatic residue, like arginine.
2). Is it possible to place
​a
 pseudo
​ ​
atom in the centre of a cavity in the protein? I am thinking how can I
define the co ordinates of the position where I wan t to place the pseudo
​ ​
atom?

​Thanks ​

-- 
*Best,*

*Kanika*

Dear PyMol Users,

I am struggling here two things.
1). I want to place a pseudoatom in the charge centre of a non aromatic
residue, like arginine.
2). Is it possible to place another pseudoatom in the centre of a cavity in
the protein? I am thinking how can I define the co ordinates of the
position where I wan t to place the pseudoatom?

​Thanks ​

-- 
*Best,*

*Kanika*

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

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 <mai...@gm...> 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.

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

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

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 <hdu...@gm...> 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 <command-name>" 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.

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 <mai...@gm...> 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.

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 <hi...@sa...> 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.

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

Hi Filip,

This is already done. The update was in PyMOL 1.8.4.2 and in Open-Source PyMOL rev 4165. The object names are still the same, so it's backwards compatible. The only difference is the file format, previously we downloaded omap format, now it's ccp4 map format (larger files but higher data precision).

Cheers,
  Thomas

On 24 Jan 2017, at 12:42, Filip Leonarski <leo...@un...> wrote:

> Hi,
> 
> I'm writing in regards of downloading electron density maps in Pymol. As you know EDS is soon to be decomissioned and PDBe (PDB in Europe) is a new source of electron density maps for crystal structures. Is it possible with next update of Pymol to change "fetch xxxx, type=2fofc" command to get maps from PDBe instead of EDS. Is it also possible to leave old names "xxxx_2fofc" and "xxxx_fofc" (PDBe uses "xxxx" and "xxxx_diff" as map names), so scripts are backward compatible?
> 
> Thanks,
> Filip

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi,

I'm writing in regards of downloading electron density maps in Pymol. As
you know EDS is soon to be decomissioned and PDBe (PDB in Europe) is a new
source of electron density maps for crystal structures. Is it possible with
next update of Pymol to change "fetch xxxx, type=2fofc" command to get maps
from PDBe instead of EDS. Is it also possible to leave old names
"xxxx_2fofc" and "xxxx_fofc" (PDBe uses "xxxx" and "xxxx_diff" as map
names), so scripts are backward compatible?

Thanks,
Filip

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