[PyMOL] opensource for commercial use?

2015-07-03 Thread Albert
Hello:

I just got a question: can we use the open source version of pymol for 
commercial usage? Or can we develop some commercial tool based on Pymol?

thank you very much.

Albert

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[PyMOL] how can we change GUI font size?

2015-07-06 Thread Albert
Hello:

I notice that my screen resolution is too high that the font of pymol 
GUI looks extremely small. I am just wondering is it possible to 
increase them?

thank you very much.

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[PyMOL] problem of Pymol git install

2015-07-06 Thread Albert
Hello:

I've installed pymol git repo following steps:

http://www.pymolwiki.org/index.php/Git_install

However, when I start pymol, it always showed the following messages:

No module named tkintertable.Tables
Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui).
No module named wx
Unable to initialize plugin 'mtsslTrilaterate' 
(pmg_tk.startup.mtsslTrilaterate).

I am just wondering how can we solve the problem?

thank you very much.




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[PyMOL] how can we rotate torsion angle of a molecule?

2015-07-06 Thread Albert
Hello:

I am just wondering is it possible to rotate the torsion angle of a 
molecule in Pymol? I search in pymolwiki, and I only find how to 
translate a molecule or move the atom positions, but I didn't find 
anything about how to rotate a torsion angle of a molecule.

Meanwhile, I am just wondering is it possible for pymol give alternative 
rotamer conformation of a protein residue?

thanks a lot

Albert

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[PyMOL] GTX980Ti for Pymol 3D?

2015-10-28 Thread Albert
Hello:

Does anybody know whether Nvidia GTX980Ti support Pymol active stereo 
3D? I saw someone said that some GTX graphic card may also work, but I 
am not sure for this one.

Thx a lot

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Re: [PyMOL] Stacking Interactions

2015-11-09 Thread Albert
I think the major concern is how Pymol depicts the pi-pi stacking Of 
course we can identify such interaction immediately as soon as we open 
the system in Pymol.


However there is no any  components to indicate this, eg: we can depict 
the H-bond with a dash between two atoms but how could pi-pi interaction 
be depicted?




On 11/10/2015 07:03 AM, Osvaldo Martin wrote:

Hi Amali,

I am not aware that PyMOL has this feature implemented out-of-the-box. 
Nevertheless this can be done with PyMOL. A crude approximation will 
be to measure the distance between the center of aromatic rings and 
consider a pi-pi stacking for distances shorter than a threshold 
value. A better model will probably include a distance threshold and 
one or two angles in the definition.


Are you trying to estimate pi-pi stacking interactions in general or 
for a particular system?


Cheers,
Osvaldo.


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[PyMOL] how to setup environment for APBS?

2015-10-08 Thread Albert
Hello:

I noticed that each time when I try to use APBS plugin, pymol always ask 
to specify the location of:

apbs
psize.py
pdb2pqr.py

I am just wondering can we somehow write the location of those program 
into .pymolrc file so that each time Pymol APBS plugin can find it 
automatically?

thanks a lot

Albert

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[PyMOL] APBS problem

2015-10-08 Thread Albert
Hello:

I am trying to calculate the protein surface electstatic properities by 
APBS plugin in pymol. But it always failed with messages:

Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist?

Does anybody has any idea how to solve this problem?

thx a lot



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Re: [PyMOL] APBS problem

2015-10-08 Thread Albert


thanks a lot for reply.

Problem solved after I specify the maloc library path explicitly in my 
tcsh environment.


setenv FETK_LIBRARY /home/albert/install/apbs/apbs-1.4.0/lib



On 10/08/2015 05:02 PM, Andreas Forster wrote:

Hi Albert,

I apologize that I take your email for a grumpy old man's rant, but I 
feel this mailing list is getting washed out with poorly formulated 
questions.


What happened to specifying what OS you use, what version of PyMOL, 
what version of the apbs plugin.  Also, to give answers, it would help 
to know what settings you chose for the calculation of the 
electrostatic potential.  There's a bunch of buttons to click.  Which 
ones did you choose?  What step have you already taken to overcome the 
problem?


Basically, I'm asking new users to spend a leisurely coffee break 
reading http://www.catb.org/~esr/faqs/smart-questions.html 
<http://www.catb.org/%7Eesr/faqs/smart-questions.html> and then ask 
better question.


The answer to your problem: /tmp/1-PE0.dx needs to be generated.  
That's all I can infer from the information you gave.


All best.


Andreas


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[PyMOL] how to enable 3D

2015-10-19 Thread Albert
Hello:

I just notice that nowadays the webGL and xml5 technology developed so 
fast that many new tools emerging these days. I am really impressed by 
the GLMOL tool for pymol recently. It is really powerful.

I am just wondering is it possible to enable anaglyph or side by side 
stereo for GLMOL tool? I just find a  a tool based in GLmol, called 
iview which support such kind of function. Is it possible for the 
developer integrate them into GLmol python script so that the generated 
.html file can also support some simple stereo view?

Here is the link of website:

http://istar.cse.cuhk.edu.hk/iview/

and here is script for this tool

https://github.com/HongjianLi/istar/tree/master/public/iview

Thank you very much.

Albert

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Re: [PyMOL] pymol to webGL?

2015-10-19 Thread Albert

Dear Osvaldo:

Thanks a lot for further information.

I just run the command

|set pse_export_version, 1.72 |


before I load anything to pymol, then followed the step for exporting. 
But it still failed with messages:


Traceback (most recent call last):
  File "/home/albert/install/pymol/modules/pymol/parser.py", line 256, 
in parse

self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File "exportToWeb.py", line 119, in dump_rep
ret += parseObjMol(obj)
  File "exportToWeb.py", line 57, in parseObjMol
if (rep[7] == 1):
IndexError: list index out of range


Thank you very much.
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[PyMOL] pymol to webGL?

2015-10-17 Thread Albert

Hello:

I noticed that there is a plugin called

exportToWeb.py

I try to rum it with command:

python exportToWeb.py test.pse

However, no any new file generated I am just wondering how shall we 
use this script correctly?


thanks a lot

Albert

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Re: [PyMOL] pymol to webGL?

2015-10-17 Thread Albert

Thanks a lot for further advice.

Here is what I got:

PyMOL> run exportToWeb.py
PyMOL>exportToWeb my
Traceback (most recent call last):
  File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line 
256, in parse

self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File "exportToWeb.py", line 118, in dump_rep
ret += parseObjMol(obj)
  File "exportToWeb.py", line 50, in parseObjMol
if (rep[5] == 1):
TypeError: 'int' object has no attribute '__getitem__'


If possible, would you please give me some suggestions?

Thanks a lot

Albert




On 10/17/2015 04:36 PM, Osvaldo Martin wrote:


Hi Albert,

I do the following steps and I get a .html file as expected.

 1. I download and unpack this

<http://sourceforge.jp/projects/webglmol/downloads/54536/pymol-exporter-0.01.zip/>
file. The script there seems to be similar to the one you attached.
 2. Lauch PyMOL and do some stuff
 3. cd to the folder creating during unpacking
 4. run the script by doing
|run exportToWeb.py |
 5. then run the commnand
|exportToWeb PymolObjectName |
where PymolObjectName is the name of the pymol object you want to
export
 6. check the unpacked folder for a file with the name
PymolObjectName.html

Could you try to follow these steps and tell us what you get?

Cheers,

Osvaldo.



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[PyMOL] how to copy color?

2015-08-28 Thread Albert
Hello:

I've colored object1 in various color in different regions. I am just 
wondering how can we copy the color scheme for object1 to object2? 
Object 2 is the same protein with object1 but with different conformations.

Thank you very much

Albert

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[PyMOL] any hotkey?

2015-09-03 Thread Albert
Hello:

I am just wondering is there any hotkey in Pymol so that we can center 
in the Ligand automatically? For instance:

If I press keyboard "L", Pymol zoom to ligand binding pocket 
automatically

Thanks a lot

Albert

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[PyMOL] can we show ligand in 2D?

2015-09-14 Thread Albert
Hello:

I've got a 3D coordinate in 3D.  I am just wondering is it possible to 
show it in 2D diagram in Pymol for a ligand so that we can get more 
clear idea how exactly the ligand looks like?

thanks a lot

Albert

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[PyMOL] label

2015-09-16 Thread Albert
Hello:

Does anybody have any idea whether pymol could label the absolute 
configuration (R/S) for a chiarity atom?

Thank you very much.

Albert

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[PyMOL] pymol crashed reading any structure file

2015-12-13 Thread Albert
Dear:

I've compiled pymol-1.8.0 under my Linux X64 OS. I found that Pymol can 
start by command:

pymol

without any complaints or erros. However, when I try to load a .pdb file 
into pymol, pymol always failed with following messages:


---
stephen@linux:~/tmp> pymol 4eiy.pdb
  PyMOL(TM) Molecular Graphics System, Version 1.8.0.0.
  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 1.30.
  OpenGL graphics engine:
   GL_VENDOR:   VMware, Inc.
   GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.4, 256 bits)
   GL_VERSION:  2.1 Mesa 10.0.3
  Detected 4 CPU cores.  Enabled multithreaded rendering.
HEADERMEMBRANE PROTEIN06-APR-12   4EIY
TITLE CRYSTAL STRUCTURE OF THE CHIMERIC PROTEIN OF A2AAR-BRIL IN COMPLEX
TITLE2 WITH ZM241385 AT 1.8A RESOLUTION
COMPNDMOL_ID: 1;
COMPND   2 MOLECULE: ADENOSINE RECEPTOR A2A/SOLUBLE CYTOCHROME B562 CHIMERA;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: CYTOCHROME B-562;
COMPND   5 ENGINEERED: YES;
COMPND   6 MUTATION: YES
  ObjectMolecule: Read secondary structure assignments.
  ObjectMolecule: Read crystal symmetry information.
  CmdLoad: "4eiy.pdb" loaded as "4eiy".
/home/stephen/install/pymol-1.8.0/pymol: line 3: 10490 Segmentation 
fault  "/usr/bin/python" 
"/home/stephen/install/pymol-1.8.0/modules/pymol/__init__.py" "$@"
-

I am just wondering what's the problem? I also tried .cif, .mol2 files, 
and all of them failed.

thx a lot

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Re: [PyMOL] how to close displaying a molecule

2015-12-10 Thread Albert

just click the b.pdb on the Pymol object manager bar to undisplay it.

That's the basic of basic usage of Pymol. Wouldn't it be nice if you 
spend a few minutes to go through Pymol manual?




On 12/11/2015 08:19 AM, Smith Liu wrote:

Dear All,

Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close 
B.pdb and have only A.pdb displayed?


Smith



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[PyMOL] default fetch format

2015-11-19 Thread Albert
Hello:

I noticed that if we run command:

fetch 2ac1

to get PDB into pymol in Version 1.8.0, it downloaded .cif file by 
default. I am just wondering is it possible to change the default format 
as .pdb file?

thanks a lot

Albert

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Re: [PyMOL] problem of pymol 1.8

2015-11-18 Thread Albert
Hi Thomas:

thanks a lot for helpful advice.

HOwever, I got something new warnings:

No module named cPluginManager
Unable to initialize plugin 'xPyder' (pmg_tk.startup.xPyder).
No module named backend_wxagg
Unable to initialize plugin 'mtsslPlotter' (pmg_tk.startup.mtsslPlotter).

I google it, and cannot find any helpful information


thanks again

ALbert


On 11/18/2015 11:16 PM, Thomas Holder wrote:
> Hi Albert,
>
> These messages come from third-party plugins that you have installed, see:
> http://pymolwiki.org/index.php/MtsslDock
> http://pymolwiki.org/index.php/MtsslTrilaterate
>
> Cheers,
>Thomas


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[PyMOL] real time minization in Pymol

2015-11-23 Thread Albert
Hello:

I just found a a very nice module of pymol, called "Molecular 
Sculpting". However, according to the description in Pymolwiki, it works 
like a real-time energy minimizer, except that it isn't minimizing the 
energy. Instead, its just trying to return local atomic geometries 
(bonds, angles, chirality, planarity) to the configuration the molecules 
possess when they were first loaded into PyMOL.

So I am just wondering does the developer have any planning to improve 
this nice too? For instance introducing forcefiled for this tool (eg: 
Amber FF for protein, GAFF for the ligand). There is a "optimize" plugin 
in Pymol, maybe the developer can consider merge them together?

Thank you very much

Albert

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[PyMOL] can we clone representation?

2015-11-21 Thread Albert
Hello:

I've shown an object as cartoon and displaced sticks with various 
colors. I am just wondering, can we clone all representation from object 
1 to object 2 with some command in Pymol? As far as I known, this is 
possible in VMD:

http://www.ks.uiuc.edu/Research/vmd/plugins/clonerep/

Thank you very much

Albert

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Re: [PyMOL] default fetch format

2015-11-22 Thread Albert
Hi Thomas:

thanks a lot for helpful advice.

May I ask is there any superior features of mmCIF format against PDB format?

regards

Albert

On 11/22/2015 04:15 PM, Thomas Holder wrote:
> Hi Albert,
>
> Unfortunately the default fetch type can't be configured. But you can 
> override the fetch command. Example which you could place in your ~/.pymolrc 
> file:
>
> python
> from pymol import cmd
>
> def fetchpdb(*args, **kwargs):
>  if 'type' not in kwargs:
>  kwargs['type'] = 'pdb'
>  return cmd.fetch(*args, **kwargs)
>
> cmd.extend('fetch', fetchpdb)
> python end
>
> However, if you don't have a compelling reason to work with PDB instead of 
> mmCIF, then I recommend to give the new mmCIF default a try.
>
> Cheers,


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Re: [PyMOL] real time minization in Pymol

2015-11-23 Thread Albert
Yes, I also really love this function. However, for the sake of 
accuracy, I believe many users will also strongly demand for introducing 
forcefield for minimization..I am looking forward to see that 
"optimize" plugin would somehow merged into "Molecular Sculpting".At 
least, it is very easy and free to get access to Amber and GAFF forcefield.

Thanks again.

On 11/23/2015 05:07 PM, H. Adam Steinberg wrote:
> I would love to see this feature improved!
>
> Try it out if you have never used it. It works quite well. It is quite 
> processor intensive and it can take over your computer when it is running…. I 
> have also found when you uncheck it in the menu, it will still continue to 
> run and I end up force quitting to get it to stop.


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[PyMOL] VR for Pymol?

2016-06-17 Thread Albert
Hello:

Does anybody have any idea whether PyMol support Virtual Reality (VR)? 
Can we use the following VR devices to visualize PyMOl in computer?

http://www.polygon.com/2016/1/5/10719326/nvidia-virtual-reality-performance-power

https://www.youtube.com/watch?v=U4JPhUr_d7g

If yes, will any VR device on the market work for PyMol?

Thanks a lot

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[PyMOL] how to get an atom coordinates information

2016-02-25 Thread Albert
Hello:

I would like to know the XYZ information of a specific atom. I am just 
wondering how can we do this? Is there any command line?

thank you very much

Albert

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[PyMOL] how to convert .pse to html?

2017-01-23 Thread Albert
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


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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


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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


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Re: [PyMOL] New plugin: PyMOLProbity

2017-01-17 Thread Albert

fantastic job!!

Thanks a lot.

Albert

On 01/16/2017 10:16 PM, Sampson, Jared M. wrote:

Dear PyMOL Users,

I am pleased to introduce a new plugin called PyMOLProbity 
<https://github.com/jaredsampson/pymolprobity> which allows a PyMOL 
user to visualize MolProbity-style structural validation data directly 
in a PyMOL session. The programs Reduce, Flipkin, and Probe from the 
well-known MolProbity <http://molprobity.biochem.duke.edu/> software 
package allow generation of data in "kinemage" (kinetic image) format 
to illustrate atom-atom contacts (dots) and clashes (spikes), and the 
new plugin now makes it possible to utilize the same programs to 
produce similar results in PyMOL scenes.


I have put together a page on the PyMOL Wiki 
<https://pymolwiki.org/index.php/PyMOLProbity> with a brief summary of 
its features and basic how-to information.  (Please note that the 
MolProbity executables are only available for Linux/MacOS, so 
PyMOLProbity isn't yet useful on Windows.)


My work on this plugin was supported by the Warren L. DeLano Memorial 
PyMOL Open-Source Fellowship.  I would like once again to thank 
Schrödinger for the opportunity to work on this project, and in 
particular would like to thank the PyMOL developers for their support 
and feedback along the way.


I hope many of you will find it useful.  If you come across any bugs 
or have any feature requests or other suggestions, please feel free to 
email me directly or create a new issue 
<https://github.com/jaredsampson/pymolprobity/issues> on Github.


Happy PyMOLing!

Cheers,
Jared


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[PyMOL] how to hide dashed artificial cartoon?

2016-09-09 Thread Albert
Hello:

I noticed that if I show my structure as cartoon, there would be a 
"dashed loop" cartoon filling in the missing part of my structure. I am 
just wondering how can we disable PyMol show the missing part automatically?

Thank you very much

Albert

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[PyMOL] problem of internal_gui

2016-10-06 Thread Albert
Hello:

I used commad line:

set internal_gui, off

to hide the internal gui. Then I save my pymol session as a .pse file.

However, when I reopen this .pse file, the internal_gui is still there. 
When I insert .pse file to a PPT file, the internal_gui is also there.

I am just wondering how to solve this problem? I am using PyMOL-1.8.2.3.

I also tested in the latest 1.8.4, it has the same issue.

Thank you very much.

Albert

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Re: [PyMOL] problem of internal_gui

2016-10-07 Thread Albert
I see.

It works very well now.

Thanks a lot


On 10/06/2016 10:32 PM, Thomas Holder wrote:
> Hi Albert,
>
> "internal_gui" is now a blacklisted setting not be stored or restored from 
> session files.
>
> You can launch PyMOL without internal gui like this from a Terminal:
>
> pymol -i session.pse
>
> When inserting in AxPyMOL, please check the option
>
> [x] PyMOL Show (Hide controls)
>
> For older versions of AxPyMOL (before 1.7 I think) the session needs to be 
> saved as a "PyMOL Show file" (with .psw Extension) to be loaded without 
> controls into AxPyMOL.
>
> Hope that helps.
>
> Cheers,
>Thomas


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[PyMOL] problem of optirun in Pymol

2016-10-10 Thread Albert
Hello:

I've got 2 graphic card in my laptop:

Intel® HD Graphics 4600+ Nvidia M1100M

I have installed Bumblee optirun in my Linux OS. Currently, command line

optirun pymol

works fine for Pymol-1.8.2.3. However, I found that it doesn't work for 
Pymol-1.8.4. When I type

optirun pymol

Pymol doesn't start and I didn't get any error messages from terminal 
either.

I am just wondering how can we solve the problem?

Thx a lot

Albert


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Re: [PyMOL] problem of optirun in Pymol

2016-10-10 Thread Albert
Hello:

I am using openSUSE 13.2 X64 OS.

Pymol works fine without optirun in 1.8.4.

Here is output from ./pymol -c

PyMOL>python end
  PyMOL: normal program termination.

However, when I type

optirun ./pymol -c

I didn't obtain any information.

regards

Albert



On 10/10/2016 08:46 PM, Thomas Holder wrote:
> Hi Albert,
>
> Which Linux OS and version (e.g. Ubuntu 12.04 64bit) is this?
> Does PyMOL work without optirun?
> Does it work in headless mode (pymol -c)?
>
> Thanks,
>Thomas


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[PyMOL] how to show PBC box?

2016-12-07 Thread Albert
Hello:

I am visualizing a MD simulation system in PyMOL. It contains the PBC 
information. I am just wondering how can we show the PBC box in PyMOL? 
As far as I know the PBC box can be shown in VMD using the following 
command line:

 >pbc box

Is there any similar command line in PyMOL?

Thank you very much.

Albert


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Re: [PyMOL] how to show PBC box?

2016-12-07 Thread Albert

Dear Tsjerk:

Thanks a lot for such prompt reply.

It works very well.

Cheers.

Albert


On 12/07/2016 08:46 PM, Tsjerk Wassenaar wrote:

Hi Albert,

You can do:

show cell

Cheers,

Tsjerk



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Re: [PyMOL] Save command output to a file in pymol

2017-01-13 Thread Albert

I think you can obtain it from your Linux  terminal



On 01/13/2017 10:34 AM, Academic Research wrote:


Pymol Professionals I need your help,

I have the following command:

|iterate n. CA, print resi + ':' + ss |

I use this command in pymol to print out each residue number and its 
corresponding secondary structure. The command prints out the result 
in pymol itself.


My question is: *How can I save the output from this command into a file?*

AC Research



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[PyMOL] rms_cur, rms, fit - No atoms selected

2009-04-23 Thread Albert Solernou
I'm new at pymol, and I'm trying to use the commands rms and rms_cur.

I have two pdb files, with two proteins in each.
First, I load the files

 load 1acb_321000.pdb, c321
 load 1acb_dock.pdb, dock

then I select the backbone of the B chain of each complex,
 select lc, /c321//b//ca+c+n+o
 select lr, /dock//b//ca+c+n+o

Everything works until here. Each selection is showed on the screen, and
they are 207 atoms each. Now I want to get the rms value without
superimposing:

 rms_cur lc, lr

but it does not work:
ExecutiveRMS-Error: No atoms selected.
It also does not work with rms or fit commands, although it works with
align:

 align lc, lr
 Match: read scoring matrix.
 Match: assigning 69 x 69 pairwise scores.
 MatchAlign: aligning residues (69 vs 69)...
 ExecutiveAlign: 207 atoms aligned.
 ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=0.01).
 ExecutiveRMS: 2 atoms rejected during cycle 2 (RMS=0.01).
 Executive: RMS =0.006 (200 to 200 atoms)


I've seen that someone has reported a bug at debian's, under the version
0.99rc6:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=486254


I've tried the 1.0r2-1 version (commming with ubuntu, apt-get), and
compliling the source code from the svn of the current version, 1.2-x.
Same results.

Hope someone can help me,
albert



[PyMOL] unable to export obj

2015-01-21 Thread Albert Solernou
Hi,
I am trying to get a .obj file, but fail when setting up surface_type to 
2. More explicitly:
 load 1ppe.pdb, 1ppe
 set surface_type, 2
 hide everything
 show surface
shows a nice triangulated surface. However,
 save myscene.obj
saves an empty file.

I've tried pymol versions 1.7.4 and 1.6.0. Saving into an obj file works 
well when surface_type is set to 0, or 1. Any help?

Best,
Albert


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[PyMOL] RMS over a MD trajectory.

2015-05-06 Thread Albert Solernou
Hi,
I am trying to compute the RMS between a PDB file and a Gromacs 
trajectory. I can see that align does things correctly when:
  align trj, pdb1, mobile_state=1
i. e., when I align the first snapshot of the trajectory with the PDB 
file. I also understand that PyMOL does compute the RMS along the 
trajectory if I simply:
  align trj, pdb1
as it is told in:
  http://www.pymolwiki.org/index.php/Align
However, I am unable to get the list of RMS values printed out. How 
could I do that?

Thanks,
Albert

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Re: [PyMOL] RMS over a MD trajectory.

2015-05-08 Thread Albert Solernou
Thanks Thomas,
I was already printing k[i][3] (RMSD before refinement) instead of 
k[i][0] (RMSD after refinement) but your cycles=0 looks cleaner.

Cheers,
Albert

On 05/06/2015 05:14 PM, Thomas Holder wrote:
 Hi Albert,

 Please pay attention to the difference between all-atom RMSD and RMSD after 
 outlier rejection.
 http://pymolwiki.org/index.php/Align#RMSD

 If your trj and pdb1 have identical topology and matching atom 
 identifiers, then you can also use cmd.rms().
 http://pymolwiki.org/index.php/Rms

 Cheers,
Thomas

 On 06 May 2015, at 11:56, Albert Solernou a.soler...@leeds.ac.uk wrote:

 Terribly useful Carsten!

 I could easily do a loop and get the RMS along the trajectory:
   k = []
   for i in range(1,101): k.append(cmd.align(trj,pdb1,mobile_state=i))
   for i in range(100): print k[i][0]

 Cheers,
 Albert


 On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
 Hi Al,

 you would need to go through the Python API:

 python
 rms=cmd.align(mobCA,tarCA, quiet=0)
 print rms
 python end

 rms contains a tuple with various parameters related to the superposition. 
 The first value in the tuple i.e. rms[0] should be the RMS value.

 HTH

 Carsten

 -Original Message-
 From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
 Sent: Wednesday, May 06, 2015 8:32 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] RMS over a MD trajectory.

 Hi,
 I am trying to compute the RMS between a PDB file and a Gromacs trajectory. 
 I can see that align does things correctly when:
align trj, pdb1, mobile_state=1
 i. e., when I align the first snapshot of the trajectory with the PDB file. 
 I also understand that PyMOL does compute the RMS along the trajectory if I 
 simply:
align trj, pdb1
 as it is told in:
http://www.pymolwiki.org/index.php/Align
 However, I am unable to get the list of RMS values printed out. How could I 
 do that?

 Thanks,
 Albert

 --
 -
 Dr Albert Solernou
 EPSRC Research Fellow,
 Department of Physics and Astronomy,
 University of Leeds
 Tel: +44 (0)1133 431451

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   University of Leeds
   Tel: +44 (0)1133 431451


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Re: [PyMOL] RMS over a MD trajectory.

2015-05-11 Thread Albert Solernou
Oh, I see...
It looks like I'll need to end up writing a short script that does the 
loop along the trajectory together with a correct RMS calculation.

Thanks for the tip, Carsten.

Cheers,
Albert


On 05/08/2015 04:11 PM, Schubert, Carsten [JRDUS] wrote:
 Hi Al,

 based on my experience running align or super with cycles=0 has the 
 tendency to produce inferior alignment results. So depending on how similar 
 the conformation of your structures are you may end up with skewed 
 statistics. What I've done in the past and for a paper I'm working on now is 
 to run the alignment with default parameters to get the best superposition 
 and then calculate the statistics by hand from the superposed structures. Not 
 sure if cmd.rms() would do this for all residues w/o outlier rejection, so I 
 ended up writing code for myself. The colorbyrmsd.py 
 (http://pymolwiki.org/index.php/ColorByRMSD) script gives a nice illustration 
 on how to approach this this.

 Carsten

 -Original Message-
 From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
 Sent: Friday, May 08, 2015 10:04 AM
 To: Thomas Holder
 Cc: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] RMS over a MD trajectory.

 Thanks Thomas,
 I was already printing k[i][3] (RMSD before refinement) instead of k[i][0] 
 (RMSD after refinement) but your cycles=0 looks cleaner.

 Cheers,
 Albert

 On 05/06/2015 05:14 PM, Thomas Holder wrote:
 Hi Albert,

 Please pay attention to the difference between all-atom RMSD and RMSD after 
 outlier rejection.
 http://pymolwiki.org/index.php/Align#RMSD

 If your trj and pdb1 have identical topology and matching atom 
 identifiers, then you can also use cmd.rms().
 http://pymolwiki.org/index.php/Rms

 Cheers,
 Thomas

 On 06 May 2015, at 11:56, Albert Solernou a.soler...@leeds.ac.uk wrote:

 Terribly useful Carsten!

 I could easily do a loop and get the RMS along the trajectory:
k = []
for i in range(1,101): k.append(cmd.align(trj,pdb1,mobile_state=i))
for i in range(100): print k[i][0]

 Cheers,
 Albert


 On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
 Hi Al,

 you would need to go through the Python API:

 python
 rms=cmd.align(mobCA,tarCA, quiet=0) print rms python end

 rms contains a tuple with various parameters related to the superposition. 
 The first value in the tuple i.e. rms[0] should be the RMS value.

 HTH

Carsten

 -Original Message-
 From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
 Sent: Wednesday, May 06, 2015 8:32 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] RMS over a MD trajectory.

 Hi,
 I am trying to compute the RMS between a PDB file and a Gromacs 
 trajectory. I can see that align does things correctly when:
 align trj, pdb1, mobile_state=1
 i. e., when I align the first snapshot of the trajectory with the PDB 
 file. I also understand that PyMOL does compute the RMS along the 
 trajectory if I simply:
 align trj, pdb1
 as it is told in:
 http://www.pymolwiki.org/index.php/Align
 However, I am unable to get the list of RMS values printed out. How could 
 I do that?

 Thanks,
 Albert

 --
 -
  Dr Albert Solernou
  EPSRC Research Fellow,
  Department of Physics and Astronomy,
  University of Leeds
  Tel: +44 (0)1133 431451
 --
 -
 Dr Albert Solernou
 EPSRC Research Fellow,
 Department of Physics and Astronomy,
 University of Leeds
 Tel: +44 (0)1133 431451


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Re: [PyMOL] RMS over a MD trajectory.

2015-05-06 Thread Albert Solernou
Terribly useful Carsten!

I could easily do a loop and get the RMS along the trajectory:
  k = []
  for i in range(1,101): k.append(cmd.align(trj,pdb1,mobile_state=i))
  for i in range(100): print k[i][0]

Cheers,
Albert


On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
 Hi Al,

 you would need to go through the Python API:

 python
 rms=cmd.align(mobCA,tarCA, quiet=0)
 print rms
 python end

 rms contains a tuple with various parameters related to the superposition. 
 The first value in the tuple i.e. rms[0] should be the RMS value.

 HTH

   Carsten

 -Original Message-
 From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
 Sent: Wednesday, May 06, 2015 8:32 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] RMS over a MD trajectory.

 Hi,
 I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I 
 can see that align does things correctly when:
align trj, pdb1, mobile_state=1
 i. e., when I align the first snapshot of the trajectory with the PDB file. I 
 also understand that PyMOL does compute the RMS along the trajectory if I 
 simply:
align trj, pdb1
 as it is told in:
http://www.pymolwiki.org/index.php/Align
 However, I am unable to get the list of RMS values printed out. How could I 
 do that?

 Thanks,
 Albert

 --
 -
 Dr Albert Solernou
 EPSRC Research Fellow,
 Department of Physics and Astronomy,
 University of Leeds
 Tel: +44 (0)1133 431451


 --
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Re: [PyMOL] selecting faces and vertices in CGOs

2016-04-12 Thread Albert Solernou
Hi Thomas,
thanks for your answer. Even if it is challenging, I could still be
interested in coding that. I have written a plugin for PyMOL that we
plan to release as soon as it proves to be stable, together with another
piece of software, and that functionality would help us very much.

I would be very grateful if you could give me some hints on the code
structure, and on how to tackle the inclusion of this new feature.

Cheers,
Albert


On 04/08/2016 09:18 PM, Thomas Holder wrote:
> Hi Albert,
> 
> This is currently not possible and adding this would be a very major project.
> 
> Cheers,
>   Thomas
> 
> On 30 Mar 2016, at 10:40, Albert Solernou <a.soler...@leeds.ac.uk> wrote:
> 
>> Dear All,
>> I was wondering if there is a way to select faces, vertices and/or edges
>> from a CGO either using the mouse or the command line. How difficult
>> would be to add this, and how would you do that?
>>
>> It would be very useful for us if we could get that working.
>>
>> Thanks,
>> Albert
>>
>> -- 
>> -
>>  Dr Albert Solernou
>>  EPSRC Research Fellow,
>>  Department of Physics and Astronomy,
>>  University of Leeds
>>  Tel: +44 (0)1133 431451
> 

-- 
-
  Dr Albert Solernou
  EPSRC Research Fellow,
  Department of Physics and Astronomy,
  University of Leeds
  Tel: +44 (0)1133 431451

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[PyMOL] selecting faces and vertices in CGOs

2016-03-30 Thread Albert Solernou
Dear All,
I was wondering if there is a way to select faces, vertices and/or edges
from a CGO either using the mouse or the command line. How difficult
would be to add this, and how would you do that?

It would be very useful for us if we could get that working.

Thanks,
Albert



-- 
-
  Dr Albert Solernou
  EPSRC Research Fellow,
  Department of Physics and Astronomy,
  University of Leeds
  Tel: +44 (0)1133 431451

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[PyMOL] loading StringIO

2016-10-26 Thread Albert Solernou
Dear All,
I was wondering if there was a way to load a PDB file stored in memory 
instead of disk, i. e., a memory file, defined through StringIO or 
tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could 
handle an open file instead of a file?

Thanks,
Albert


-- 
-
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

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Re: [PyMOL] loading StringIO

2016-10-26 Thread Albert Solernou
Hi Jordan,
I still don't figure out how to do that with "load_object". What is the 
"type" for a file handler? Would be "object" the file handler itself?

Albert

On 10/26/2016 10:58 AM, Jordan Willis wrote:
> Probably could use load_object instead.
>
>
>def load_object(type,object,name,state=0,finish=1,discrete=0,
>  quiet=1,zoom=-1,_self=cmd):
> '''
> DESCRIPTION
>
> "load_object" is a general developer function for loading Python objects
> into PyMOL.
>> On Oct 26, 2016, at 1:55 AM, Albert Solernou <a.soler...@leeds.ac.uk
>> <mailto:a.soler...@leeds.ac.uk>> wrote:
>>
>> Dear All,
>> I was wondering if there was a way to load a PDB file stored in memory
>> instead of disk, i. e., a memory file, defined through StringIO or
>> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could
>> handle an open file instead of a file?
>>
>> Thanks,
>> Albert
>>
>>
>> --
>> -
>>   Dr Albert Solernou
>>   EPSRC Research Fellow,
>>   Department of Physics and Astronomy,
>>   University of Leeds
>>   Tel: +44 (0)1133 431451
>>
>> --
>> The Command Line: Reinvented for Modern Developers
>> Did the resurgence of CLI tooling catch you by surprise?
>> Reconnect with the command line and become more productive.
>> Learn the new .NET and ASP.NET <http://ASP.NET> CLI. Get your free copy!
>> http://sdm.link/telerik
>> ___
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>

-- 
-
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

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Re: [PyMOL] loading StringIO

2016-10-26 Thread Albert Solernou
That's lovely, David.

Thanks,
Albert

On 10/26/2016 11:56 AM, David Hall wrote:
> https://pymolwiki.org/index.php/Read_Pdbstr
>
> -David
>
> On Oct 26, 2016, at 3:55 AM, Albert Solernou <a.soler...@leeds.ac.uk
> <mailto:a.soler...@leeds.ac.uk>> wrote:
>
>> Dear All,
>> I was wondering if there was a way to load a PDB file stored in memory
>> instead of disk, i. e., a memory file, defined through StringIO or
>> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could
>> handle an open file instead of a file?
>>
>> Thanks,
>> Albert
>>
>>
>> --
>> -
>>   Dr Albert Solernou
>>   EPSRC Research Fellow,
>>   Department of Physics and Astronomy,
>>   University of Leeds
>>   Tel: +44 (0)1133 431451
>>
>> --
>> The Command Line: Reinvented for Modern Developers
>> Did the resurgence of CLI tooling catch you by surprise?
>> Reconnect with the command line and become more productive.
>> Learn the new .NET and ASP.NET <http://ASP.NET> CLI. Get your free copy!
>> http://sdm.link/telerik
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net
>> <mailto: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

-- 
-
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

--
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[PyMOL] sources for PyMOL 2

2017-11-23 Thread Albert Solernou

Dear All,
we have been writing a plugin for PyMOL during the last years, released 
as GPL. I would like to support PyMOL2, but need to know whether the 
code will be made accessible or not. Is PyMOL2 still free software? And 
if so, can we get access to the source code?


Thanks,
Albert

--
-
  Dr Albert Solernou
  EPSRC Research Fellow,
  Department of Physics and Astronomy,
  University of Leeds
  Tel: +44 (0)1133 431451

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Re: [PyMOL] sources for PyMOL 2

2017-11-23 Thread Albert Solernou

OK,
I found the answer myself, googling in this email list. Sources will be 
released early next year, I understood. I'll wait patiently :)


Cheers,
Albert

On 22/11/17 11:49, Albert Solernou wrote:

Dear All,
we have been writing a plugin for PyMOL during the last years, released 
as GPL. I would like to support PyMOL2, but need to know whether the 
code will be made accessible or not. Is PyMOL2 still free software? And 
if so, can we get access to the source code?


Thanks,
Albert



--
-
  Dr Albert Solernou
  EPSRC Research Fellow,
  Department of Physics and Astronomy,
  University of Leeds
  Tel: +44 (0)1133 431451

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