pymol-users Mailing List for PyMOL Molecular Graphics System

Greetings,

This is just a quick note to let you know that as of revision 3997
PyMOL has an improved plugin/script manager. This system was written
by Thomas Holder as part of his PyMOL Open Source Fellowship. Some new
features include:
 * install script/plugin from the PyMOLWiki directly
 * install from a URL
 * install from a custom path on your file system
 * setup and install into multiple repositories
 * scripts/plugins requiring a citation will bring up a dialog telling
you so (authors, please see the docs for information on how to require
a citation)
 * ...and more.

Please feel free to test the code and get used to the new manager. If
you like it, please send Thomas a note of thanks.

We will be starting another round of the PyMOL Open Source Fellowship
soon. If you're interested keep an eye out for the call for
applications.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Dear Pymol users
We are trying to generate a number of mutated structures using the 
mutagenesis wizard. However, after mutating a position and saving to a 
new PDB file, the mutated residue ends up being "mixed" into the 
coordinate lines of the first residue. Some two coordinate lines are 
separated by TER statements. At the position, where the residue should 
sit, there is a TER statement, and the residue is skipped (e.g Res ID 
139, TER, Res ID 141).
We also observe this using

set retain_order
set pdb_retain_ids

Is there a fix for this?

Any help is appreciated.

Thanks,
Martin








On 13.12.10 16:52, Jason Vertrees wrote:
> Hi Martin,
>
> As you've found, the mutagenesis wizard destroys the ordering in some
> cases.  I'll look into it.
>
> Cheers,
>
> -- Jason
>
> On Tue, Dec 7, 2010 at 11:34 AM, Martin Hediger<ma...@bl...>  wrote:
>> Good day
>> I use PyMOL to introduce mutations into a structure. It occured to me that
>> when saving the modified structure, atom sequence was not preserved. Using
>>
>> set retain_order
>> set pdb_retain_ids
>>
>> is supposed to control this. It seems now, as if mutating a structure does a
>> really weired thing:
>> Once the mutation is introduced, the sequence becomes completely disordered
>> in a sense that the atoms of the "new" residue are placed in between the
>> atoms of the very first residue, in terms of sequence (not geometry).
>> This results in a PDB file like this (PRO is the first residue, PHE is the
>> residue to which the mutation is being carried out):
>>
>> ATOM      1  N   PRO A   1      53.611  -4.470  40.679  1.00  0.00      PROT
>> N
>> TER       2      PRO A   1
>> ATOM      0  N   PHE D  14      55.428  -5.717  38.365  1.00  0.00      PROT
>> N
>> TER       1      PHE D  14
>> ATOM      2  CA  PRO A   1      52.399  -3.722  40.197  1.00  0.00      PROT
>> C
>> TER       3      PRO A   1
>> ATOM      1  CA  PHE D  14      55.821  -4.897  37.223  1.00  0.00      PROT
>> C
>> TER       2      PHE D  14
>> ATOM      3  C   PRO A   1      52.805  -2.296  39.783  1.00  0.00      PROT
>> C
>> TER       4      PRO A   1
>> ATOM      2  CB  PHE D  14      54.681  -4.879  36.160  1.00  0.00      PROT
>> C
>> TER       3      PHE D  14
>> ATOM      4  O   PRO A   1      53.381  -1.530  40.550  1.00  0.00      PROT
>> O
>> TER       5      PRO A   1
>> ATOM      3  CG  PHE D  14      54.928  -4.027  34.905  1.00  0.00      PROT
>> C
>> TER       4      PHE D  14
>> ATOM      5  CB  PRO A   1      51.360  -3.675  41.342  1.00  0.00      PROT
>> C
>> TER       6      PRO A   1
>> ATOM      4  CD1 PHE D  14      56.116  -4.189  34.183  1.00  0.00      PROT
>> C
>> TER       5      PHE D  14
>> ATOM      6  CG  PRO A   1      52.019  -4.362  42.549  1.00  0.00      PROT
>> C
>> TER       7      PRO A   1
>> ATOM      5  CD2 PHE D  14      54.011  -3.049  34.512  1.00  0.00      PROT
>> C
>> TER       6      PHE D  14
>> ATOM      7  CD  PRO A   1      53.253  -5.096  41.996  1.00  0.00      PROT
>> C
>> TER       8      PRO A   1
>> ATOM      6  CE1 PHE D  14      56.391  -3.370  33.093  1.00  0.00      PROT
>> C
>> TER       7      PHE D  14
>> ATOM      8  HA  PRO A   1      51.990  -4.297  39.323  1.00  0.00      PROT
>> H
>> TER       9      PRO A   1
>> ATOM      7  CE2 PHE D  14      54.282  -2.238  33.413  1.00  0.00      PROT
>> C
>> TER       8      PHE D  14
>> ATOM      9 1HB  PRO A   1      50.434  -4.192  41.043  1.00  0.00      PROT
>> H
>> TER      10      PRO A   1
>> ATOM      8  CZ  PHE D  14      55.473  -2.397  32.707  1.00  0.00      PROT
>> C
>> TER       9      PHE D  14
>> ATOM     10 2HB  PRO A   1      51.070  -2.637  41.594  1.00  0.00      PROT
>> H
>> TER      11      PRO A   1
>> ATOM      9  C   PHE D  14      56.113  -3.478  37.649  1.00  0.00      PROT
>> C
>> TER      10      PHE D  14
>> ATOM     11 1HG  PRO A   1      51.327  -5.056  43.052  1.00  0.00      PROT
>> H
>> TER      12      PRO A   1
>> ATOM     10  O   PHE D  14      55.357  -2.867  38.421  1.00  0.00      PROT
>> O
>> TER      11      PHE D  14
>> ATOM     12 2HG  PRO A   1      52.313  -3.615  43.311  1.00  0.00      PROT
>> H
>> TER      13      PRO A   1
>> ATOM     11 1HD  PHE D  14      56.847  -4.922  34.497  1.00  0.00      PROT
>> H
>> TER      12      PHE D  14
>> ATOM     13 1HD  PRO A   1      54.110  -5.062  42.704  1.00  0.00      PROT
>> H
>>
>>
>> Can this be explained somehow?
>>
>> Thanks for your answers.
>> Martin
>>
>>
>>
>>
>>
>>
>>
>>
>> On 09.11.10 13:26, Jason Vertrees wrote:
>>> Hi Martin,
>>>
>>> set retain_order
>>> set pdb_retain_ids
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>> On Tue, Nov 9, 2010 at 4:30 AM, Martin Hediger<ma...@bl...>    wrote:
>>>> Dear all
>>>> It occured to me that PyMOL is resequencing a structure when saving. I
>>>> am trying to interpolate between two structures where it is critical to
>>>> have identical sequence in both structures. Is it possible submit a
>>>> <DO_NOT_RESEQUENCE>-option to the save command?
>>>>
>>>> Thanks for your help
>>>> Martin
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>>>> David G. Thomson, author of the best-selling book "Blueprint to a
>>>> Billion" shares his insights and actions to help propel your
>>>> business during the next growth cycle. Listen Now!
>>>> http://p.sf.net/sfu/SAP-dev2dev
>>>> _______________________________________________
>>>> 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 James and Joel,

I would use a homology modeling tool to add missing atoms (basically 
rebuild the structure, given the incomplete structure as template).

Examples for web servers:
  * http://toolkit.tuebingen.mpg.de/modeller
  * http://swissmodel.expasy.org/

pdb2pqr can also add a limited number of missing atoms, see 
http://www.poissonboltzmann.org/pdb2pqr/d/web-servers

Hope that helps.

Cheers,
   Thomas

Joel Tyndall wrote, On 04/30/12 00:07:
> Surely you could use pymol mutagenesis wizard to do tis.
> 
> Also James, It is a good practice to  start a new thread (new email with 
> new subject for each set of questions you have
> 
> Regards
> 
> Joel
> 
> From: James Starlight [mailto:jms...@gm...]
> Sent: Friday, 27 April 2012 8:25 p.m.
> To: pymol-users
> Subject: Re: [PyMOL] Editing of the pdb structure
> 
> Dear all!
> 
> I want to prepare my pdb structure for MD simulation. I've done all 
> required things but my protein consist of some missing heavy atoms the 
> list of which I've obtained from my pdb hedader
> 
> REMARK 470   M RES CSSEQI  ATOMS                                                
> REMARK 470     ARG A 220    CG   CD   NE   CZ   NH1  NH2                        
> REMARK 470     ARG A 222    CG   CD   NE   CZ   NH1  NH2                        
> REMARK 470     ASN B 212    O    CG   OD1  ND2                                  
> REMARK 470     LYS C  43    CG   CD   CE   NZ                                   
> REMARK 470     GLY C 225    O 
> 
> I've heard that there are some web servers wich could be usefull to build such missing atoms.
> In particular in my structure there are lack not only side chain atoms but also two backbone Oxygens in the Gly and Asn wich could be the main problem of such task.
> 
> In any case I'll be very thankfull if you provide me with such server 
> 
> James

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Surely you could use pymol mutagenesis wizard to do tis.

Also James, It is a good practice to  start a new thread (new email with new subject for each set of questions you have

Regards

Joel

From: James Starlight [mailto:jms...@gm...]
Sent: Friday, 27 April 2012 8:25 p.m.
To: pymol-users
Subject: Re: [PyMOL] Editing of the pdb structure

Dear all!

I want to prepare my pdb structure for MD simulation. I've done all required things but my protein consist of some missing heavy atoms the list of which I've obtained from my pdb hedader

REMARK 470   M RES CSSEQI  ATOMS

REMARK 470     ARG A 220    CG   CD   NE   CZ   NH1  NH2

REMARK 470     ARG A 222    CG   CD   NE   CZ   NH1  NH2

REMARK 470     ASN B 212    O    CG   OD1  ND2

REMARK 470     LYS C  43    CG   CD   CE   NZ

REMARK 470     GLY C 225    O


I've heard that there are some web servers wich could be usefull to build such missing atoms.
In particular in my structure there are lack not only side chain atoms but also two backbone Oxygens in the Gly and Asn wich could be the main problem of such task.


In any case I'll be very thankfull if you provide me with such server

James

26 апреля 2012 г. 12:55 пользователь James Starlight <jms...@gm...<mailto:jms...@gm...>> написал:
Thanks Thomas!


Another question-
I have my protein.pdb with some inserted crystall waters within protein interiour as well as water surrounded of my protein. I want to remove only sorrounding water but prevent internal water ( wich could be functional relevant ).

How I could to select such surrounded water ( e.g via some cutoff radius relative my protein etc) wich I'd like to remove further ?
26 апреля 2012 г. 11:22 пользователь Thomas Holder <sp...@us...<mailto:sp...@us...>> написал:

Hi James,

use the alter command:

alter chain "", chain="A"

See also http://pymolwiki.org/index.php/Alter

Cheers,
 Thomas

James Starlight wrote, On 04/26/12 09:18:

Dear PyMol users!


I have some structure.pdb from the md simulation wich consist of 1 chain not defined in the pdb file explicitly ( missing chain id in the pdb file). So the pymol recognise that chain as the  ' '  . I need to rename this chain to the desired name ( e.g to chain A ).

How I could do it?

James

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Dear all!

I want to prepare my pdb structure for MD simulation. I've done all
required things but my protein consist of some missing heavy atoms the list
of which I've obtained from my pdb hedader

REMARK 470   M RES CSSEQI  ATOMS
REMARK 470     ARG A 220    CG   CD   NE   CZ   NH1  NH2
REMARK 470     ARG A 222    CG   CD   NE   CZ   NH1  NH2
REMARK 470     ASN B 212    O    CG   OD1  ND2
REMARK 470     LYS C  43    CG   CD   CE   NZ
REMARK 470     GLY C 225    O


I've heard that there are some web servers wich could be usefull to
build such missing atoms.
In particular in my structure there are lack not only side chain atoms
but also two backbone Oxygens in the Gly and Asn wich could be the
main problem of such task.

In any case I'll be very thankfull if you provide me with such server

James



26 апреля 2012 г. 12:55 пользователь James Starlight <jms...@gm...
> написал:

> Thanks Thomas!
>
>
> Another question-
> I have my protein.pdb with some inserted crystall waters within protein
> interiour as well as water surrounded of my protein. I want to remove only
> sorrounding water but prevent internal water ( wich could be functional
> relevant ).
>
> How I could to select such surrounded water ( e.g via some cutoff radius
> relative my protein etc) wich I'd like to remove further ?
>
> 26 апреля 2012 г. 11:22 пользователь Thomas Holder <
> sp...@us...> написал:
>
> Hi James,
>>
>> use the alter command:
>>
>> alter chain "", chain="A"
>>
>> See also " rel="nofollow">http://pymolwiki.org/index.**php/Alter<http://pymolwiki.org/index.php/Alter>
>>
>> Cheers,
>>  Thomas
>>
>> James Starlight wrote, On 04/26/12 09:18:
>>
>>  Dear PyMol users!
>>>
>>>
>>> I have some structure.pdb from the md simulation wich consist of 1 chain
>>> not defined in the pdb file explicitly ( missing chain id in the pdb file).
>>> So the pymol recognise that chain as the  ' '  . I need to rename this
>>> chain to the desired name ( e.g to chain A ).
>>>
>>> How I could do it?
>>>
>>> James
>>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>

Hi Martin & James,

is it just a coincident that you both ask almost the same question?

You could remove all water atoms with few protein contacts or with a 
small surface area. For example:

remove solvent beyond 3.5 of polymer
set dot_solvent
get_area solvent, load_b=1
remove solvent and b > 20

Hope that helps.

Cheers,
   Thomas

On 04/26/2012 10:55 AM, James Starlight wrote:
> Another question- I have my protein.pdb with some inserted crystall
> waters within protein interiour as well as water surrounded of my
> protein. I want to remove only sorrounding water but prevent internal
> water ( wich could be functional relevant ).
>
> How I could to select such surrounded water ( e.g via some cutoff
> radius relative my protein etc) wich I'd like to remove further ?

On 04/25/2012 05:34 PM, Martin Hediger wrote:
> In a crystal structure, there are usually a number of relevant crystal
> waters, as well as water molecules on the surface. In our approach, we
> model the protein structure within a dielectric continuum, so surface
> water molecules are not required (to save computer time). However,
> waters in the interior should remain in our model. How could we discard
> the surface waters while keeping the internal waters?

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Thanks Thomas!


Another question-
I have my protein.pdb with some inserted crystall waters within protein
interiour as well as water surrounded of my protein. I want to remove only
sorrounding water but prevent internal water ( wich could be functional
relevant ).

How I could to select such surrounded water ( e.g via some cutoff radius
relative my protein etc) wich I'd like to remove further ?

26 апреля 2012 г. 11:22 пользователь Thomas Holder <
sp...@us...> написал:

> Hi James,
>
> use the alter command:
>
> alter chain "", chain="A"
>
> See also " rel="nofollow">http://pymolwiki.org/index.**php/Alter<http://pymolwiki.org/index.php/Alter>
>
> Cheers,
>  Thomas
>
> James Starlight wrote, On 04/26/12 09:18:
>
>  Dear PyMol users!
>>
>>
>> I have some structure.pdb from the md simulation wich consist of 1 chain
>> not defined in the pdb file explicitly ( missing chain id in the pdb file).
>> So the pymol recognise that chain as the  ' '  . I need to rename this
>> chain to the desired name ( e.g to chain A ).
>>
>> How I could do it?
>>
>> James
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>

Hi James,

use the alter command:

alter chain "", chain="A"

See also http://pymolwiki.org/index.php/Alter

Cheers,
   Thomas

James Starlight wrote, On 04/26/12 09:18:
> Dear PyMol users!
> 
> 
> I have some structure.pdb from the md simulation wich consist of 1 chain 
> not defined in the pdb file explicitly ( missing chain id in the pdb 
> file). So the pymol recognise that chain as the  ' '  . I need to rename 
> this chain to the desired name ( e.g to chain A ).
> 
> How I could do it?
> 
> James

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Dear PyMol users!


I have some structure.pdb from the md simulation wich consist of 1 chain
not defined in the pdb file explicitly ( missing chain id in the pdb file).
So the pymol recognise that chain as the  ' '  . I need to rename this
chain to the desired name ( e.g to chain A ).

How I could do it?

James

1 апреля 2012 г. 15:04 пользователь James Starlight
<jms...@gm...>написал:

> Thomas,
>
>
> thank you I'll test your script with modeller after obtaining of this
> software on my workstation and post here results :)
>
>
> James
>
> 1 апреля 2012 г. 12:30 пользователь Thomas Holder <
> sp...@us...> написал:
>
> Hi James,
>>
>> I use Modeller for exactly such tasks (build missing residues). It's free
>> for academic use.
>>
>> http://salilab.org/modeller/
>>
>> Using modeller is also not "comfortable" since it only has a python
>> scripting interface and thus requires you to write a script for each task.
>> But I wrote a general purpose automodel client which is quite convenient
>> for simple modelling tasks. See attachment.
>>
>> Usage:
>> python automodeller.py sequence.fasta template.pdb
>>
>> I provide this script "as is" without any warranty :) Let me know if it
>> works for you.
>>
>> Cheers,
>>  Thomas
>>
>> James Starlight wrote, On 04/01/12 08:55:
>>
>>  Hi Thomas!
>>>
>>> Thanks for help- this works good :)
>>>
>>>
>>> By the way I have some question not about pymol :)
>>>  I've already looked for some software for processing of my PDB
>>> structure for a long time ( often I need to build missing residues and
>>> flexible LOOP fragments with some refining of the result ). For such
>>> purposes I've used amber tools software but I've found that this tools are
>>> not very comfortable for me :)
>>>
>>> Also I've found exactly what I need for in the MAESTRO's prime module
>>> but this tools avialable for the licensing only.
>>>
>>> Is there any other free software for structure processing with
>>> easy-to-use interface and free academical ussage ?
>>>
>>> Thanks again
>>>
>>> James
>>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>

Dear List
In a crystal structure, there are usually a number of relevant crystal 
waters, as well as water molecules on the surface. In our approach, we 
model the protein structure within a dielectric continuum, so surface 
water molecules are not required (to save computer time). However, 
waters in the interior should remain in our model. How could we discard 
the surface waters while keeping the internal waters?

Thanks for any feedback.
Martin

Hi Mary,

I suggest to use a real modeling tool like MODELLER for this task.

Some modeling is possible with the sculpting feature, but you should 
keep in mind that it only tries to restore the starting conformation and 
to avoid clashes. There is no "real" molecular forcefield.

Cheers,
   Thomas

On 04/23/2012 08:36 PM, Mary Hall wrote:
> Hello! I am a student at the Potomac School and I have been trying to learn
> how to use PYMOL based off of online support and online tutorials.
> Currently, I am attempting to use the program to build an isolated section
> of a protein with a known structure. I was just wondering how long does it
> take to sculpt a protein segment? Is it possible to build an entire
> protein  with a known structure from scratch using PYMOL?
>
> Thank you

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

> Hello! I am a student at the Potomac School and I have been trying to
>learn
>> how to use PYMOL based off of online support and online tutorials.
>> Currently, I am attempting to use the program to build an isolated
>section
>> of a protein with a known structure. I was just wondering how long does
>it
>> take to sculpt a protein segment? Is it possible to build an entire
>protein
>> with a known structure from scratch using PYMOL?
>>
>> Thank you

Hi Bishwa,

PyMOL lacks the feature to save secondary structure to PDB files. But 
you could install "psico" which is a add-on to PyMOL. It adds a 
"save_pdb" command (or overloads the save command if you like) which 
does write PDB files including secondary structure header.

http://pymolwiki.org/index.php/Psico

Hope that helps.

Cheers,
   Thomas

On 04/23/2012 12:07 AM, Bishwa Subedi wrote:
> Hi,
>
> I altered the secondary structure of the protein using alter command.
> I have the PDB file with the correct secondary structure and their
> appropriate length. But how can I save this information into my PDB
> coordinate file such that when I reopen the file I do not have to
> repeat the command again?
>
> Thank you in advance
>
> Bishwa

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Hi,

I altered the secondary structure of the protein using alter command. I have the PDB file with the correct secondary structure and their appropriate length. But how can I save this information into my PDB coordinate file such that when I reopen the file I do not have to repeat the command again?

Thank you in advance

Bishwa

Dear Jason,
Thanks for the tip about anaglyph_mode settings. I am using PyMOL version  
1.5.0.3. However, I usually work with carbon atoms painted either black or  
dark gray (over a light blue background). The optimized anaglyph setting  
makes it hard to differentiate red oxygens from black carbons. I guess  
that I will need some time to decide what combination of colors and  
anaglyph_mode setting suits me better.

On Fri, 20 Apr 2012 16:52:41 +0200, Jason Vertrees  
<jas...@sc...> wrote:
> Hi Luis,
>
> We've had "optimized anaglyph" in PyMOL for a  little while now. The
> default mode is to attenuate intensities in the left and right eyes to
> reduce strain and improve the 3D experience. If you have a recent
> build (eg. after v1.5.0) try anaglyph. Versions before that don't have
> the optimized colors. The new version also has a few different modes
> (see the alaglyph_mode setting).
>
> Cheers,
>
> -- Jason
>
> 2012/4/20 Luis M. Sánchez <lm...@un...>:
>> Hi,
>> Red-cyan and red-blue anaglyphs are affected by the chromatic aberration
>> of our eyes. If I use PyMOL's anaglyph stereo and close one of my eyes,
>> the red image is blurrier than the other one. Also, most of the red  
>> color is lost.
>>
>> Nowadays there are better color combinations for anaglyphs:
>> http://en.wikipedia.org/wiki/Anaglyph_3D . Suitable glasses are also
>> available from Amazon and other companies.
>>
>> Is there an option to change the colors used by PyMOL's anaglyp stereo?  
>> If
>> not, maybe we could have a magenta-cyan anaglyph option in the future?
>>
>> Thanks for a great program and best regards
>>
>> ------------------------------------------------------------------------------
>> For Developers, A Lot Can Happen In A Second.
>> Boundary is the first to Know...and Tell You.
>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
>> http://p.sf.net/sfu/Boundary-d2dvs2
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...

-- 
Luis M. Sánchez
IUOPA
Edificio Severo Ochoa
Campus del Cristo
33006 Oviedo
Teléfono: 985 10 9620

Hi Rolf,

The new code should fix this problem. Alternatively, put this in your
~/.pymolrc and see if it helps:

set use_shaders, 0
set sphere_mode, 0

Cheers,

-- Jason

On Fri, Apr 20, 2012 at 5:11 AM, Rolf S. Arvidson <rs...@gm...> wrote:
> Hi
> This is not a pymol problem per se, but I'm trying to figure out
> whether the error below is hardware-related (video card) or
> software-related (i.e., video driver/mesa/opengl libraries, etc.). If
> I run pymol from the command line (loading one of the demo files,
> pept.r3d), the pymol graphics and interface windows appear briefly and
> then close almost immediately. At the command line, the result is:
>
>  $ pymol /usr/share/pymol/test/dat/pept.r3d
>  Detected OpenGL version 2.0 or greater.  Shaders available.
>  Detected GLSL version 1.20.
>  Executive: object "pept" created.
>  python2.7: nv50_pc.h:351: nv_alloc_instruction: Assertion
> `pc->num_instructions < 2048' failed.
>  /usr/bin/pymol: line 2:  5112 Aborted                 python2.7 -O
> ${PYMOL_PATH}/__init__.py -q $*
>
> Also, pymol seems to function OK if I do not try to load a file, i.e.,
> the UI opens correctly and I can close it gracefully. If I try to load
> the demo file from the interface, it crashes with the above error.
> Starting pymol with -h yields the following:
>
>  $ pymol -h
>   PyMOL(TM) Molecular Graphics System, Version 1.5.0.3.
>   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 1.20.
>   OpenGL graphics engine:
>   GL_VENDOR: nouveau
>   GL_RENDERER: Gallium 0.4 on NV96
>   GL_VERSION: 2.1 Mesa 8.0.2
>   Detected 16 CPU cores.  Enabled multithreaded rendering.
>   PyMOL>quit
>   PyMOL: normal program termination.
>
> Alternatively, I can successfully generate png output from a script
> (provided I disable screen output), e.g.
>  $ cat makePNG.pml
> center origin
> zoom complete=0
> draw 2400
> png test.png, dpi=600
> $ pymol /usr/share/pymol/test/dat/pept.r3d -c -d "@./makePNG.pml"
>  Executive: object "pept" created.
> PyMOL>@./makePNG.pml
> PyMOL>center origin
> PyMOL>zoom complete=0
> PyMOL>draw 2400
> PyMOL>png test.png, dpi=600
>  Ray: render time: 0.08 sec. = 45537.9 frames/hour (0.08 sec. accum.).
>  ScenePNG: wrote 640x480 pixel image to file "test.png".
>
> If I ssh (with X-forwarding) to a remote machine with the identical
> pymol setup, the display works fine. I've searched for the above
> nv_alloc_instruction error, and it crops up on bugs related to the
> nouveau video driver
> (https://bugs.freedesktop.org/show_bug.cgi?id=46597). However, both
> the local and remote machine both use this same driver, and all
> supporting libraries as well. I've rebuilt the driver on the local
> machine and all its dependencies, mesa, opengl, etc., with no change
> in the above result. I've been pulling my hair out over this, and
> thought I'd ask here if anyone had any ideas. Thanks in advance.
>
> Cheers //Rolf
>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Luis,

We've had "optimized anaglyph" in PyMOL for a  little while now. The
default mode is to attenuate intensities in the left and right eyes to
reduce strain and improve the 3D experience. If you have a recent
build (eg. after v1.5.0) try anaglyph. Versions before that don't have
the optimized colors. The new version also has a few different modes
(see the alaglyph_mode setting).

Cheers,

-- Jason

2012/4/20 Luis M. Sánchez <lm...@un...>:
> Hi,
> Red-cyan and red-blue anaglyphs are affected by the chromatic aberration
> of our eyes. If I use PyMOL's anaglyph stereo and close one of my eyes,
> the red image is blurrier than the other one. Also, most of the red color
> is lost.
>
> Nowadays there are better color combinations for anaglyphs:
> http://en.wikipedia.org/wiki/Anaglyph_3D . Suitable glasses are also
> available from Amazon and other companies.
>
> Is there an option to change the colors used by PyMOL's anaglyp stereo? If
> not, maybe we could have a magenta-cyan anaglyph option in the future?
>
> Thanks for a great program and best regards
>
> --
> Luis M. Sánchez
> IUOPA
> Edificio Severo Ochoa
> Campus del Cristo
> 33006 Oviedo
> Teléfono: 985 10 9620
>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi,
Red-cyan and red-blue anaglyphs are affected by the chromatic aberration  
of our eyes. If I use PyMOL's anaglyph stereo and close one of my eyes,  
the red image is blurrier than the other one. Also, most of the red color  
is lost.

Nowadays there are better color combinations for anaglyphs:  
http://en.wikipedia.org/wiki/Anaglyph_3D . Suitable glasses are also  
available from Amazon and other companies.

Is there an option to change the colors used by PyMOL's anaglyp stereo? If  
not, maybe we could have a magenta-cyan anaglyph option in the future?

Thanks for a great program and best regards

--
Luis M. Sánchez
IUOPA
Edificio Severo Ochoa
Campus del Cristo
33006 Oviedo
Teléfono: 985 10 9620

Hi Julien,

how did you prepare the 2-state object?

If you like you can try to install "psico", it provides a quite robust 
"morpheasy" command.
http://pymolwiki.org/index.php/Psico

Cheers,
   Thomas

On 19.04.2012 19:43, Julien LV wrote:
> Hi,
>
> I'm trying to use rigimol for the first time.
>
> After creating an object with the 2 states, I run these commands
>
> from epymol import rigimol
> rigimol.morph("morph_in","morph_out",refinement=5,async=1)
>
> It runs for a few seconds, and then, error:
>
> Write-Interpolation>    end
> Morph-Error: no rigimol output received!
> Saved 'rigimol.inp' for troubleshooting...
>
> I have not attached rigimol.inp. It is too big (600Kb) for this mailing
> list and I didn't see anything informative.
>
> This is my version of pymol:
>
>   This Executable Build integrates and extends Open-Source PyMOL 1.5.0.4.
>   Detected OpenGL version 2.0 or greater. Shaders available.
>   Detected GLSL version 1.20.
>   Detected 4 CPU cores.  Enabled multithreaded rendering.
>
> Thanks!

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Hi
This is not a pymol problem per se, but I'm trying to figure out
whether the error below is hardware-related (video card) or
software-related (i.e., video driver/mesa/opengl libraries, etc.). If
I run pymol from the command line (loading one of the demo files,
pept.r3d), the pymol graphics and interface windows appear briefly and
then close almost immediately. At the command line, the result is:

  $ pymol /usr/share/pymol/test/dat/pept.r3d
  Detected OpenGL version 2.0 or greater.  Shaders available.
  Detected GLSL version 1.20.
  Executive: object "pept" created.
  python2.7: nv50_pc.h:351: nv_alloc_instruction: Assertion
`pc->num_instructions < 2048' failed.
  /usr/bin/pymol: line 2:  5112 Aborted                 python2.7 -O
${PYMOL_PATH}/__init__.py -q $*

Also, pymol seems to function OK if I do not try to load a file, i.e.,
the UI opens correctly and I can close it gracefully. If I try to load
the demo file from the interface, it crashes with the above error.
Starting pymol with -h yields the following:

  $ pymol -h
   PyMOL(TM) Molecular Graphics System, Version 1.5.0.3.
   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 1.20.
   OpenGL graphics engine:
   GL_VENDOR: nouveau
   GL_RENDERER: Gallium 0.4 on NV96
   GL_VERSION: 2.1 Mesa 8.0.2
   Detected 16 CPU cores.  Enabled multithreaded rendering.
   PyMOL>quit
   PyMOL: normal program termination.

Alternatively, I can successfully generate png output from a script
(provided I disable screen output), e.g.
  $ cat makePNG.pml
center origin
zoom complete=0
draw 2400
png test.png, dpi=600
$ pymol /usr/share/pymol/test/dat/pept.r3d -c -d "@./makePNG.pml"
 Executive: object "pept" created.
PyMOL>@./makePNG.pml
PyMOL>center origin
PyMOL>zoom complete=0
PyMOL>draw 2400
PyMOL>png test.png, dpi=600
 Ray: render time: 0.08 sec. = 45537.9 frames/hour (0.08 sec. accum.).
 ScenePNG: wrote 640x480 pixel image to file "test.png".

If I ssh (with X-forwarding) to a remote machine with the identical
pymol setup, the display works fine. I've searched for the above
nv_alloc_instruction error, and it crops up on bugs related to the
nouveau video driver
(https://bugs.freedesktop.org/show_bug.cgi?id=46597). However, both
the local and remote machine both use this same driver, and all
supporting libraries as well. I've rebuilt the driver on the local
machine and all its dependencies, mesa, opengl, etc., with no change
in the above result. I've been pulling my hair out over this, and
thought I'd ask here if anyone had any ideas. Thanks in advance.

Cheers //Rolf

Thomas,

Thanks--we'll add the fix ASAP.

Cheers,

-- J

On Thu, Apr 19, 2012 at 9:46 AM, Thomas Holder
<sp...@us...> wrote:
> Hi Rolf,
>
> the count_atoms command is fine. PyMOL truncates the first line of the
> xyz file to 6 characters, so it actually stopped reading the file after
> 139814 atoms. The fix is easy:
>
> --- layer2/ObjectMolecule.c     (revision 3996)
> +++ layer2/ObjectMolecule.c     (working copy)
> @@ -3481,7 +3481,7 @@
>    atInfo = *atInfoPtr;
>
>    p_store = p;
> -  p = ncopy(cc, p, 6);
> +  p = ncopy(cc, p, 9);
>    if(sscanf(cc, "%d", &nAtom) != 1) {
>      nAtom = 0;
>      tinker_xyz = false;
>
> Cheers,
>   Thomas
>
> On 04/19/2012 04:00 PM, Rolf S. Arvidson wrote:
>> Hi Jason,
>>
>> I've also posted a screen cap of VMD with the same file loaded
>>
>> http://www.ruf.rice.edu/~rsa4046/_private/pymol/cap4.png
>>
>> in which the correct atom count is reported. In addition, I tried this
>> with my licensed copy of PyMOL on my laptop (win7), also with same
>> (truncated) result as Linux session. Thanks again for any help you can
>> provide.
>>
>> Cheers //Rolf
>>
>> On Thu, Apr 19, 2012 at 07:58:56AM -0500, Rolf S. Arvidson wrote:
>>> Hi Jason,
>>>
>>> Thanks for the speedy reply. I've posted the ASCII .xyz data file,
>>> compressed equivalent, and screen caps at
>>>
>>> http://www.ruf.rice.edu/~rsa4046/_private/pymol/
>>>
>>> I have had some recent problems with pymol apparently hanging on this
>>> machine (possibly due to an opengl + nouveau-nvidia driver issue), that
>>> has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't
>>> know if my problem with atom count was related. You're right, it does
>>> indeed seem as if the last digit is just truncated. To test if this was
>>> just a display issue, I also tried loading the same data file within
>>> pymol (without the LIBGL statement) on a remote machine (although same
>>> version, OS, and libraries) via ssh X-forwarding, and derived the same
>>> result in terms of reported number of atoms from count_atoms, although I
>>> don't know if such a test is really definitive. Thanks very much for any
>>> insight you can provide.
>>>
>>> Cheers //Rolf
>>>
>>> On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote:
>>>> Hi Rolf,
>>>>
>>>> That's pretty strange. Any chance you can share the file? It looks
>>>> like PyMOL's somehow missing the last number in the result. I've
>>>> easily loaded millions of atoms before and got the correct atom count.
>>>>
>>>> Cheers,
>>>>
>>>> -- Jason
>>>>
>>>> On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson<rs...@gm...>  wrote:
>>>>> I am using pymol to display the surface of inorganic crystals, and
>>>>> have used it successfully in the past for relatively small molecules.
>>>>> I am not trying to display larger surfaces (>1e6 atoms), and now
>>>>> notice a discrepancy between the number of atoms present in and loaded
>>>>> from the source file, and that reported by pymol. I have included an
>>>>> example using a file with 1398146 atoms. VMD loads and displays the
>>>>> same file and reports the correct number of atom entries. However,
>>>>> pymol oddly reports 139814 atoms, not 1398146. However, as far as I
>>>>> can tell, the atoms do *appear* in the graphical display. I've posted
>>>>> some screen captures at
>>>>>
>>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png
>>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png
>>>>>
>>>>> to illustrate this. Can anyone guess at the cause of this? I am using
>>>>> version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1
>>>>> kernel, 12012MB RAM).
>>>>> Many thanks //Rolf
>>>>
>>>> --
>>>> Jason Vertrees, PhD
>>>> PyMOL Product Manager
>>>> Schrödinger, LLC
>>>>
>>>> (e) Jas...@sc...
>>>> (o) +1 (603) 374-7120
>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Thomas,

Your patch got the file loaded in its entirety, thanks!

	$ pymol $SIM -c -d "@./png.pml"
	 ExecutiveLoad: "output/flicker-1811000.xyz" loaded as "flicker-1811000", through state 1.
	PyMOL>@./png.pml
	 Selector: selection "cube" defined with 1398146 atoms.
	PyMOL>count_atoms cube
	 Selector: selection "cube" defined with 1398146 atoms.
	 count_atoms: 1398146 atoms
	...

I posted the result at

http://www.ruf.rice.edu/~rsa4046/_private/pymol/flicker-1811000.png

Thanks again-
Cheers //Rolf

On Thu, Apr 19, 2012 at 12:11:56PM -0500, Rolf S. Arvidson wrote:
> Hi Thomas,
> Thanks very much for this patch, I will apply and post back results. Cheers!
> // Rolf
> 
> On Thu, Apr 19, 2012 at 11:46 AM, Thomas Holder
> <sp...@us...> wrote:
> > Hi Rolf,
> >
> > the count_atoms command is fine. PyMOL truncates the first line of the
> > xyz file to 6 characters, so it actually stopped reading the file after
> > 139814 atoms. The fix is easy:
> >
> > --- layer2/ObjectMolecule.c     (revision 3996)
> > +++ layer2/ObjectMolecule.c     (working copy)
> > @@ -3481,7 +3481,7 @@
> >    atInfo = *atInfoPtr;
> >
> >    p_store = p;
> > -  p = ncopy(cc, p, 6);
> > +  p = ncopy(cc, p, 9);
> >    if(sscanf(cc, "%d", &nAtom) != 1) {
> >      nAtom = 0;
> >      tinker_xyz = false;
> >
> > Cheers,
> >   Thomas
> >
> > On 04/19/2012 04:00 PM, Rolf S. Arvidson wrote:
> >> Hi Jason,
> >>
> >> I've also posted a screen cap of VMD with the same file loaded
> >>
> >> http://www.ruf.rice.edu/~rsa4046/_private/pymol/cap4.png
> >>
> >> in which the correct atom count is reported. In addition, I tried this
> >> with my licensed copy of PyMOL on my laptop (win7), also with same
> >> (truncated) result as Linux session. Thanks again for any help you can
> >> provide.
> >>
> >> Cheers //Rolf
> >>
> >> On Thu, Apr 19, 2012 at 07:58:56AM -0500, Rolf S. Arvidson wrote:
> >>> Hi Jason,
> >>>
> >>> Thanks for the speedy reply. I've posted the ASCII .xyz data file,
> >>> compressed equivalent, and screen caps at
> >>>
> >>> http://www.ruf.rice.edu/~rsa4046/_private/pymol/
> >>>
> >>> I have had some recent problems with pymol apparently hanging on this
> >>> machine (possibly due to an opengl + nouveau-nvidia driver issue), that
> >>> has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't
> >>> know if my problem with atom count was related. You're right, it does
> >>> indeed seem as if the last digit is just truncated. To test if this was
> >>> just a display issue, I also tried loading the same data file within
> >>> pymol (without the LIBGL statement) on a remote machine (although same
> >>> version, OS, and libraries) via ssh X-forwarding, and derived the same
> >>> result in terms of reported number of atoms from count_atoms, although I
> >>> don't know if such a test is really definitive. Thanks very much for any
> >>> insight you can provide.
> >>>
> >>> Cheers //Rolf
> >>>
> >>> On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote:
> >>>> Hi Rolf,
> >>>>
> >>>> That's pretty strange. Any chance you can share the file? It looks
> >>>> like PyMOL's somehow missing the last number in the result. I've
> >>>> easily loaded millions of atoms before and got the correct atom count.
> >>>>
> >>>> Cheers,
> >>>>
> >>>> -- Jason
> >>>>
> >>>> On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson<rs...@gm...>  wrote:
> >>>>> I am using pymol to display the surface of inorganic crystals, and
> >>>>> have used it successfully in the past for relatively small molecules.
> >>>>> I am not trying to display larger surfaces (>1e6 atoms), and now
> >>>>> notice a discrepancy between the number of atoms present in and loaded
> >>>>> from the source file, and that reported by pymol. I have included an
> >>>>> example using a file with 1398146 atoms. VMD loads and displays the
> >>>>> same file and reports the correct number of atom entries. However,
> >>>>> pymol oddly reports 139814 atoms, not 1398146. However, as far as I
> >>>>> can tell, the atoms do *appear* in the graphical display. I've posted
> >>>>> some screen captures at
> >>>>>
> >>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png
> >>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png
> >>>>>
> >>>>> to illustrate this. Can anyone guess at the cause of this? I am using
> >>>>> version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1
> >>>>> kernel, 12012MB RAM).
> >>>>> Many thanks //Rolf
> >>>>
> >>>> --
> >>>> Jason Vertrees, PhD
> >>>> PyMOL Product Manager
> >>>> Schrödinger, LLC
> >>>>
> >>>> (e) Jas...@sc...
> >>>> (o) +1 (603) 374-7120
> >
> >
> > --
> > Thomas Holder
> > MPI for Developmental Biology
> > Spemannstr. 35
> > D-72076 Tübingen
> >
> > ------------------------------------------------------------------------------
> > For Developers, A Lot Can Happen In A Second.
> > Boundary is the first to Know...and Tell You.
> > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> > http://p.sf.net/sfu/Boundary-d2dvs2
> > _______________________________________________
> > 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,

I'm trying to use rigimol for the first time.


After creating an object with the 2 states, I run these commands

from epymol import rigimol
rigimol.morph("morph_in","morph_out",refinement=5,async=1)

It runs for a few seconds, and then, error:

Write-Interpolation>    end
Morph-Error: no rigimol output received!
Saved 'rigimol.inp' for troubleshooting...

I have not attached rigimol.inp. It is too big (600Kb) for this mailing
list and I didn't see anything informative.

This is my version of pymol:

 This Executable Build integrates and extends Open-Source PyMOL 1.5.0.4.
 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.20.
 Detected 4 CPU cores.  Enabled multithreaded rendering.

Thanks!

JLV

Hi Thomas,
Thanks very much for this patch, I will apply and post back results. Cheers!
// Rolf

On Thu, Apr 19, 2012 at 11:46 AM, Thomas Holder
<sp...@us...> wrote:
> Hi Rolf,
>
> the count_atoms command is fine. PyMOL truncates the first line of the
> xyz file to 6 characters, so it actually stopped reading the file after
> 139814 atoms. The fix is easy:
>
> --- layer2/ObjectMolecule.c     (revision 3996)
> +++ layer2/ObjectMolecule.c     (working copy)
> @@ -3481,7 +3481,7 @@
>    atInfo = *atInfoPtr;
>
>    p_store = p;
> -  p = ncopy(cc, p, 6);
> +  p = ncopy(cc, p, 9);
>    if(sscanf(cc, "%d", &nAtom) != 1) {
>      nAtom = 0;
>      tinker_xyz = false;
>
> Cheers,
>   Thomas
>
> On 04/19/2012 04:00 PM, Rolf S. Arvidson wrote:
>> Hi Jason,
>>
>> I've also posted a screen cap of VMD with the same file loaded
>>
>> http://www.ruf.rice.edu/~rsa4046/_private/pymol/cap4.png
>>
>> in which the correct atom count is reported. In addition, I tried this
>> with my licensed copy of PyMOL on my laptop (win7), also with same
>> (truncated) result as Linux session. Thanks again for any help you can
>> provide.
>>
>> Cheers //Rolf
>>
>> On Thu, Apr 19, 2012 at 07:58:56AM -0500, Rolf S. Arvidson wrote:
>>> Hi Jason,
>>>
>>> Thanks for the speedy reply. I've posted the ASCII .xyz data file,
>>> compressed equivalent, and screen caps at
>>>
>>> http://www.ruf.rice.edu/~rsa4046/_private/pymol/
>>>
>>> I have had some recent problems with pymol apparently hanging on this
>>> machine (possibly due to an opengl + nouveau-nvidia driver issue), that
>>> has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't
>>> know if my problem with atom count was related. You're right, it does
>>> indeed seem as if the last digit is just truncated. To test if this was
>>> just a display issue, I also tried loading the same data file within
>>> pymol (without the LIBGL statement) on a remote machine (although same
>>> version, OS, and libraries) via ssh X-forwarding, and derived the same
>>> result in terms of reported number of atoms from count_atoms, although I
>>> don't know if such a test is really definitive. Thanks very much for any
>>> insight you can provide.
>>>
>>> Cheers //Rolf
>>>
>>> On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote:
>>>> Hi Rolf,
>>>>
>>>> That's pretty strange. Any chance you can share the file? It looks
>>>> like PyMOL's somehow missing the last number in the result. I've
>>>> easily loaded millions of atoms before and got the correct atom count.
>>>>
>>>> Cheers,
>>>>
>>>> -- Jason
>>>>
>>>> On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson<rs...@gm...>  wrote:
>>>>> I am using pymol to display the surface of inorganic crystals, and
>>>>> have used it successfully in the past for relatively small molecules.
>>>>> I am not trying to display larger surfaces (>1e6 atoms), and now
>>>>> notice a discrepancy between the number of atoms present in and loaded
>>>>> from the source file, and that reported by pymol. I have included an
>>>>> example using a file with 1398146 atoms. VMD loads and displays the
>>>>> same file and reports the correct number of atom entries. However,
>>>>> pymol oddly reports 139814 atoms, not 1398146. However, as far as I
>>>>> can tell, the atoms do *appear* in the graphical display. I've posted
>>>>> some screen captures at
>>>>>
>>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png
>>>>> http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png
>>>>>
>>>>> to illustrate this. Can anyone guess at the cause of this? I am using
>>>>> version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1
>>>>> kernel, 12012MB RAM).
>>>>> Many thanks //Rolf
>>>>
>>>> --
>>>> Jason Vertrees, PhD
>>>> PyMOL Product Manager
>>>> Schrödinger, LLC
>>>>
>>>> (e) Jas...@sc...
>>>> (o) +1 (603) 374-7120
>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
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Rolf,

Thanks for posting the file. I will look at it later tonight and get back
to you.

Cheers ,

Sent from my Android.
On Apr 19, 2012 5:58 AM, "Rolf S. Arvidson" <rs...@gm...> wrote:

> Hi Jason,
>
> Thanks for the speedy reply. I've posted the ASCII .xyz data file,
> compressed equivalent, and screen caps at
>
> http://www.ruf.rice.edu/~rsa4046/_private/pymol/
>
> I have had some recent problems with pymol apparently hanging on this
> machine (possibly due to an opengl + nouveau-nvidia driver issue), that
> has necessitated use of "LIBGL_ALWAYS_SOFTWARE=1 pymol ...", and didn't
> know if my problem with atom count was related. You're right, it does
> indeed seem as if the last digit is just truncated. To test if this was
> just a display issue, I also tried loading the same data file within
> pymol (without the LIBGL statement) on a remote machine (although same
> version, OS, and libraries) via ssh X-forwarding, and derived the same
> result in terms of reported number of atoms from count_atoms, although I
> don't know if such a test is really definitive. Thanks very much for any
> insight you can provide.
>
> Cheers //Rolf
>
> On Thu, Apr 19, 2012 at 12:40:09AM -0700, Jason Vertrees wrote:
> > Hi Rolf,
> >
> > That's pretty strange. Any chance you can share the file? It looks
> > like PyMOL's somehow missing the last number in the result. I've
> > easily loaded millions of atoms before and got the correct atom count.
> >
> > Cheers,
> >
> > -- Jason
> >
> > On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson <rs...@gm...>
> wrote:
> > > I am using pymol to display the surface of inorganic crystals, and
> > > have used it successfully in the past for relatively small molecules.
> > > I am not trying to display larger surfaces (>1e6 atoms), and now
> > > notice a discrepancy between the number of atoms present in and loaded
> > > from the source file, and that reported by pymol. I have included an
> > > example using a file with 1398146 atoms. VMD loads and displays the
> > > same file and reports the correct number of atom entries. However,
> > > pymol oddly reports 139814 atoms, not 1398146. However, as far as I
> > > can tell, the atoms do *appear* in the graphical display. I've posted
> > > some screen captures at
> > >
> > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap1.png
> > > http://i1111.photobucket.com/albums/h464/lokidawg/pymol/cap2.png
> > >
> > > to illustrate this. Can anyone guess at the cause of this? I am using
> > > version 1.5.0.2, compiled from source (Funtoo Linux x86_64, 3.3.1
> > > kernel, 12012MB RAM).
> > > Many thanks //Rolf
> > >
> > >
> ------------------------------------------------------------------------------
> > > For Developers, A Lot Can Happen In A Second.
> > > Boundary is the first to Know...and Tell You.
> > > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> > > http://p.sf.net/sfu/Boundary-d2dvs2
> > > _______________________________________________
> > > PyMOL-users mailing list (PyM...@li...)
> > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > Archives:
> http://www.mail-archive.com/pym...@li...
> >
> >
> >
> > --
> > Jason Vertrees, PhD
> > PyMOL Product Manager
> > Schrödinger, LLC
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
>