pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Babban,

regarding your questions on peptide building:

> My last doubt is about creating polymers out a given PDB ?
> I am studying the fibrils of some proteins and although the structure of 
> fibril is not know but through some analysis I have come to understand 
> the region in peptide which is leading to fibrillation.

PyMOL has a builder where you can create a peptide with given secondary 
structure. In the external GUI click on "Builder" on the right and then 
"Protein" on the left side.

You may also check this PyMOLWiki page:
http://www.pymolwiki.org/index.php/Peptide_Sequence

> I want to be able to create a PDB which has like 4/8/16 monomeric 
> peptide combined through some BETA PLEATED region(i.e the peptides will 
> join/aggregate around that region (beta region) of the peptide ) and all 
> I have is the PDB of the monomeric peptide.

As far as I know there's no build-in PyMOL function that sticks together 
two beta-strands.

In editing mode you can freely drag around objects: Right-click, "drag 
object coords", SHIFT+Middle-Mouse-Drag.

More precide movements can be achived with translate and rotate commands:
http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures#Translate_or_rotate_individual_objects

If this is not precise enough for you and you want real beta-sheet 
modeling, you should use something like modeller.

Cheers,
   Thomas

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

Hi Jeff,

> I have several questions about extending PyMOL via modules or plugins.
>
> It appears that the primary difference between the two is windows for
> modules are created at during start up and plugin windows can be brought up
> on demand (from the plugins menu). Are there other differences?

I would say a pymol plugin is just a module that provides a
__init_plugin__ (or __init__) function which gets as argument the
PMGApp instance, which is PyMOLs external GUI. This is of course
required if the module wants to add items to the plugins menu or open
dialogs. But extending the plugins menu or opening any windows is not
mandatory for plugins or other modules.

> What is the current status of wxPython versus Tkinter for the future of
> PyMOL? I could look at wxPython, but I seem to be at a loss to find the
> python binary for the prebuilt Mac OS PyMOL Application.
>
> This has probably been brought up before, what are the issues with using an
> egg for extensions that have more than one file?

If you stay with pure python and just import your module, there should
be no issues. However the plugin architecture (modules within the
pmg_tk/startup directory) so far only recognizes single python files
(this will most likely change in the future).

Cheers,
  Thomas

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

Hi Everyone,

I`m writing a Python plug-in that depends on a certain Python module. For
Linux users It would be easy to install this module because is available
through the repositories (I think Mac OsX has a repositories system too, but
I am not sure) . But for Windows this could be a little more complicated, 1)
They don´t have a repository system and 2) Python is not installed by
default in Windows, hence if they install any Python module this module will
not be available to PyMol.

I think there are at least two options.

1) The easy one (for me): To distribute a "README" file with the
instructions to install the plugin in each platform and to make my plug-in
to check if the module if available, if not ask the user to install it.

2) The easy one (for the user): To distribute this module with my plug-in,
and create some "installer" to perform the installation in a more or less
automatic way.

Which option would be the better? It is option 2 to complicated to
implement?, it is worthwhile? which are the easiest way to install Python
modules on Windows and Mac OsX (and making them available to PyMol)?

Thanks in advance.

Cheers,

Osvaldo.

Dear users,

Is there some program to calculate the zeta potential or streaming
potential
of protein molecules (PDB files )

Is there some program to calculate the dipole moment of protein molecules
at
different PH values?


My last doubt is about creating polymers out a given PDB ?
I am studying the fibrils of some proteins and although the structure of
fibril is not know but through some analysis I have come to understand the
region in peptide which is leading to fibrillation.

I want to be able to create a PDB which has like 4/8/16 monomeric peptide
combined through some BETA PLEATED region(i.e the peptides will
join/aggregate around that region (beta region) of the peptide ) and all I
have is the PDB of the monomeric peptide.

Is there a possibility to make such peptides in Pymol or something ? Please
advise.


Thanks for your help.

Sincerely

I have several questions about extending PyMOL via modules or plugins.

It appears that the primary difference between the two is windows for 
modules are created at during start up and plugin windows can be brought up 
on demand (from the plugins menu). Are there other differences?

What is the current status of wxPython versus Tkinter for the future of 
PyMOL? I could look at wxPython, but I seem to be at a loss to find the 
python binary for the prebuilt Mac OS PyMOL Application.

This has probably been brought up before, what are the issues with using an 
egg for extensions that have more than one file?

Regards,

Jeff Van Voorst

Hi!

Is it possible to run pymol without libGL libraries? I want to render a
movie on a compute cluster. The cluster has no X server/sophisticated
graphical libraries.

The stuff that I found in this list about "libGL" is written by people
who have problems with the GUI, but since I do not want to see any
GUI... ^^

I tried pymol -c, but this results in the following error:
pymol.exe: error while loading shared libraries: libGL.so.1: cannot open
shared object file: No such file or directory

Greets,
Christian


-- 
Christian Seifert, M.Sc.
HPC Administrator
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: cse...@bp...
Web: http://www.bph.rub.de

I have a slightly different answer using (almost:) only PyMOL commands:

# take 1acb as example
fetch 1acb, async=0
import numpy
# center is [x0,y0,z0]
x0,y0,z0=[1,2,3]
alldist = []
iterate_state 1,  1acb, 
alldist.append(numpy.sqrt(numpy.sum([(x-x0)**2,(y-y0)**2,(z-z0)**2])))
# assign dist to b-factors!
di = iter(alldist)
alter 1acb, b=di.next()
spectrum b, rainbow, 1acb

The distance computation line is awkward. I thought of using distance() 
command to replace it. It is also much faster to use distance(). But I 
failed to dig distance values out of the object generated by distance(). 
Anybody knows how to do that?

cheers,hongbo

On 28.07.2011 5:06, Thomas Holder wrote:
> Hi Robert,
>
> you can set the distance between each atom and the center as b-factor, 
> and then use spectrum (or spectrumany [1]) for coloring.
>
> I wrote a small python script that will do that, see attachment.
>
> Example (in PyMOL command line):
>
> run distancecoloring.py
> centerdistance2b (all)
> spectrum b, blue_white_red, (all)
>
> Cheers,
>   Thomas
>
> [1] http://pymolwiki.org/index.php/Spectrumany
>
> On 07/28/2011 04:29 PM, Muench, Robert wrote:
>> Dear community,
>>
>> I was searching the internet for several days now to find out how to
>> perform a distance dependent coloring in pymol.
>>
>> The idea is to color the surface of a viral (spherical) structure. I
>> would like to define the xyz-coordinates of the center of the viral
>> structure an color all residues with a gradient depending on the
>> distance from these xyz coordinates.
>>
>> Can anyone please help me out?
>>
>> All the best
>>
>> Robert
>>
>> *Robert Münch***
>>
>> ---------------------------------------------------------
>>
>> Dipl. Biologist / PhD-Student
>>
>> *Paul-Ehrlich-Institut*
>>
>> Federal Institute for Vaccines and Biomedicines
>>
>> Division of Medical Biotechnology
>>
>> Section 6/5 - Viral Gene Transfer Medicinal Products
>>
>> 63225 Langen, Germany
>>
>> Phone: +49-6103-77-4222
>>
>> Fax: +49-6103-77-1255
>
>
> ------------------------------------------------------------------------------
> Got Input?   Slashdot Needs You.
> Take our quick survey online.  Come on, we don't ask for help often.
> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
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>
>
> _______________________________________________
> 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 Robert,

I did something like this in the past. Check out the ramp_new command
page on the PyMOLWiki for an example
(http://pymolwiki.org/index.php/Ramp_new#Elaborate_examples) for
arbitrary functions.

Here's a very quick way to color a surface by distance from a given
point--here I chose the origin (0,0,0):

# fetch a friendly protein

fetch 1hug, async=0

# show it as a surface

as surface

# create a pseudoatom at the origin; we will
# measure the distance from this point

pseudoatom pOrig, pos=(0,0,0), label=origin

# create a new color ramp, measuring the distance
# from pOrig to 1hug, colored as rainbow

ramp_new proximityRamp, pOrig, selection=1hug, range=[5,65], color=rainbow

# set the surface color to the ramp coloring

set surface_color, proximityRamp, 1hug

# some older PyMOLs need this recoloring/rebuilding

recolor; rebuild

Cheers,

-- Jason


On Thu, Jul 28, 2011 at 10:29 AM, Muench, Robert <Rob...@pe...> wrote:
> Dear community,
>
>
>
> I was  searching the internet for several days now to find out how to
> perform a distance dependent coloring in pymol.
>
> The idea is to color the surface of a viral (spherical) structure. I would
> like to define the xyz-coordinates of the center of the viral structure an
> color all residues with a gradient depending on the distance from these xyz
> coordinates.
>
> Can anyone please help me out?
>
>
>
> All the best
>
>
>
> Robert
>
>
>
>
>
> Robert Münch
>
> ---------------------------------------------------------
>
> Dipl. Biologist / PhD-Student
>
> Paul-Ehrlich-Institut
>
> Federal Institute for Vaccines and Biomedicines
>
> Division of Medical Biotechnology
>
> Section 6/5 - Viral Gene Transfer Medicinal Products
>
> 63225 Langen, Germany
>
>
>
> Phone: +49-6103-77-4222
>
> Fax: +49-6103-77-1255
>
> ---------------------------------------------------------
>
>
>
> ------------------------------------------------------------------------------
> Got Input?   Slashdot Needs You.
> Take our quick survey online.  Come on, we don't ask for help often.
> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
> http://p.sf.net/sfu/slashdot-survey
> _______________________________________________
> 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
Schrodinger, LLC

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

Hi Robert,

you can set the distance between each atom and the center as b-factor, 
and then use spectrum (or spectrumany [1]) for coloring.

I wrote a small python script that will do that, see attachment.

Example (in PyMOL command line):

run distancecoloring.py
centerdistance2b (all)
spectrum b, blue_white_red, (all)

Cheers,
   Thomas

[1] http://pymolwiki.org/index.php/Spectrumany

On 07/28/2011 04:29 PM, Muench, Robert wrote:
> Dear community,
>
> I was searching the internet for several days now to find out how to
> perform a distance dependent coloring in pymol.
>
> The idea is to color the surface of a viral (spherical) structure. I
> would like to define the xyz-coordinates of the center of the viral
> structure an color all residues with a gradient depending on the
> distance from these xyz coordinates.
>
> Can anyone please help me out?
>
> All the best
>
> Robert
>
> *Robert Münch***
>
> ---------------------------------------------------------
>
> Dipl. Biologist / PhD-Student
>
> *Paul-Ehrlich-Institut*
>
> Federal Institute for Vaccines and Biomedicines
>
> Division of Medical Biotechnology
>
> Section 6/5 - Viral Gene Transfer Medicinal Products
>
> 63225 Langen, Germany
>
> Phone: +49-6103-77-4222
>
> Fax: +49-6103-77-1255

-- 
Thomas Holder
MPI for Developmental Biology

Hi Jason,

Thanks for your prompt reply.

2011/7/28 Jason Vertrees <jas...@sc...>

>
> > This only happens if I use the "set use_shaders, 1". If I don't use this
> > command, the "cartoon" and "stick" are displayed in the right colour, but
> > then I have problems coloring the sticks (it's a known bug :
> >
> http://www.mail-archive.com/pym...@li.../msg09181.html
> ).
>
>
> The stick coloring bug was fixed not too long ago. Please try pulling
> the source code and rebuilding or ask your package maintainer rebuild.
>
>
Sorry I am not sure I understand you.

I still have the stick coloring bug. But also now I have a problem with
cartoon.

I am using latest Pymol 1.4.1 downloaded from schrodinger website (we're
customers). I haven't found any newer source code around, but only a beta.

Which source code you mean ?


>
> > Is this a known bug ? Does anybody know what to do ?
>
> What does PyMOL report upon launching? Does it emit any messages about
> shaders? For my computer I see:
> """
> PyMOL(TM) Incentive Product - PyMOL Executable Build
>  Copyright (C) Schrodinger, LLC
>
>  This PyMOL Executable Build is available only to PyMOL Power, Casual, and
>  Developer Users who have a valid license to use this software product. Any
>  other usage is specifically prohibited and may constitute a violation of
>  United States and international copyright laws.
>
>  This Executable Build integrates and extends Open-Source PyMOL 1.5.0.
>  Detected OpenGL version 2.0 or greater.  Shaders available.
>  Detected GLSL version 1.20.
>  Adjusting settings to improve performance for ATI cards.
>  Detected 16 CPU cores.  Enabled multithreaded rendering.
> """
>
> So please copy/paste that block from your version of PyMOL.
>
>
 This Executable Build integrates and extends Open-Source PyMOL 1.4.1.
 Detected OpenGL version 2.0 or greater.  Shaders available.
 Detected GLSL version 1.20.
 Detected 2 CPU cores.  Enabled multithreaded rendering.





>
> > By the way, this is a relevant piece of output of my glxinfo command on
> > linux :
> > OpenGL vendor string: Tungsten Graphics, Inc
> > OpenGL renderer string: Mesa DRI Mobile Intel® GM45 Express Chipset GEM
> > 20100330 DEVELOPMENT x86/MMX/SSE2
> > OpenGL version string: 2.1 Mesa 7.9-devel
>
> After seeing this, my suggestions are: (1) update your video driver to
> the most recent (stable) version; (2) use the latest PyMOL source
> code.
>
>
(1) I think I am already using the latest stable, but another user suggested
using the latest unstable version has fixed it. I am going to give it a try.

(2) As said above, where can I find this latest pymol source ?

Thanks.

Regards



> Cheers,
>
> -- Jason
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>

Dear community,

I was  searching the internet for several days now to find out how to perform a distance dependent coloring in pymol.
The idea is to color the surface of a viral (spherical) structure. I would like to define the xyz-coordinates of the center of the viral structure an color all residues with a gradient depending on the distance from these xyz coordinates.
Can anyone please help me out?

All the best

Robert


Robert Münch
---------------------------------------------------------
Dipl. Biologist / PhD-Student
Paul-Ehrlich-Institut
Federal Institute for Vaccines and Biomedicines
Division of Medical Biotechnology
Section 6/5 - Viral Gene Transfer Medicinal Products
63225 Langen, Germany

Phone: +49-6103-77-4222
Fax: +49-6103-77-1255
---------------------------------------------------------

Hi Santiago,

> I've found a problem with Pymol version 1.4.1. I am using Ubuntu 10.10 in a
> laptop with Intel Mobile 4 graphics controller.
>
> The problem comes when I load any PDB file, then try to show it as a
> cartoon. It displays the cartoon but in black color, so I cannot see it
> unless I turn the background to white. With "lines" it's correctly displayed
> but "cartoon" or "sticks" show the same behaviour (colored black).

There was an older Linux bug that caused PyMOL to improperly
initialize shaders on some systems. There are also driver issues with
the Intel Mobile GMx45 cards.


> This only happens if I use the "set use_shaders, 1". If I don't use this
> command, the "cartoon" and "stick" are displayed in the right colour, but
> then I have problems coloring the sticks (it's a known bug :
> http://www.mail-archive.com/pym...@li.../msg09181.html).

The stick coloring bug was fixed not too long ago. Please try pulling
the source code and rebuilding or ask your package maintainer rebuild.


> I don't know if this is related but immediately after loading the pdb I get
> this message in the pymol console :
> PyMOL>load FILE.pdb
>  ObjectMoleculeGuessValences(
> 1,1): Unreasonable connectivity in heteroatom,
>   unsuccessful in guessing valences.

This message is unrelated.


> Is this a known bug ? Does anybody know what to do ?

What does PyMOL report upon launching? Does it emit any messages about
shaders? For my computer I see:
"""
PyMOL(TM) Incentive Product - PyMOL Executable Build
 Copyright (C) Schrodinger, LLC

 This PyMOL Executable Build is available only to PyMOL Power, Casual, and
 Developer Users who have a valid license to use this software product. Any
 other usage is specifically prohibited and may constitute a violation of
 United States and international copyright laws.

 This Executable Build integrates and extends Open-Source PyMOL 1.5.0.
 Detected OpenGL version 2.0 or greater.  Shaders available.
 Detected GLSL version 1.20.
 Adjusting settings to improve performance for ATI cards.
 Detected 16 CPU cores.  Enabled multithreaded rendering.
"""

So please copy/paste that block from your version of PyMOL.


> By the way, this is a relevant piece of output of my glxinfo command on
> linux :
> OpenGL vendor string: Tungsten Graphics, Inc
> OpenGL renderer string: Mesa DRI Mobile Intel® GM45 Express Chipset GEM
> 20100330 DEVELOPMENT x86/MMX/SSE2
> OpenGL version string: 2.1 Mesa 7.9-devel

After seeing this, my suggestions are: (1) update your video driver to
the most recent (stable) version; (2) use the latest PyMOL source
code.

Cheers,

-- Jason

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

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

Hi Bernhard,

I just installed this new driver :
xserver-xorg-video-intel_2.13.901-2ubuntu2~xup~maverick_i386.deb

And the problem remains the same. Also tried installing the combo of :

libdrm-intel1_2.4.23+git20110119.550fe2ca-0ubuntu0sarvatt~maverick_i386.deb
xserver-xorg-video-intel_2.14.0+git20110220.9599fde6-0ubuntu0sarvatt~maverick_i386.deb

And no luck either.

Which Ubuntu version are you using, 10.10 or 11.04 ?

Also, could you please tell me exactly which driver version are you using ?
Or how did you install them, so I can follow your steps.

Thanks


2011/7/28 Bernhard Lechtenberg <bc...@ca...>

> Hello Santiago,
>
> have you tried using the graphics drivers from the xorg-edgers project?
>
> That helped me with the stick coloring problem:
> http://www.mail-archive.com/pym...@li.../msg09210.html
>
> and may also help with your problem.
>
> Bernhard
>
>
> -----Original Message-----
> From: Santi Rios <sri...@gm...>
> To: pym...@li...
> Subject: [PyMOL] Pymol 1.4.1 problem coloring cartoons. They turn to
> black.
> Date: Thu, 28 Jul 2011 11:37:56 +0200
>
> Dear Pymol Users,
>
> I've found a problem with Pymol version 1.4.1. I am using Ubuntu 10.10
> in a laptop with Intel Mobile 4 graphics controller.
>
> The problem comes when I load any PDB file, then try to show it as a
> cartoon. It displays the cartoon but in black color, so I cannot see it
> unless I turn the background to white. With "lines" it's correctly
> displayed but "cartoon" or "sticks" show the same behaviour (colored
> black).
>
> This only happens if I use the "set use_shaders, 1". If I don't use this
> command, the "cartoon" and "stick" are displayed in the right colour,
> but then I have problems coloring the sticks (it's a known bug :
> http://www.mail-archive.com/pym...@li.../msg09181.html
> ).
>
> I don't know if this is related but immediately after loading the pdb I
> get this message in the pymol console :
> PyMOL>load FILE.pdb
>  ObjectMoleculeGuessValences(
> 1,1): Unreasonable connectivity in heteroatom,
>  unsuccessful in guessing valences.
>
> Is this a known bug ? Does anybody know what to do ?
>
> Thanks
>
> Regards,
> Santiago
>
> By the way, this is a relevant piece of output of my glxinfo command on
> linux :
> OpenGL vendor string: Tungsten Graphics, Inc
> OpenGL renderer string: Mesa DRI Mobile Intel® GM45 Express Chipset GEM
> 20100330 DEVELOPMENT x86/MMX/SSE2
> OpenGL version string: 2.1 Mesa 7.9-devel
>
> ------------------------------------------------------------------------------
> Got Input?   Slashdot Needs You.
> Take our quick survey online.  Come on, we don't ask for help often.
> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
> http://p.sf.net/sfu/slashdot-survey
> _______________________________________________ PyMOL-users mailing list (
> PyM...@li...) Info Page:
> https://lists.sourceforge.net/lists/listinfo/pymol-users Archives:
> http://www.mail-archive.com/pym...@li...
>
>
>
> ------------------------------------------------------------------------------
> Got Input?   Slashdot Needs You.
> Take our quick survey online.  Come on, we don't ask for help often.
> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
> http://p.sf.net/sfu/slashdot-survey
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hello Santiago,

have you tried using the graphics drivers from the xorg-edgers project?

That helped me with the stick coloring problem:
http://www.mail-archive.com/pym...@li.../msg09210.html

and may also help with your problem.

Bernhard


-----Original Message-----
From: Santi Rios <sri...@gm...>
To: pym...@li...
Subject: [PyMOL] Pymol 1.4.1 problem coloring cartoons. They turn to
black.
Date: Thu, 28 Jul 2011 11:37:56 +0200

Dear Pymol Users,

I've found a problem with Pymol version 1.4.1. I am using Ubuntu 10.10
in a laptop with Intel Mobile 4 graphics controller.

The problem comes when I load any PDB file, then try to show it as a
cartoon. It displays the cartoon but in black color, so I cannot see it
unless I turn the background to white. With "lines" it's correctly
displayed but "cartoon" or "sticks" show the same behaviour (colored
black).

This only happens if I use the "set use_shaders, 1". If I don't use this
command, the "cartoon" and "stick" are displayed in the right colour,
but then I have problems coloring the sticks (it's a known bug :
http://www.mail-archive.com/pym...@li.../msg09181.html).

I don't know if this is related but immediately after loading the pdb I
get this message in the pymol console :
PyMOL>load FILE.pdb
 ObjectMoleculeGuessValences(
1,1): Unreasonable connectivity in heteroatom,
  unsuccessful in guessing valences.

Is this a known bug ? Does anybody know what to do ?

Thanks

Regards,
Santiago

By the way, this is a relevant piece of output of my glxinfo command on
linux :
OpenGL vendor string: Tungsten Graphics, Inc
OpenGL renderer string: Mesa DRI Mobile Intel® GM45 Express Chipset GEM
20100330 DEVELOPMENT x86/MMX/SSE2
OpenGL version string: 2.1 Mesa 7.9-devel
------------------------------------------------------------------------------
Got Input?   Slashdot Needs You.
Take our quick survey online.  Come on, we don't ask for help often.
Plus, you'll get a chance to win $100 to spend on ThinkGeek.
http://p.sf.net/sfu/slashdot-survey
_______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li...

Dear Pymol Users,

I've found a problem with Pymol version 1.4.1. I am using Ubuntu 10.10 in a
laptop with Intel Mobile 4 graphics controller.

The problem comes when I load any PDB file, then try to show it as a
cartoon. It displays the cartoon but in black color, so I cannot see it
unless I turn the background to white. With "lines" it's correctly displayed
but "cartoon" or "sticks" show the same behaviour (colored black).

This only happens if I use the "set use_shaders, 1". If I don't use this
command, the "cartoon" and "stick" are displayed in the right colour, but
then I have problems coloring the sticks (it's a known bug :
http://www.mail-archive.com/pym...@li.../msg09181.html
).

I don't know if this is related but immediately after loading the pdb I get
this message in the pymol console :
PyMOL>load FILE.pdb
 ObjectMoleculeGuessValences(
1,1): Unreasonable connectivity in heteroatom,
  unsuccessful in guessing valences.

Is this a known bug ? Does anybody know what to do ?

Thanks

Regards,
Santiago

By the way, this is a relevant piece of output of my glxinfo command on
linux :
OpenGL vendor string: Tungsten Graphics, Inc
OpenGL renderer string: Mesa DRI Mobile Intel® GM45 Express Chipset GEM
20100330 DEVELOPMENT x86/MMX/SSE2
OpenGL version string: 2.1 Mesa 7.9-devel

Greetings,

Just a quick note to let you know that the latest versions of MacPyMOL
(1.4.x+) should work without issue on Mac OS X 10.7 (Lion). I did some
quick testing and everything worked well. If you update and find any
problems with PyMOL, please let me know.

Cheers,

-- Jason

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

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

Hi Peter,

I suggest you post a concomitant page on the PyMOLWiki
(http://pymolwiki.org). If you need a PyMOLWiki account, please email
me and I'll set it up for you.

The scripts look pretty good; my suggestion would be to save the
identified residues in named selections
(http://www.pymolwiki.org/index.php/Named_Atom_Selections) as well.
This makes it easier for PyMOL users to interact with the data.

Cheers,

-- Jason


> (e.g., protein-protein or protein-DNAcontact surfaces), or if modification
> sites that are separated by many residues in the primary structure might lie
> close to each other in the tertiary structure, suggesting possible mechanism
> for cross-talk between modification sites.
> Please let colleagues that may be interested in this feature and who use
> Pymol know about this feature.
> I would welcome feedback on this implementation might be improved.
> Peter
>
> Peter Hornbeck, Ph.D.
> Senior Scientist, Director of PhosphoSitePlus®
> http://www.phosphosite.org
> Cell Signaling Technology
> 3 Trask Lane
> Danvers, MA 01923
> Phone: (978) 867-2368
>
>
> ------------------------------------------------------------------------------
> Magic Quadrant for Content-Aware Data Loss Prevention
> Research study explores the data loss prevention market. Includes in-depth
> analysis on the changes within the DLP market, and the criteria used to
> evaluate the strengths and weaknesses of these DLP solutions.
> http://www.accelacomm.com/jaw/sfnl/114/51385063/
> _______________________________________________
> 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
Schrodinger, LLC

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

We have added a subroutine to the structure viewer window of PhosphoSitePlus® (PSP)
 (http://www.phosphosite.org) that generates downloadable scripts that label and color amino acids  that are known to be post-translationally modified.

Only the reactive groups on each amino acid are colored, e.g. -OH on Ser, Thr or Tyr.

For example, go to the PKACa page on PSP (http://www.phosphosite.org/proteinAction.do?id=637&showAllSites=true), select 2GUB, and open the viewer. By clicking on "Get PyMOL Script", a rendering script will be downloaded onto your desktop which can be opened in PyMOL.

The intent of this routine is to allow users to determine if known modification sites might lie within known functional regions of the protein (e.g., protein-protein or protein-DNAcontact surfaces), or if modification sites that are separated by many residues in the primary structure might lie close to each other in the tertiary structure, suggesting possible mechanism for cross-talk between modification sites.

Please let colleagues that may be interested in this feature and who use Pymol know about this feature.

I would welcome feedback on this implementation might be improved.

Peter


Peter Hornbeck, Ph.D.
Senior Scientist, Director of PhosphoSitePlus®
http://www.phosphosite.org
Cell Signaling Technology
3 Trask Lane
Danvers, MA 01923
Phone: (978) 867-2368

On Mon, Jul 25, 2011 at 1:27 AM, Thomas Holder
<sp...@us...> wrote:
> Hi lina,
>
> lina wrote, On 07/22/11 12:55:
>>
>> Thanks very much for your advice, but I don't know which part is wrong,
>> the new saved one is not the ideal one I wanted, which was supposed to
>> be the one I saw from screen.
>>
>> do I need to modify the transfrom_by_camera_rotation scrips a bit.
>> actually I don't get it very well.
>
> looks like I confused you, I'm sorry for that. No, you don't need to modify
> the script. The script defines a new command, so you first need to run the
> script, and then call the command, otherwise nothing will happen actually.
>
> run transform_by_camera_rotation.py    # run the script
> transform_by_camera_rotation           # call the new command

Last time I forget calling the new command,

It works very well.

Thanks with best regards,


lina
> save /tmp/withneworientation.pdb       # save the file
>
> Is that clear?
>
> Cheers,
>  Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>

Hi lina,

lina wrote, On 07/22/11 12:55:
> Thanks very much for your advice, but I don't know which part is wrong,
> the new saved one is not the ideal one I wanted, which was supposed to
> be the one I saw from screen.
> 
> do I need to modify the transfrom_by_camera_rotation scrips a bit.
> actually I don't get it very well.

looks like I confused you, I'm sorry for that. No, you don't need to 
modify the script. The script defines a new command, so you first need 
to run the script, and then call the command, otherwise nothing will 
happen actually.

run transform_by_camera_rotation.py    # run the script
transform_by_camera_rotation           # call the new command
save /tmp/withneworientation.pdb       # save the file

Is that clear?

Cheers,
   Thomas

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

Hi jpd,

> from the get_object_matrix output,
> i can use the euler-rodrigues transformation
> http://en.wikipedia.org/wiki/Euler%E2%80%93Rodrigues_formula
> and get the axis and angle of rotation.
> 
> is there a way to place the axis?

if I understand you correct, you are looking for the translation T so 
that for object matrix M it yields:

M = T * R * T^-1

With python (and numpy):

from numpy import reshape, linalg, identity
M = cmd.get_object_matrix(object_name)
M = reshape(M, (4,4))
t = linalg.solve(identity(3) - M[0:3,0:3], M[0:3,3])

see if this is correct:

from numpy import identity, matrix
R = identity(4)
T = identity(4)
R[0:3,0:3] = M[0:3,0:3]
T[0:3,3] = t
# should print two times the same matrix
print M
print matrix(T) * matrix(R) * matrix(T).I

Hope that helps.

Cheers,
   Thomas

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

hi,
from the get_object_matrix output,
i can use the euler-rodrigues transformation
http://en.wikipedia.org/wiki/Euler%E2%80%93Rodrigues_formula
and get the axis and angle of rotation.

is there a way to place the axis?
perhaps from the translation vector in the matrix?

thanks
jpd

Thank you all for your help.  Looks like both ProFit and rms_cur will do
just what I needed.

Thanks!

Tom


--
Thomas D. Grant
Graduate Research Assistant
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203



On Fri, Jul 22, 2011 at 10:59 AM, Michael Lerner <mgl...@gm...> wrote:

> PyMOL's rms_cur command will do what you want. E.g.
>
> fetch 1rx1
> fetch 1ra1
>
> # reports "Executive: RMS =   34.329 (159 to 159 atoms)"
> # because the structures still need to be translated and rotated
> rms_cur (1rx1 and name CA), (1ra1 and name CA)
>
> # reports "Executive: RMS =    0.862 (159 to 159 atoms)"
> # because it calculates translated/rotated value, but does now
> # apply the translation/rotation to the molecules
> rms (1rx1 and name CA), (1ra1 and name CA)
>
>
> # reports "Executive: RMS =    0.391 (1026 to 1026 atoms)"
> # standard PyMOL align, which also translates and rotates
> align 1rx1, 1ra1
>
> # both of these report "Executive: RMS =    0.862 (159 to 159 atoms)"
> # because the structures have now been translated and rotated
> rms_cur (1rx1 and name CA), (1ra1 and name CA)
> rms (1rx1 and name CA), (1ra1 and name CA)
>
> Cheers,
>
> -Michael
>
>
> On Fri, Jul 22, 2011 at 10:19 AM, Thomas Grant <tg...@hw...>wrote:
>
>> Dear all,
>>
>> I'm attempting to align a series of structures using the CEAlign plug-in
>> in PyMOL due to a lack of any detectable sequence homology.  CEAlign does a
>> good job of aligning and the fits are very reasonable.  However, the RMSD
>> that is calculated is based only on the c-alphas that were actually aligned,
>> not based on the total number of c-alphas in the structure.  After searching
>> online I have been unable to find any software or servers that will simply
>> calculate the RMSD of two structures as is, without aligning them first.  I
>> would think this would be a relatively straightforward thing to do, just to
>> calculate RMSD from two existing structures without translation or rotation
>> for alignment.
>>
>> Does anyone know of a way either in PyMOL or in general to simply
>> calculate the RMSD between all c-alphas of two structures?  Obviously it
>> won't necessarily be a one-to-one ratio of c-alphas, but I can manually
>> curate the pdb to include only the equivalent and "aligned" residues, even
>> if not used in the CEAlign algorithm, so that there are the same number of
>> c-alphas in both structures.
>>
>> Thank you for any help and suggestions,
>>
>> Tom
>>
>>
>> ------------------------------------------------------------------------------
>> 10 Tips for Better Web Security
>> Learn 10 ways to better secure your business today. Topics covered
>> include:
>> Web security, SSL, hacker attacks & Denial of Service (DoS), private keys,
>> security Microsoft Exchange, secure Instant Messaging, and much more.
>> http://www.accelacomm.com/jaw/sfnl/114/51426210/
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
> as of August 15th:
>
> Department of Physics and Astronomy
> Earlham College
> 801 National Road West
> Richmond, IN   47374-4095
>
>

PyMOL's rms_cur command will do what you want. E.g.

fetch 1rx1
fetch 1ra1

# reports "Executive: RMS =   34.329 (159 to 159 atoms)"
# because the structures still need to be translated and rotated
rms_cur (1rx1 and name CA), (1ra1 and name CA)

# reports "Executive: RMS =    0.862 (159 to 159 atoms)"
# because it calculates translated/rotated value, but does now
# apply the translation/rotation to the molecules
rms (1rx1 and name CA), (1ra1 and name CA)


# reports "Executive: RMS =    0.391 (1026 to 1026 atoms)"
# standard PyMOL align, which also translates and rotates
align 1rx1, 1ra1

# both of these report "Executive: RMS =    0.862 (159 to 159 atoms)"
# because the structures have now been translated and rotated
rms_cur (1rx1 and name CA), (1ra1 and name CA)
rms (1rx1 and name CA), (1ra1 and name CA)

Cheers,

-Michael


On Fri, Jul 22, 2011 at 10:19 AM, Thomas Grant <tg...@hw...>wrote:

> Dear all,
>
> I'm attempting to align a series of structures using the CEAlign plug-in in
> PyMOL due to a lack of any detectable sequence homology.  CEAlign does a
> good job of aligning and the fits are very reasonable.  However, the RMSD
> that is calculated is based only on the c-alphas that were actually aligned,
> not based on the total number of c-alphas in the structure.  After searching
> online I have been unable to find any software or servers that will simply
> calculate the RMSD of two structures as is, without aligning them first.  I
> would think this would be a relatively straightforward thing to do, just to
> calculate RMSD from two existing structures without translation or rotation
> for alignment.
>
> Does anyone know of a way either in PyMOL or in general to simply calculate
> the RMSD between all c-alphas of two structures?  Obviously it won't
> necessarily be a one-to-one ratio of c-alphas, but I can manually curate the
> pdb to include only the equivalent and "aligned" residues, even if not used
> in the CEAlign algorithm, so that there are the same number of c-alphas in
> both structures.
>
> Thank you for any help and suggestions,
>
> Tom
>
>
> ------------------------------------------------------------------------------
> 10 Tips for Better Web Security
> Learn 10 ways to better secure your business today. Topics covered include:
> Web security, SSL, hacker attacks & Denial of Service (DoS), private keys,
> security Microsoft Exchange, secure Instant Messaging, and much more.
> http://www.accelacomm.com/jaw/sfnl/114/51426210/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

as of August 15th:

Department of Physics and Astronomy
Earlham College
801 National Road West
Richmond, IN   47374-4095

Tom-

Try ProFit
http://www.bioinf.org.uk/software/profit/

Jed

Thomas Grant wrote:
> Dear all,
>
> I'm attempting to align a series of structures using the CEAlign 
> plug-in in PyMOL due to a lack of any detectable sequence homology. 
>  CEAlign does a good job of aligning and the fits are very reasonable. 
>  However, the RMSD that is calculated is based only on the c-alphas 
> that were actually aligned, not based on the total number of c-alphas 
> in the structure.  After searching online I have been unable to find 
> any software or servers that will simply calculate the RMSD of two 
> structures as is, without aligning them first.  I would think this 
> would be a relatively straightforward thing to do, just to calculate 
> RMSD from two existing structures without translation or rotation for 
> alignment.
>
> Does anyone know of a way either in PyMOL or in general to simply 
> calculate the RMSD between all c-alphas of two structures?  Obviously 
> it won't necessarily be a one-to-one ratio of c-alphas, but I can 
> manually curate the pdb to include only the equivalent and "aligned" 
> residues, even if not used in the CEAlign algorithm, so that there are 
> the same number of c-alphas in both structures.
>
> Thank you for any help and suggestions,
>
> Tom
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> 10 Tips for Better Web Security
> Learn 10 ways to better secure your business today. Topics covered include:
> Web security, SSL, hacker attacks & Denial of Service (DoS), private keys,
> security Microsoft Exchange, secure Instant Messaging, and much more.
> http://www.accelacomm.com/jaw/sfnl/114/51426210/
> ------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

-- 
------------------------
Jed Goldstone, PhD
Research Specialist
Woods Hole Oceanographic Institution
Redfield 3-52 MS#32
Woods Hole, MA 02543
http://www.whoi.edu/hpb/Site.do?id=481
Phone: 508-289-4823