pymol-users Mailing List for PyMOL Molecular Graphics System

Der Pymol users!

I wounder to know if it possible to increase rendering rate mainly at the
expense of the GPU usage. At my desktop with core i7 and 6 cpu (12 cpus in
the hyper-threading mode) I've spend  ~ 2 hours to render image consisted
of ensemble of conformations (~ 30 aligned pdbs) using only CPUs.

set ray_trance mode, 1
ray 3000
png ./1.png


Does it possible to add some loading to the gpu as well?


James

Hello List,

is there any good reason why PyMOL can not read PDBML data files ?


Cheers,
Jerome 

Thanks for the clarification.

Osvaldo.


On Thu, Nov 28, 2013 at 2:11 PM, Tsjerk Wassenaar <ts...@gm...> wrote:

> Hi Osvaldo,
>
> The problem can be understood from the description of 'super'.
>
> #---------------------
> PyMOL>help super
>
> DESCRIPTION
>
>         NOTE: This feature is experimental and unsupported.
>
>         "super" performs a residue-based pairwise alignment followed by a
>         structural superposition, and then carries out zero or more cycles
>         of refinement in order to reject outliers.
> #---------------------
>
> The point is the alignment. Pymol needs the C-alphas for that. You can
> achieve what you want with 'rms'.
>
> Cheers,
>
> Tsjerk
>
>
>
>
> On Thu, Nov 28, 2013 at 5:13 PM, Osvaldo Martin <alo...@gm...>wrote:
>
>> Hi,
>>
>> I am trying to use the comand cmd.super() to calculate the rmsd between
>> the sidechains of two proteins using
>>
>> cmd.super('%s and not name ca+c+o+n' % obj0, '%s and not name ca+c+o+n' %
>> obj1)
>>
>> And I get this error
>> ExecutiveAlign: invalid selections for alignment.
>>
>> It seems to me that the problem is related to the exclusion of the "ca"
>> atoms. because:
>>
>> cmd.super('%s and not name c+o+n' % obj0, '%s and not name c+o+n' % obj1)
>>
>> works, but
>>
>> cmd.super('%s and not name ca' % obj0, '%s and not name ca' % obj1)
>>
>> does not work.
>>
>>
>> Osvaldo.
>>
>>
>> ------------------------------------------------------------------------------
>> Rapidly troubleshoot problems before they affect your business. Most IT
>> organizations don't have a clear picture of how application performance
>> affects their revenue. With AppDynamics, you get 100% visibility into your
>> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>

Hi Osvaldo,

The problem can be understood from the description of 'super'.

#---------------------
PyMOL>help super

DESCRIPTION

        NOTE: This feature is experimental and unsupported.

        "super" performs a residue-based pairwise alignment followed by a
        structural superposition, and then carries out zero or more cycles
        of refinement in order to reject outliers.
#---------------------

The point is the alignment. Pymol needs the C-alphas for that. You can
achieve what you want with 'rms'.

Cheers,

Tsjerk




On Thu, Nov 28, 2013 at 5:13 PM, Osvaldo Martin <alo...@gm...>wrote:

> Hi,
>
> I am trying to use the comand cmd.super() to calculate the rmsd between
> the sidechains of two proteins using
>
> cmd.super('%s and not name ca+c+o+n' % obj0, '%s and not name ca+c+o+n' %
> obj1)
>
> And I get this error
> ExecutiveAlign: invalid selections for alignment.
>
> It seems to me that the problem is related to the exclusion of the "ca"
> atoms. because:
>
> cmd.super('%s and not name c+o+n' % obj0, '%s and not name c+o+n' % obj1)
>
> works, but
>
> cmd.super('%s and not name ca' % obj0, '%s and not name ca' % obj1)
>
> does not work.
>
>
> Osvaldo.
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Hi,

I am trying to use the comand cmd.super() to calculate the rmsd between the
sidechains of two proteins using

cmd.super('%s and not name ca+c+o+n' % obj0, '%s and not name ca+c+o+n' %
obj1)

And I get this error
ExecutiveAlign: invalid selections for alignment.

It seems to me that the problem is related to the exclusion of the "ca"
atoms. because:

cmd.super('%s and not name c+o+n' % obj0, '%s and not name c+o+n' % obj1)

works, but

cmd.super('%s and not name ca' % obj0, '%s and not name ca' % obj1)

does not work.


Osvaldo.

You can try installing the ATI proprietary driver (fglrx, Catalyst) 
instead of using the open source driver that come with Ubuntu. Check to 
see if this driver is compatible with your card.

I've had nothing but trouble and bad luck getting ATI graphics cards to 
work under linux. If building from scratch, I install an NVidia graphic 
card. Their proprietary drivers seem to have fewer problems. You can get 
a capable GeForce card for $30-$40 if you don't want 3D stereo.

Cheers,

_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rro...@co...

On 11/26/2013 10:51 AM, Hitesh Patel wrote:
> Hello all,
> I installed ubuntu 13.10 on my PC. It has ATI Radeon HD 4650 graphics 
> card.
> When I am trying to load a pdb file in PyMol, It gives following error.
> Which drivers do I need to install?
> *EE ../../../../../../src/gallium/drivers/r600/r600_state.c:2373 
> r600_adjust_gprs - ps & vs shader require too many register (109 + 20) 
> for a combined maximum of 128
> EE ../../../../../../src/gallium/drivers/r600/r600_shader.c:1580 
> r600_shader_from_tgsi - GPR limit exceeded - shader requires 128 registers
> EE ../../../../../../src/gallium/drivers/r600/r600_shader.c:158 
> r600_pipe_shader_create - translation from TGSI failed !
> EE ../../../../../../src/gallium/drivers/r600/r600_state_common.c:754 
> r600_shader_select - Failed to build shader variant (type=1) -12
> EE ../../../../../../src/gallium/drivers/r600/r600_state.c:2373 
> r600_adjust_gprs - ps & vs shader require too many register (109 + 20) 
> for a combined maximum of 128
> *
> Thanks,
>
> Regards,
>
> Hitesh Patel
>
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
>
>
> _______________________________________________
> 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 all,
I installed ubuntu 13.10 on my PC. It has ATI Radeon HD 4650 graphics card.
When I am trying to load a pdb file in PyMol, It gives following error.
Which drivers do I need to install?





*EE ../../../../../../src/gallium/drivers/r600/r600_state.c:2373
r600_adjust_gprs - ps & vs shader require too many register (109 + 20) for
a combined maximum of 128 EE
../../../../../../src/gallium/drivers/r600/r600_shader.c:1580
r600_shader_from_tgsi - GPR limit exceeded - shader requires 128
registersEE ../../../../../../src/gallium/drivers/r600/r600_shader.c:158
r600_pipe_shader_create - translation from TGSI failed ! EE
../../../../../../src/gallium/drivers/r600/r600_state_common.c:754
r600_shader_select - Failed to build shader variant (type=1) -12EE
../../../../../../src/gallium/drivers/r600/r600_state.c:2373
r600_adjust_gprs - ps & vs shader require too many register (109 + 20) for
a combined maximum of 128 *
Thanks,

Regards,

Hitesh Patel

  many thanks jason…..worked a treat…..

    j.


Dr. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
University Research Lecturer
DIAMOND Research Fellow

Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK

Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547       

On 25 Nov 2013, at 14:29, Jason Vertrees <jas...@sc...> wrote:

> Jon,
> 
> You can also iterate over a selection and show the color index for each color
> 
> iterate *, color
> 
> You can then color by those indices, eg:
> 
> color 26
> 
> Cheers,
> 
> -- Jason
> 
> 
> On Mon, Nov 25, 2013 at 5:42 AM, Jonathan Grimes <jon...@st...> wrote:
> 
>  dear all,
> 
>   i am having implementing these instructions.
> 
>   i would like to work out what color an object is……
> 
>   how is this defined …..
> 
> > s["names"][1][5][0][1]
> >
> > equals your object name.
> 
>   if I have an object called A1…i am unsure how to
>    make A1 equal to s["names"][1][5][0][1]
> 
> 
>   many thanks
> 
>   jon
> 
> 
> Dr. Jonathan M. Grimes,
> NDM Senior Reseach Fellow
> University Research Lecturer
> DIAMOND Research Fellow
> 
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> University of Oxford
> Roosevelt Drive,
> Oxford OX3 7BN, UK
> 
> Email: Jon...@st..., Web: www.strubi.ox.ac.uk
> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
> 
> On 12 Dec 2012, at 17:24, Jason Vertrees <jas...@sc...> wrote:
> 
> > Hi Jon,
> >
> >> ive been given a pse file.....and i am trying to work out what color
> >>   an object is......
> >>
> >>   i used the command
> >>
> >> get cartoon_color, pT_A
> >>
> >>  and got back....
> >>
> >> get: cartoon_color = default in object pT_A
> >
> > You're right, that's not very helpful. This will get you the answer,
> > but it's not very straightforward:
> >
> > s = cmd.get_session()
> >
> > print cmd.get_color_tuple(s["names"][1][5][0][2])
> >
> > To make sure you have right object ensure that,
> >
> > s["names"][1][5][0][1]
> >
> > equals your object name.
> >
> > Cheers,
> >
> > -- Jason
> >
> > --
> > Jason Vertrees, PhD
> > Director of Core Modeling Product Management
> > Schrödinger, Inc.
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
> 
> 
> 
> 
> -- 
> Jason Vertrees, PhD
> Director of Core Modeling Products
> Schrödinger, Inc.
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

  many thanks……much appreciated.
 
    jon


Dr. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
University Research Lecturer
DIAMOND Research Fellow

Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK

Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547       

On 25 Nov 2013, at 18:29, Sampson, Jared <Jar...@ny...> wrote:

> Hi Jonathan - 
> 
> There is a script by Christoph Gohlke on the PyMOL Wiki called transformations.py  which may be useful.  It provides several functions that can be used to manipulate quaternions.  I used it to calculate pseudo-twofold axes for my Fab elbow angle script last year.  The implementation would be different, using camera matrices instead of object matrices, but the general idea would be similar.
> 
> Cheers,
> Jared
> 
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> 550 First Avenue
> New York, NY 10016
> 212-263-7898
> http://kong.med.nyu.edu/
> 
> 
> 
> 
> 
> 
> On Nov 25, 2013, at 11:20 AM, Robert Hanson <ha...@st...>
>  wrote:
> 
>> Jonathan, this is called the quaternion difference, but I don't know how you get access to quaternions in PyMOL. If you could, you would just take the difference between the two quaternion representations of the views and get it's angle for the corresponding axis-angle.
>> 
>> Jason, are there standard Python utilities that one can use to get the quaternion equivalents of PyMOL matrices?
>> 
>> Bob
>>  
>> 
>> 
>> On Mon, Nov 25, 2013 at 9:14 AM, Jonathan Grimes <jon...@st...> wrote:
>> 
>>    is there a script available to calculate the min rotation about a vector
>>    that describes the relationship between 2 views……
>> 
>>    i am happy to ignore any translational component but i have 2 views
>>    of a molecule and want to say that theres a *** deg rotation between the
>>     2 views ?
>> 
>>    thanks
>>     jon
>> 
>> 
>> Dr. Jonathan M. Grimes,
>> NDM Senior Reseach Fellow
>> University Research Lecturer
>> DIAMOND Research Fellow
>> 
>> Division of Structural Biology
>> Wellcome Trust Centre for Human Genetics
>> University of Oxford
>> Roosevelt Drive,
>> Oxford OX3 7BN, UK
>> 
>> Email: Jon...@st..., Web: www.strubi.ox.ac.uk
>> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
>> 
>> 
>> ------------------------------------------------------------------------------
>> Shape the Mobile Experience: Free Subscription
>> Software experts and developers: Be at the forefront of tech innovation.
>> Intel(R) Software Adrenaline delivers strategic insight and game-changing
>> conversations that shape the rapidly evolving mobile landscape. Sign up now.
>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>> 
>> 
>> 
>> -- 
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>> 
>> 
>> If nature does not answer first what we want,
>> it is better to take what answer we get. 
>> 
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>> 
>> ------------------------------------------------------------------------------
>> Shape the Mobile Experience: Free Subscription
>> Software experts and developers: Be at the forefront of tech innovation.
>> Intel(R) Software Adrenaline delivers strategic insight and game-changing 
>> conversations that shape the rapidly evolving mobile landscape. Sign up now. 
>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk_______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
> 
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
> =================================

Hi Suzanne,

the showbumps.py script uses the sculpting mechanism, which is no real energy forcefield and thus those units are arbitrary.

Calculating the stability of a mutant is a very advanced task, and PyMOL is not made for that. PyMOL can give you visual clues for your reasoning, like obvious vdw clashes.

A tool that I've used in the past to calculate mutant ddG: http://foldx.crg.es/
There are of course others, like ROSETTA, or MD simulations.

For sculpting, see also:
http://www.mail-archive.com/pym...@li.../msg00359.html
http://pymolwiki.org/index.php/Molecular_Sculpting

Cheers,
  Thomas

On 25 Nov 2013, at 14:40, Lapolla, Suzanne M (HSC) <suz...@ou...> wrote:

> I noticed my question was truncated when I submitted it so will try again.
> When I run showbumps.py on Pymol I get a vanderwaal value of about 163.
> I need a good ref point as to what that number represents.
> Thanks, Suzanne

I noticed my question was truncated when I submitted it so will try again.
When I run showbumps.py on Pymol I get a vanderwaal value of about 163.
I need a good ref point as to what that number represents.
Thanks, Suzanne

Hi Jonathan -

There is a script by Christoph Gohlke on the PyMOL Wiki called transformations.py<" rel="nofollow">http://pymolwiki.org/index.php/Transformations>  which may be useful.  It provides several functions that can be used to manipulate quaternions.  I used it to calculate pseudo-twofold axes for my Fab elbow angle<" rel="nofollow">http://pymolwiki.org/index.php/Elbow_angle> script last year.  The implementation would be different, using camera matrices instead of object matrices, but the general idea would be similar.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Nov 25, 2013, at 11:20 AM, Robert Hanson <ha...@st...<mailto:ha...@st...>>
 wrote:

Jonathan, this is called the quaternion difference, but I don't know how you get access to quaternions in PyMOL. If you could, you would just take the difference between the two quaternion representations of the views and get it's angle for the corresponding axis-angle.

Jason, are there standard Python utilities that one can use to get the quaternion equivalents of PyMOL matrices?

Bob



On Mon, Nov 25, 2013 at 9:14 AM, Jonathan Grimes <jon...@st...<mailto:jon...@st...>> wrote:

   is there a script available to calculate the min rotation about a vector
   that describes the relationship between 2 views……

   i am happy to ignore any translational component but i have 2 views
   of a molecule and want to say that theres a *** deg rotation between the
    2 views ?

   thanks
    jon


Dr. Jonathan M. Grimes,
NDM Senior Reseach Fellow
University Research Lecturer
DIAMOND Research Fellow

Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK

Email: Jon...@st...<mailto:Jon...@st...>, Web: www.strubi.ox.ac.uk<" rel="nofollow">http://www.strubi.ox.ac.uk/>
Tel: (+44) - 1865 - 287561<tel:%28%2B44%29%20-%201865%20-%20287561>, FAX: (+44) - 1865 - 287547<tel:%28%2B44%29%20-%201865%20-%20287547>


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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

------------------------------------------------------------------------------
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conversations that shape the rapidly evolving mobile landscape. Sign up now.
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------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

Jonathan, this is called the quaternion difference, but I don't know how
you get access to quaternions in PyMOL. If you could, you would just take
the difference between the two quaternion representations of the views and
get it's angle for the corresponding axis-angle.

Jason, are there standard Python utilities that one can use to get the
quaternion equivalents of PyMOL matrices?

Bob



On Mon, Nov 25, 2013 at 9:14 AM, Jonathan Grimes
<jon...@st...>wrote:

>
>    is there a script available to calculate the min rotation about a vector
>    that describes the relationship between 2 views……
>
>    i am happy to ignore any translational component but i have 2 views
>    of a molecule and want to say that theres a *** deg rotation between the
>     2 views ?
>
>    thanks
>     jon
>
>
> Dr. Jonathan M. Grimes,
> NDM Senior Reseach Fellow
> University Research Lecturer
> DIAMOND Research Fellow
>
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> University of Oxford
> Roosevelt Drive,
> Oxford OX3 7BN, UK
>
> Email: Jon...@st..., Web: www.strubi.ox.ac.uk
> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
>
>
>
> ------------------------------------------------------------------------------
> Shape the Mobile Experience: Free Subscription
> Software experts and developers: Be at the forefront of tech innovation.
> Intel(R) Software Adrenaline delivers strategic insight and game-changing
> conversations that shape the rapidly evolving mobile landscape. Sign up
> now.
> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

   is there a script available to calculate the min rotation about a vector
   that describes the relationship between 2 views……
 
   i am happy to ignore any translational component but i have 2 views
   of a molecule and want to say that theres a *** deg rotation between the 
    2 views ?

   thanks
    jon


Dr. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
University Research Lecturer
DIAMOND Research Fellow

Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK

Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547       

Jon,

You can also iterate over a selection and show the color index for each
color

iterate *, color

You can then color by those indices, eg:

color 26

Cheers,

-- Jason


On Mon, Nov 25, 2013 at 5:42 AM, Jonathan Grimes
<jon...@st...>wrote:

>
>  dear all,
>
>   i am having implementing these instructions.
>
>   i would like to work out what color an object is……
>
>   how is this defined …..
>
> > s["names"][1][5][0][1]
> >
> > equals your object name.
>
>   if I have an object called A1…i am unsure how to
>    make A1 equal to s["names"][1][5][0][1]
>
>
>   many thanks
>
>   jon
>
>
> Dr. Jonathan M. Grimes,
> NDM Senior Reseach Fellow
> University Research Lecturer
> DIAMOND Research Fellow
>
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> University of Oxford
> Roosevelt Drive,
> Oxford OX3 7BN, UK
>
> Email: Jon...@st..., Web: www.strubi.ox.ac.uk
> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
>
> On 12 Dec 2012, at 17:24, Jason Vertrees <jas...@sc...>
> wrote:
>
> > Hi Jon,
> >
> >> ive been given a pse file.....and i am trying to work out what color
> >>   an object is......
> >>
> >>   i used the command
> >>
> >> get cartoon_color, pT_A
> >>
> >>  and got back....
> >>
> >> get: cartoon_color = default in object pT_A
> >
> > You're right, that's not very helpful. This will get you the answer,
> > but it's not very straightforward:
> >
> > s = cmd.get_session()
> >
> > print cmd.get_color_tuple(s["names"][1][5][0][2])
> >
> > To make sure you have right object ensure that,
> >
> > s["names"][1][5][0][1]
> >
> > equals your object name.
> >
> > Cheers,
> >
> > -- Jason
> >
> > --
> > Jason Vertrees, PhD
> > Director of Core Modeling Product Management
> > Schrödinger, Inc.
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
>
>


-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

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

Hi Jon,

this will give you the A1 object color:

s = cmd.get_session("A1", partial=1, compress=0)
print cmd.get_color_tuple(s["names"][0][5][0][2])

I use to query the color of the first atom instead of the "object color", see psico.querying.get_color:
https://github.com/speleo3/pymol-psico/blob/master/psico/querying.py

Cheers,
  Thomas

On 25 Nov 2013, at 06:42, Jonathan Grimes <jon...@st...> wrote:
> dear all,
> 
>  i am having implementing these instructions.  
> 
>  i would like to work out what color an object is……
> 
>  how is this defined …..
> 
>> s["names"][1][5][0][1]
>> 
>> equals your object name.
> 
>  if I have an object called A1…i am unsure how to 
>   make A1 equal to s["names"][1][5][0][1]
> 
> 
>  many thanks
> 
>  jon
> 
> 
> Dr. Jonathan M. Grimes, 
> NDM Senior Reseach Fellow
> University Research Lecturer
> DIAMOND Research Fellow
> 
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> University of Oxford
> Roosevelt Drive,
> Oxford OX3 7BN, UK
> 
> Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547       

 dear all,

  i am having implementing these instructions.  

  i would like to work out what color an object is……

  how is this defined …..

> s["names"][1][5][0][1]
> 
> equals your object name.

  if I have an object called A1…i am unsure how to 
   make A1 equal to s["names"][1][5][0][1]


  many thanks

  jon


Dr. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
University Research Lecturer
DIAMOND Research Fellow

Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK

Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547       

On 12 Dec 2012, at 17:24, Jason Vertrees <jas...@sc...> wrote:

> Hi Jon,
> 
>> ive been given a pse file.....and i am trying to work out what color
>>   an object is......
>> 
>>   i used the command
>> 
>> get cartoon_color, pT_A
>> 
>>  and got back....
>> 
>> get: cartoon_color = default in object pT_A
> 
> You're right, that's not very helpful. This will get you the answer,
> but it's not very straightforward:
> 
> s = cmd.get_session()
> 
> print cmd.get_color_tuple(s["names"][1][5][0][2])
> 
> To make sure you have right object ensure that,
> 
> s["names"][1][5][0][1]
> 
> equals your object name.
> 
> Cheers,
> 
> -- Jason
> 
> --
> Jason Vertrees, PhD
> Director of Core Modeling Product Management
> Schrödinger, Inc.
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Hi Pawel,

Have a look here:
http://euclideanspace.com/maths/algebra/realNormedAlgebra/quaternions/index.htm

It should provide some insight into what quaternions are and how you can
use them to rotate or obtain an axis-angle representation.

Cheers,

Tsjerk


On Sun, Nov 24, 2013 at 11:31 PM, Павел Томашевский <cro...@gm...>wrote:

> Hi all,
>
> Ok, so today I have to admit that I don't know what quaternions are
> but I <probably> will need to use them.
> I'm working on PyMOL and Sensable Phantom Omni haptic device
> integration using Virtual Reality Peripherial Network (VRPN).
>
> So far I have a nicely working plugin for PyMOL that can retreive
> X,Y,Z coordinates and vector of four quaternion values.
>
> My CGO pointer (cone) can smoothly move according to X,Y and Z
> changes. Now I need to do some rotations of the pointer. AFAIK
> 'rotate' function accepts only degree value of rotation around axis.
>
> My question is: is there any build in PyMOL function that accepts four
> quaternion values and do rotation (instead of degree for each axis)?
>
> If not: do you have any simple hint or math formulas for me :) to
> calculate angles for rotation of CGO out of four quaternion value?
>
> Cheers
> Pawel 'crooveck' Tomaszewski
>
>
> ------------------------------------------------------------------------------
> Shape the Mobile Experience: Free Subscription
> Software experts and developers: Be at the forefront of tech innovation.
> Intel(R) Software Adrenaline delivers strategic insight and game-changing
> conversations that shape the rapidly evolving mobile landscape. Sign up
> now.
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Jason,
My drivers are newest Nvidia 331.82 from
http://www.nvidia.pl/download/driverResults.aspx/70559.
I'm not sure if the problem is on my site or no. Maybe my pymol
distribution is badly built? What else can I do to get rid of that
bug?

Cheers,
Pawel

2013/11/24 Jason Vertrees <jas...@sc...>:
> Hi Pawel,
>
> I suggest making sure that your video drivers are up to date at all times
> when using software like PyMOL. Mobile video cards notoriously badly
> implement the OpenGL spec.
>
> If that's a bug in our part, we'll try to track it down.
>
> Cheers,
>
> -- Jason
>
>
> On Sun, Nov 24, 2013 at 3:42 PM, Павел Томашевский <cro...@gm...>
> wrote:
>>
>> 2013/11/24 Jason Vertrees <jas...@sc...>:
>> > Hi,
>> Hi Jason
>>
>> > Is there any chance you can send me your input file(s)? Also, please let
>> > me
>> > know what computer, video card, and architecture (32-bit/64-bit) you're
>> > running on.
>>
>> So basically this problem occurs every time I start pymol, even
>> without loading any input files.
>> My computer is Dell Latitude E6400, running Windows 7 64-bits, I have
>> Nvidia Quadro NVS160M.
>> I've installed newest drivers a few days ago, but the problem still
>> exists.
>>
>> If it matters... I've obtained PyMol executables (already compiled)
>> from
>> http://www.lfd.uci.edu/~gohlke/pythonlibs/3msnvi49/pymol-1.6.0.0.win-amd64-py2.7.exe.
>> Executable comes with integrated Python 2.7 distribution...
>>
>>
>> > Cheers,
>> >
>> > -- Jason
>>
>> Cheers
>> Pawel
>>
>>
>> >
>> >
>> > On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский <cro...@gm...>
>> > wrote:
>> >>
>> >> Hello
>> >> I run PyMol 1.6.0 on windows 7 and I get this error:
>> >> ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns
>> >> err=1282
>> >> or
>> >> ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282
>> >>
>> >> over and over again.
>> >> Is there any way to get rid of that? That's really annoying.
>> >>
>> >> crooveck
>> >>
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >> Shape the Mobile Experience: Free Subscription
>> >> Software experts and developers: Be at the forefront of tech
>> >> innovation.
>> >> Intel(R) Software Adrenaline delivers strategic insight and
>> >> game-changing
>> >> conversations that shape the rapidly evolving mobile landscape. Sign up
>> >> now.
>> >>
>> >>
>> >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
>> >> _______________________________________________
>> >> 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
>> > Director of Core Modeling Products
>> > Schrödinger, Inc.
>> >
>> > (e) Jas...@sc...
>> > (o) +1 (603) 374-7120
>
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Products
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Hi Pawel,

I suggest making sure that your video drivers are up to date at all times
when using software like PyMOL. Mobile video cards notoriously badly
implement the OpenGL spec.

If that's a bug in our part, we'll try to track it down.

Cheers,

-- Jason


On Sun, Nov 24, 2013 at 3:42 PM, Павел Томашевский <cro...@gm...>wrote:

> 2013/11/24 Jason Vertrees <jas...@sc...>:
> > Hi,
> Hi Jason
>
> > Is there any chance you can send me your input file(s)? Also, please let
> me
> > know what computer, video card, and architecture (32-bit/64-bit) you're
> > running on.
>
> So basically this problem occurs every time I start pymol, even
> without loading any input files.
> My computer is Dell Latitude E6400, running Windows 7 64-bits, I have
> Nvidia Quadro NVS160M.
> I've installed newest drivers a few days ago, but the problem still exists.
>
> If it matters... I've obtained PyMol executables (already compiled)
> from
> http://www.lfd.uci.edu/~gohlke/pythonlibs/3msnvi49/pymol-1.6.0.0.win-amd64-py2.7.exe
> .
> Executable comes with integrated Python 2.7 distribution...
>
>
> > Cheers,
> >
> > -- Jason
>
> Cheers
> Pawel
>
>
> >
> >
> > On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский <cro...@gm...>
> > wrote:
> >>
> >> Hello
> >> I run PyMol 1.6.0 on windows 7 and I get this error:
> >> ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns
> >> err=1282
> >> or
> >> ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282
> >>
> >> over and over again.
> >> Is there any way to get rid of that? That's really annoying.
> >>
> >> crooveck
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Shape the Mobile Experience: Free Subscription
> >> Software experts and developers: Be at the forefront of tech innovation.
> >> Intel(R) Software Adrenaline delivers strategic insight and
> game-changing
> >> conversations that shape the rapidly evolving mobile landscape. Sign up
> >> now.
> >>
> >>
> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
> >> _______________________________________________
> >> 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
> > Director of Core Modeling Products
> > Schrödinger, Inc.
> >
> > (e) Jas...@sc...
> > (o) +1 (603) 374-7120
>



-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

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

Hi all,

Ok, so today I have to admit that I don't know what quaternions are
but I <probably> will need to use them.
I'm working on PyMOL and Sensable Phantom Omni haptic device
integration using Virtual Reality Peripherial Network (VRPN).

So far I have a nicely working plugin for PyMOL that can retreive
X,Y,Z coordinates and vector of four quaternion values.

My CGO pointer (cone) can smoothly move according to X,Y and Z
changes. Now I need to do some rotations of the pointer. AFAIK
'rotate' function accepts only degree value of rotation around axis.

My question is: is there any build in PyMOL function that accepts four
quaternion values and do rotation (instead of degree for each axis)?

If not: do you have any simple hint or math formulas for me :) to
calculate angles for rotation of CGO out of four quaternion value?

Cheers
Pawel 'crooveck' Tomaszewski

2013/11/24 Jason Vertrees <jas...@sc...>:
> Hi,
Hi Jason

> Is there any chance you can send me your input file(s)? Also, please let me
> know what computer, video card, and architecture (32-bit/64-bit) you're
> running on.

So basically this problem occurs every time I start pymol, even
without loading any input files.
My computer is Dell Latitude E6400, running Windows 7 64-bits, I have
Nvidia Quadro NVS160M.
I've installed newest drivers a few days ago, but the problem still exists.

If it matters... I've obtained PyMol executables (already compiled)
from http://www.lfd.uci.edu/~gohlke/pythonlibs/3msnvi49/pymol-1.6.0.0.win-amd64-py2.7.exe.
Executable comes with integrated Python 2.7 distribution...


> Cheers,
>
> -- Jason

Cheers
Pawel


>
>
> On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский <cro...@gm...>
> wrote:
>>
>> Hello
>> I run PyMol 1.6.0 on windows 7 and I get this error:
>> ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns
>> err=1282
>> or
>> ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282
>>
>> over and over again.
>> Is there any way to get rid of that? That's really annoying.
>>
>> crooveck
>>
>>
>> ------------------------------------------------------------------------------
>> Shape the Mobile Experience: Free Subscription
>> Software experts and developers: Be at the forefront of tech innovation.
>> Intel(R) Software Adrenaline delivers strategic insight and game-changing
>> conversations that shape the rapidly evolving mobile landscape. Sign up
>> now.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
>> _______________________________________________
>> 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
> Director of Core Modeling Products
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Hi,

Is there any chance you can send me your input file(s)? Also, please let me
know what computer, video card, and architecture (32-bit/64-bit) you're
running on.

Cheers,

-- Jason


On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский <cro...@gm...>wrote:

> Hello
> I run PyMol 1.6.0 on windows 7 and I get this error:
> ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282
> or
> ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282
>
> over and over again.
> Is there any way to get rid of that? That's really annoying.
>
> crooveck
>
>
> ------------------------------------------------------------------------------
> Shape the Mobile Experience: Free Subscription
> Software experts and developers: Be at the forefront of tech innovation.
> Intel(R) Software Adrenaline delivers strategic insight and game-changing
> conversations that shape the rapidly evolving mobile landscape. Sign up
> now.
> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
> _______________________________________________
> 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
Director of Core Modeling Products
Schrödinger, Inc.

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

Hello
I run PyMol 1.6.0 on windows 7 and I get this error:
ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282
or
ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282

over and over again.
Is there any way to get rid of that? That's really annoying.

crooveck

Hi Justin,

We'll fix that, too.

Cheers,

-- Jason


On Fri, Nov 22, 2013 at 1:24 AM, Justin Lecher <j.l...@fz...>wrote:

> On 22/11/13 01:02, Thomas Holder wrote:
> > Hi,
> >
> > this is fixed now in the sourceforge SVN repository.
> >
> > Cheers,
> >   Thomas
> >
>
> Thanks for working quickly on it, but it isn't fixed here.
>
> There some things I observe,
>
> The font geometry changes according to the window geometry. That means a
> tall & thin window creates tall, stretched fonts. I would say, that font
> geometry should be independent from the window size.
>
> Probably coming from the same source in the code, the fonts get ugly
> when maximizing a window on a 27'' screen.
>
> This scaling problem also depends on use_shaders.
>
> I am using rev. 4052
>
>
> Regards,
> Justin
>
>
> --
> Justin Lecher
> Institute of Complex Systems
> ICS-6 Structural Biochemistry
> Research Centre Juelich
> 52425 Juelich, Germany
> phone: +49 2461 61 2117
>
>
>
>
> ------------------------------------------------------------------------------
> Shape the Mobile Experience: Free Subscription
> Software experts and developers: Be at the forefront of tech innovation.
> Intel(R) Software Adrenaline delivers strategic insight and game-changing
> conversations that shape the rapidly evolving mobile landscape. Sign up
> now.
> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
> _______________________________________________
> 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
Director of Core Modeling Products
Schrödinger, Inc.

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