pymol-users Mailing List for PyMOL Molecular Graphics System

Dear Colleagues,

 

Building on the success of the past 3 years, we are pleased to announce
the fourth annual CCP4 summer school at Advanced Photon Source (APS),
Argonne National Laboratory (ANL). All details can be found at
http://www.ccp4.ac.uk/schools/APS-2011/index.php 

 

Title:

"CCP4 school: From data collection to structure refinement and beyond"

Dates: June 7 to 15.

Site: Advanced Photon Source, Argonne National Laboratory, Argonne,
Illinois (Near Chicago), USA

 

The school content:

Data collection workshop the first two days: beamline training and data
collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data
collection, only the participants' crystals will be used.

Software workshop: The rest of the time after data collection will
feature many modern crystallographic software packages taught by authors
and other experts. It will be organized in three

Sections - lectures, tutorials and hands-on trouble-shooting.

There will be model data sets available for tutorials but data, provided
by participants, will have higher priority for the hands-on sessions.

 

Applicants:

Graduate students, postdoctoral researchers and young scientists at the
assistant professor level are encouraged to apply. Only 20 applicants
will be selected for participation. Participants of the workshop are
strongly encouraged to bring their own problem data sets or crystals so
the problems can be addressed during data collection workshop and/or
hands-on sessions.

 

Application:

Application deadline is April 8. Application form, the program, contact
info and other details can be found at
http://www.ccp4.ac.uk/schools/APS-2011/index.php 

 

Fees: There is no fee for the workshop. The students will be responsible
for their transportation and lodging. The workshop organizers will
arrange economical lodging at the Argonne Guest House. The workshop will
also cover the expenses for all meals and refreshments.

 

Garib, Ronan and Nukri

 

 

Ruslan Sanishvili (Nukri), Ph.D.

GM/CA-CAT
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an... 

 

On Tue, Dec 21, 2010 at 2:42 PM, Jason Ferrara <ja...@di...> wrote:

> I've been using the pymol2 interface to run pymol inside Qt widgets. There
> doesn't seem to be any documentation for it, but once you figure it out it
> seems to work well.


Do you think you could put a quick summary of how to do this on the wiki?
 I've made a few futile attempts to embed it in wxPython over the last year
and a half, and it isn't even obvious how to get the modules installed
correctly.  I've been able to get as far as creating an OpenGL context and
starting PyMOL through pymol2, but after that I'm stuck with either a blank
window (if I do nothing else), or a segmentation fault (if I call the "draw"
method).

thanks,
Nat

I've been using the pymol2 interface to run pymol inside Qt widgets. There doesn't seem to be any documentation for it, but once you figure it out it seems to work well.

On Dec 21, 2010, at 12:27 AM, Jason Vertrees wrote:

> Hi Mike,
> 
> It's possible, but at this point would be more trouble than it's
> worth.  The newer pymol2 methods are not yet stable enough for
> mainstream use.  The older pymol1 methods will leave you struggling
> with synchronization and other problems.
> 
> Cheers,
> 
> -- Jason
> 
> On Fri, Dec 17, 2010 at 11:56 PM, Mike Turchenkov <mc...@gm...> wrote:
>> Hello, dear All.
>> 
>> Is it possible to use PyMOL as a whole in other python apps? I use
>> tkinter for some comfort automation and I wolud like to integrate
>> interactive visualiser windows into my app. Is it possible, or it just
>> doesn't work that way?
>> 
>> Thanks.

This works well for what I need. I don't know how I missed the group command.

Thanks!

On Dec 17, 2010, at 2:02 PM, Jason Vertrees wrote:

> Hi Jason,
> 
> Unfortunately that capability isn't yet present in PyMOL.  Improved
> state handling is something we're working on and have prioritized.
> 
> As a workaround, consider loading the object with the multiplex flag
> set, then when the user makes the selection you can record the object
> name and determine the state number from there.  You can use the group
> object to not pollute the object menu/namespace.  For example:
> 
> # models are loaded as: "name_001", "name_002", etc.
> # so we will split on the "_" and return the state number
> from string import split
> 
> # used to get data from iterate/alter commands
> from pymol import stored
> stored.name = ""
> 
> # fetch a multi-state object
> fetch 1nmr, multiplex=1
> 
> # put all these states into a group; keeps things cleaner
> group 1nmr, 1nmr*
> 
> #
> # -- Now, select an atom with the mouse, so "sele" is created
> #
> iterate first sele, stored.name = model
> 
> print "User selected model %d" % int(split(stored.name, "_")[1])
> 
> 
> This is not ideal, but should get you closer to your solution.
> 
> Cheers,
> 
> -- Jason
> 
> 
> 
> 
> On Fri, Dec 17, 2010 at 10:23 AM, Jason Ferrara <ja...@di...> wrote:
>> If I have a multi state object loaded, and all_states set to on, is there a way to select individual states with the mouse? Or if not at least some way to query which state was clicked in to generate the selection, or to query which state lies under a given x,y position in the view?
>> 
>> I'm writing a plugin where I need to have the user select a state from a multi state model.
>> 
>> Thanks
>> 
>> - J
>> ------------------------------------------------------------------------------
>> Lotusphere 2011
>> Register now for Lotusphere 2011 and learn how
>> to connect the dots, take your collaborative environment
>> to the next level, and enter the era of Social Business.
>> http://p.sf.net/sfu/lotusphere-d2d
>> _______________________________________________
>> 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 Mike,

It's possible, but at this point would be more trouble than it's
worth.  The newer pymol2 methods are not yet stable enough for
mainstream use.  The older pymol1 methods will leave you struggling
with synchronization and other problems.

Cheers,

-- Jason

On Fri, Dec 17, 2010 at 11:56 PM, Mike Turchenkov <mc...@gm...> wrote:
> Hello, dear All.
>
> Is it possible to use PyMOL as a whole in other python apps? I use
> tkinter for some comfort automation and I wolud like to integrate
> interactive visualiser windows into my app. Is it possible, or it just
> doesn't work that way?
>
> Thanks.
>
> ------------------------------------------------------------------------------
> Lotusphere 2011
> Register now for Lotusphere 2011 and learn how
> to connect the dots, take your collaborative environment
> to the next level, and enter the era of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
> _______________________________________________
> 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 Martin,

On Sun, Dec 19, 2010 at 7:37 AM, Martin Hediger <ma...@bl...> wrote:
> Dear all
> Is it possible to start a PyMOL viewer through a web browser? What I
> mean by this is, is it possible to view a protein over the internet
> where the viewing features are provided by some "limited" PyMOL server?
> The only thing able to do that right now is Jmol, but i think its very
> inconvenient to use when viewing large structures such as proteins.

Luckily, your peers have given you quite a few options so you can
weigh the pros/cons against your necessities and proposed platform
(eg. Java vs JavaScript+AJAX vs ActiveX vs HTML5).  As a developer I'd
also consider the following.  First, do you need something that can
launch a viewer from the browser or a plugin that embeds the content
inside the browser window?  If the former, Carsten noted the "p1m"
format, which you can associate with PyMOL.  If the latter, then I'd
next consider platforms (stability, speed, future):

HTML5/WebGL:
 * looks promising as the technology develops, but may be too new for
your users to quickly adopt and performance might not be what you want
(yet).

Java:
 * been around for ages, but Apple just deprecated their JVM
(http://developer.apple.com/library/mac/#releasenotes/Java/JavaSnowLeopardUpdate3LeopardUpdate8RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40010380-CH4-SW1)
 * Jmol and JyMOL both work well for their intended uses:
  -- Jmol is good software with a small footprint, fewer dependencies
than JyMOL, a large user base, and is open source in case you need to
modify the Jmol source
  -- JyMOL has PyMOL graphics, speed, and is free-to-academics, but
needs JOGL or LWJGL and is proprietary--which means you cannot modify
JyMOL itself

ActiveX:
  * Consistent cross platform deployment would be my largest concern

Use whatever's best for your project.  Hope this helps and good luck!

Cheers,

-- Jason

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

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

Hi Bjoern,

I think you answered your own question.  I think you need to use plot
over draw.  How about:

import pymol
pymol.finish_launching()
import matplotlib
import pylab

pylab.ion()
pylab.figure()
pylab.ioff()
pylab.plot([1,2],[1,2])
pylab.show()

The above gives me a fully interactive PyMOL session and matplotlib window.

Cheers,

-- Jason


On Fri, Dec 17, 2010 at 7:46 PM, Bjoern Nadrowski
<bjr...@go...> wrote:
> Hello,
> What I would like to do is write a python script that simultaneously
> drives lammps (my molecular simulation program), puts lammps output to
> pymol, and plot some pylab plots.
>
> When I try this:
>
> import pymol
> pymol.finish_launching()
>
> import matplotlib
> import pylab
>
> pylab.ion()
> pylab.figure()
> pylab.ioff()
> pylab.draw([1,2],[1,2])
> raw_input()
>
> I do get my interactive pymol gui, but the pylab window is dead. It pops
> up, but no line is drawn. I suspect that has something to do with the
> gui handlers, so I would have to attach the pylab gui to the pymol one,
> I suspect. I just don't know how to do that.
>
> Nota bene:
> replacing the pylab lines with
> pylab.figure()
> pylab.plot([1,2],[1,2])
> pylab.show()
>
> works, but then the handler is with the pylab window, and no code after
> that can be executed any more.
> So you cannot update this window during execution time.
>
> Thanks for any help!
>
>
>
> ------------------------------------------------------------------------------
> Lotusphere 2011
> Register now for Lotusphere 2011 and learn how
> to connect the dots, take your collaborative environment
> to the next level, and enter the era of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
> _______________________________________________
> 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 Martin,

not directly applicable to your question, but may be it directs your
thinking into a different direction. If I remember correctly Warren
pointed out a couple of year ago the p1m file format was supposed to
support downloading of structural information from the web with some
limited scripting options. Hope this helps.

Cheers,

	Carsten



> -----Original Message-----
> From: Martin Hediger [mailto:ma...@bl...]
> Sent: Sunday, December 19, 2010 7:38 AM
> To: pym...@li...
> Subject: [PyMOL] Start PyMOL session in web browser
> 
> Dear all
> Is it possible to start a PyMOL viewer through a web browser? What I
> mean by this is, is it possible to view a protein over the internet
> where the viewing features are provided by some "limited" PyMOL
server?
> The only thing able to do that right now is Jmol, but i think its very
> inconvenient to use when viewing large structures such as proteins.
> 
> Thanks for your answers
> Martin
> 
>
-----------------------------------------------------------------------
> -------
> Lotusphere 2011
> Register now for Lotusphere 2011 and learn how
> to connect the dots, take your collaborative environment
> to the next level, and enter the era of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
http://www.mail-archive.com/pym...@li...

I was thinking of something like a browser plug-in, just as it is 
available for PowerPoint.
We'll see, where it goes.





Am 19.12.10 17:06, schrieb Rich:
> On 19-12-2010 10:27, Martin Hediger wrote:
>> Of course, Jmol is very poweful and I am using it as well for many things.
>> Inconvenient probably is the wrong word, I just find the PyMOL handling
>> of large molecules a bit more intuitive.
> Understood.
>
>    As far as I can see, there are
>> more view options in PyMOL (Ribbons, Surfaces, etc), this would be
>> particularyl helpful.
> As long as you are basing your evaluation on the latest versions of Jmol
> because it has changed a lot over the last couple of years. Current
> versions do handle ribbons and surfaces.
>
>> Anyway, the questions remains, how one could run a PyMOL session through
>> a web browser. I will be looking at the input from the previous postings.
> As far as I know it isn't possible which is why Jmol is a choice.
> Although one of the other options may fit better with your needs even
> though they aren't PyMol either.
>
> There was some talk quite a while ago about a different version of PyMol
> that could do this but I don't think it ever got off the ground.
>
> Rich
>
> ------------------------------------------------------------------------------
> Lotusphere 2011
> Register now for Lotusphere 2011 and learn how
> to connect the dots, take your collaborative environment
> to the next level, and enter the era of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

On 19-12-2010 10:27, Martin Hediger wrote:
> Of course, Jmol is very poweful and I am using it as well for many things.
> Inconvenient probably is the wrong word, I just find the PyMOL handling
> of large molecules a bit more intuitive.

Understood.

  As far as I can see, there are
> more view options in PyMOL (Ribbons, Surfaces, etc), this would be
> particularyl helpful.

As long as you are basing your evaluation on the latest versions of Jmol 
because it has changed a lot over the last couple of years. Current 
versions do handle ribbons and surfaces.

> Anyway, the questions remains, how one could run a PyMOL session through
> a web browser. I will be looking at the input from the previous postings.

As far as I know it isn't possible which is why Jmol is a choice. 
Although one of the other options may fit better with your needs even 
though they aren't PyMol either.

There was some talk quite a while ago about a different version of PyMol 
that could do this but I don't think it ever got off the ground.

Rich

Of course, Jmol is very poweful and I am using it as well for many things.
Inconvenient probably is the wrong word, I just find the PyMOL handling 
of large molecules a bit more intuitive. As far as I can see, there are 
more view options in PyMOL (Ribbons, Surfaces, etc), this would be 
particularyl helpful.
Anyway, the questions remains, how one could run a PyMOL session through 
a web browser. I will be looking at the input from the previous postings.






Am 19.12.10 14:11, schrieb Rich:
> On 19-12-2010 7:37, Martin Hediger wrote:
>> Dear all
>> Is it possible to start a PyMOL viewer through a web browser? What I
>> mean by this is, is it possible to view a protein over the internet
>> where the viewing features are provided by some "limited" PyMOL server?
>> The only thing able to do that right now is Jmol, but i think its very
>> inconvenient to use when viewing large structures such as proteins.
> Have you tried asking about what you find inconvenient about Jmol on the
> Jmol list? Perhaps the behaviour that you don't like could be addressed?
> I know a of of people seem satisfied to use Jmol for browser-based
> rendering.
>
> Rich
>
> ------------------------------------------------------------------------------
> Lotusphere 2011
> Register now for Lotusphere 2011 and learn how
> to connect the dots, take your collaborative environment
> to the next level, and enter the era of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Martin Hediger [ma...@bl...] wrote:
> Is it possible to start a PyMOL viewer through a web browser? What I 
> mean by this is, is it possible to view a protein over the internet 
> where the viewing features are provided by some "limited" PyMOL server? 
> The only thing able to do that right now is Jmol, but i think its very 
> inconvenient to use when viewing large structures such as proteins.

Normally you do this client side by using a "mailcap" entry.
It's far more powerful  then a jmol applet. 

Old fashioned rasmol used to be popular.
It would be interesting to see pymol in this usage case.
I'm afraid it hasn't been done yet.

Cheers,

--
Michał Kurowski
<mk...@ga...>

Jmol certainly is not the only thing able to do that.

In the applet world, you have at least OpenAstexViewer http://openastexviewer.net/web/ , but I also imagine it is possible to build a (jogl-accellerated) applet using jymol http://www.pymol.org/jymol , but I'm fairly certain it is not open source.

In the html5 world, you have jolecules http://jolecule.appspot.com/ , canvasmol http://alteredqualia.com/canvasmol/ , and chemdoodle web components http://web.chemdoodle.com/

-David

On Dec 19, 2010, at 7:37 AM, Martin Hediger <ma...@bl...> wrote:

> Dear all
> Is it possible to start a PyMOL viewer through a web browser? What I 
> mean by this is, is it possible to view a protein over the internet 
> where the viewing features are provided by some "limited" PyMOL server? 
> The only thing able to do that right now is Jmol, but i think its very 
> inconvenient to use when viewing large structures such as proteins.
> 
> Thanks for your answers
> Martin
> 
> ------------------------------------------------------------------------------
> Lotusphere 2011
> Register now for Lotusphere 2011 and learn how
> to connect the dots, take your collaborative environment
> to the next level, and enter the era of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

On 19-12-2010 7:37, Martin Hediger wrote:
> Dear all
> Is it possible to start a PyMOL viewer through a web browser? What I
> mean by this is, is it possible to view a protein over the internet
> where the viewing features are provided by some "limited" PyMOL server?
> The only thing able to do that right now is Jmol, but i think its very
> inconvenient to use when viewing large structures such as proteins.

Have you tried asking about what you find inconvenient about Jmol on the 
Jmol list? Perhaps the behaviour that you don't like could be addressed? 
I know a of of people seem satisfied to use Jmol for browser-based 
rendering.

Rich

Dear all
Is it possible to start a PyMOL viewer through a web browser? What I 
mean by this is, is it possible to view a protein over the internet 
where the viewing features are provided by some "limited" PyMOL server? 
The only thing able to do that right now is Jmol, but i think its very 
inconvenient to use when viewing large structures such as proteins.

Thanks for your answers
Martin

Hello, dear All.

Is it possible to use PyMOL as a whole in other python apps? I use
tkinter for some comfort automation and I wolud like to integrate
interactive visualiser windows into my app. Is it possible, or it just
doesn't work that way?

Thanks.

Hello, 
What I would like to do is write a python script that simultaneously
drives lammps (my molecular simulation program), puts lammps output to
pymol, and plot some pylab plots. 

When I try this:

import pymol
pymol.finish_launching()

import matplotlib
import pylab

pylab.ion()
pylab.figure()
pylab.ioff()
pylab.draw([1,2],[1,2])
raw_input()

I do get my interactive pymol gui, but the pylab window is dead. It pops
up, but no line is drawn. I suspect that has something to do with the
gui handlers, so I would have to attach the pylab gui to the pymol one,
I suspect. I just don't know how to do that.

Nota bene:
replacing the pylab lines with
pylab.figure()
pylab.plot([1,2],[1,2])
pylab.show()

works, but then the handler is with the pylab window, and no code after
that can be executed any more. 
So you cannot update this window during execution time. 

Thanks for any help!

Hi Jason,

Unfortunately that capability isn't yet present in PyMOL.  Improved
state handling is something we're working on and have prioritized.

As a workaround, consider loading the object with the multiplex flag
set, then when the user makes the selection you can record the object
name and determine the state number from there.  You can use the group
object to not pollute the object menu/namespace.  For example:

# models are loaded as: "name_001", "name_002", etc.
# so we will split on the "_" and return the state number
from string import split

# used to get data from iterate/alter commands
from pymol import stored
stored.name = ""

# fetch a multi-state object
fetch 1nmr, multiplex=1

# put all these states into a group; keeps things cleaner
group 1nmr, 1nmr*

#
# -- Now, select an atom with the mouse, so "sele" is created
#
iterate first sele, stored.name = model

print "User selected model %d" % int(split(stored.name, "_")[1])


This is not ideal, but should get you closer to your solution.

Cheers,

-- Jason




On Fri, Dec 17, 2010 at 10:23 AM, Jason Ferrara <ja...@di...> wrote:
> If I have a multi state object loaded, and all_states set to on, is there a way to select individual states with the mouse? Or if not at least some way to query which state was clicked in to generate the selection, or to query which state lies under a given x,y position in the view?
>
> I'm writing a plugin where I need to have the user select a state from a multi state model.
>
> Thanks
>
> - J
> ------------------------------------------------------------------------------
> Lotusphere 2011
> Register now for Lotusphere 2011 and learn how
> to connect the dots, take your collaborative environment
> to the next level, and enter the era of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
> _______________________________________________
> 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

If I have a multi state object loaded, and all_states set to on, is there a way to select individual states with the mouse? Or if not at least some way to query which state was clicked in to generate the selection, or to query which state lies under a given x,y position in the view?

I'm writing a plugin where I need to have the user select a state from a multi state model.

Thanks

- J

Hi David,

I've never seen this problem, but can look into it.  Does this occur
in the final ray traced imaged too, or just the normal non ray traced
scene?

Cheers,

-- Jason

On Wed, Dec 15, 2010 at 12:34 AM, David Hall <li...@co...> wrote:
> Has anyone else run into a problem with label_size in pymol 1.3 on
> Mac?  For both my fink and macports build, it doesn't work.  The
> baseline of the text moves, but the size doesn't change.
>
> It does work when I compile from pymol trunk on my linux box.  I don't
> see anything in the changelog or svn log indicating a fix that might
> have been added since whatever source fink and macports declared 1.3.
>
> -David
>
> ------------------------------------------------------------------------------
> Lotusphere 2011
> Register now for Lotusphere 2011 and learn how
> to connect the dots, take your collaborative environment
> to the next level, and enter the era of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
> _______________________________________________
> 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

Dear all

Let protein P be of C1 symmetry, so no symmetry elements. It can be 
approximated by a cube C, where every face of C has its own value, say 1 
to 6.
Lets assume, the positive x-direction is coming out of the computer 
screen, the plane of the screen is the yz plane, the lower left corner 
is now (0,0,0). Lets say, C lies in first quadrant of the xy plane, and 
face 1 is visible facing towards the reader.
I now want to generate all possible orientations of the protein on the 
xy surface, so 6 in total. Are there any tools built into PyMOL? I went 
through the scripts library and saw a couple of things I might be using 
as a guide line, but so far nothing definitive. Its not a difficult 
thing to do, I just thought maybe there is something I can build on 
(instead of contributing to script inflation).

Thanks for any hints on this.

Martin

Hi Jared,

this is a numerical problem. Look in transformations.py for the lines
where values get compared to 1e-8 and change this number to something
like 1e-7.

And in your script the angle calculation missed the arccos:

elbow = 180 - numpy.degrees(numpy.arccos(numpy.dot(direction_v,direction_c)))

Cheers,
  Thomas

On Tue, Dec 14, 2010 at 7:57 PM, Sampson, Jared <Jar...@ny...> wrote:
> Hello all - I'm trying to calculate the elbow angle of an Fab locally (i.e. without uploading to a server) and decided to try it in PyMOL.  I got stuck, and thought maybe someone much wiser than I might be able to shed some light on the error(s) of my ways.
>
> I've been trying to use some of the functions in transformations.py by Christoph Gohlke (quite a thorough toolset!); what I have so far is the following .pml script:
>
> run transformations.py
>
> import numpy
> import transformations
>
> fetch 3ghe, async=0
>
> # break the fab into 4 pieces
> create vl, chain L and resi 1-107
> create vh, chain H and resi 1-113
> create cl, chain L and !vl
> create ch, chain H and !vh
>
> # align the pieces
> super vl,vh
> super cl,ch
>
> python
>
> # get the transformation matrices
> mat_v = cmd.get_object_matrix("vl")
> mat_c = cmd.get_object_matrix("cl")
>
> # turns Pymol's output into a 4x4 python array
> def mat_to_R(mat):
>    R = [[mat[0],mat[1],mat[2],mat[3]],
>         [mat[4],mat[5],mat[6],mat[7]],
>         [mat[8],mat[9],mat[10],mat[11]],
>         [mat[12],mat[13],mat[14],mat[15]]]
>    return R
>
> Rv = mat_to_R(mat_v)
> Rc = mat_to_R(mat_c)
>
> # calculate the axis & angle
> angle_v,direction_v,point_v = transformations.rotation_from_matrix(Rv)
> angle_c,direction_c,point_c = transformations.rotation_from_matrix(Rc)
>
> # calculate the elbow angle
> elbow = numpy.degrees(numpy.dot(direction_v,direction_c))
> print "Elbow angle:",elbow
>
> python end
>
> I'm getting the following error, but I'm not sure how to address it:
>
> Traceback (most recent call last):
>  File "/sw64/lib/pymol-py26/modules/pymol/parser.py", line 155, in parse
>    exec(py_block,self.pymol_names,self.pymol_names)
>  File "<string>", line 19, in <module>
>  File "transformations.py", line 348, in rotation_from_matrix
>    raise ValueError("no unit eigenvector corresponding to eigenvalue 1")
> ValueError: no unit eigenvector corresponding to eigenvalue 1
>
> Any help would be greatly appreciated!
>
> Thanks,
>
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> New York, NY 10016
> 212-263-7898

Has anyone else run into a problem with label_size in pymol 1.3 on
Mac?  For both my fink and macports build, it doesn't work.  The
baseline of the text moves, but the size doesn't change.

It does work when I compile from pymol trunk on my linux box.  I don't
see anything in the changelog or svn log indicating a fix that might
have been added since whatever source fink and macports declared 1.3.

-David

Hello all - I'm trying to calculate the elbow angle of an Fab locally (i.e. without uploading to a server) and decided to try it in PyMOL.  I got stuck, and thought maybe someone much wiser than I might be able to shed some light on the error(s) of my ways.

I've been trying to use some of the functions in transformations.py by Christoph Gohlke (quite a thorough toolset!); what I have so far is the following .pml script:

run transformations.py

import numpy
import transformations

fetch 3ghe, async=0

# break the fab into 4 pieces
create vl, chain L and resi 1-107
create vh, chain H and resi 1-113
create cl, chain L and !vl
create ch, chain H and !vh

# align the pieces
super vl,vh
super cl,ch

python

# get the transformation matrices
mat_v = cmd.get_object_matrix("vl")
mat_c = cmd.get_object_matrix("cl")

# turns Pymol's output into a 4x4 python array
def mat_to_R(mat):
    R = [[mat[0],mat[1],mat[2],mat[3]],
         [mat[4],mat[5],mat[6],mat[7]],
         [mat[8],mat[9],mat[10],mat[11]],
         [mat[12],mat[13],mat[14],mat[15]]]
    return R

Rv = mat_to_R(mat_v)
Rc = mat_to_R(mat_c)

# calculate the axis & angle
angle_v,direction_v,point_v = transformations.rotation_from_matrix(Rv)
angle_c,direction_c,point_c = transformations.rotation_from_matrix(Rc)

# calculate the elbow angle
elbow = numpy.degrees(numpy.dot(direction_v,direction_c))
print "Elbow angle:",elbow

python end

I'm getting the following error, but I'm not sure how to address it:

Traceback (most recent call last):
  File "/sw64/lib/pymol-py26/modules/pymol/parser.py", line 155, in parse
    exec(py_block,self.pymol_names,self.pymol_names)
  File "<string>", line 19, in <module>
  File "transformations.py", line 348, in rotation_from_matrix
    raise ValueError("no unit eigenvector corresponding to eigenvalue 1")
ValueError: no unit eigenvector corresponding to eigenvalue 1

Any help would be greatly appreciated!

Thanks,

Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
New York, NY 10016
212-263-7898


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=================================

Hi Sean,

since the PyMOL GUI is written in python, it's quite easy to manipulate 
menus. See attached script to get the ID into the right click menu title.

Cheers,
   Thomas

Sean Law wrote, On 12/14/10 18:20:
> Hi PyMOLers,
> 
> Is there a way to display PDB atom numbers when you right click on an 
> atom?  It normally gives information like 
> object/segment/chain/resn/resid/name but I want a quick way of comparing 
> the atom number with the PDB atom numbering.
> 
> Thanks!
> 
> Sean