Re: [PyMOL] Getting information fron selected objects

[Daniel Seeliger]

Hi Phil,

one option to get access to the coordinates is using the chempy model of a 
given selection ( named (sele) if you clicked it).

m = cmd.get_model((sele))

the chempy model contains a list of atom objects which contain most properties 
you might need.

for atom in m.atom:
 print atom.id, atom.name, atom.resn, atom.resi, atom.coord

To extract the coordinates of all atoms you can simple do:

coords = map(lambda a: a.coord, m.atom)

or if you need the coordinates as numpy arrays use:

from numpy import *
coords = map(lambda a: array(a.coord), m.atom)

gives you a list of numpy arrays

or:
coords = matrix(map(lambda a: a.coord, m.atom))

will produce a numpy matrix with your coords.

Then you might do whatever you want with the coordinates and update the 
coordinates of the chempy model.
As far as I now, you can not transfer them back easily to PyMOL but you can do 
a little trick.

Load the modified model as new pymol object:

cmd.load_model(m,modified)

and then update the original selection with the coords from the modified 
object.

cmd.update((sele),modified)

Then you can delete the modified object.
cmd.delete(modified)

Cheers,
Daniel





On Tuesday 19 January 2010 08:00:51 pm Phil Payne Local wrote:
 I am writing a Pymol plugin, in which I need to extract, manipulate, and
 replace the coordinates of selected atoms.  Are there examples out there
 I could use as a prototype?
 
 For starters, what command(s) do I use to get the name strings of
 residues that I've selected with mouse clicks.  I would like to assign
 these to a variable.
 
 Then the same question applies to coordinates.  How do I assign the
 values of atomic coordinates to a list variable in my plug_in script?
 
 
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Re: [PyMOL] Autodock/Vina Pymol Plugin Windows problem

[Florian Nachon]

On 8 Jan 2010, at 09:51, Daniel Seeliger wrote:
 
 Btw, did anyone get it to run on windows or mac? If yes, it would be nice if 
 you drop me a mail with some info about your system (operating system, 
 program 
 version, how is pymol installed).


Hi Daniel,

The plug-in works great on a Mac (snow leopard; 10.6.2) with PyMOLX11hybrid 
1.2r2 and MGLTools 1.5.4.
Though, I had to change the first line of the scripts in 
/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24 so that the 
scripts called by the plug-in get the correct python environment parameters:

#!/usr/bin/env python  changed to  
#!/usr/bin/env/Library/MGLTools/1.5.4/bin/pythonsh

Multiple errors will occur without this change.

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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

[Tsjerk Wassenaar]

Hi David,

Sorry to be more on the programmatic than on your pragmatic side.

 That seems like a modification that makes it less flexible.  Now I can't do:

 ray 2.5in, 20cm, dpi=300


Okay, let's say you could do:

ray 2.5, 20, units=(in,cm), resolution=300

providing either a single string, or a tuple of strings to indicate
the units. The reason for preferring that for me is the pymol/python
API. The x and y size should be floats, not strings, in order to make
the API intuitive and allow direct invocation in a script, without
doing something like

cmd.ray(%s%xsize+xunit,%s%ysize+yunit,...)

You'd definitely want:

xsize = calc_size(arguments)
ysize = calc_size(arguments)
cmd.ray(xsize,ysize,units=cm,...)

 Don't ask me why I might want to use two different units, I just don't see a 
 reason to make it so I cannot.  I'm frequently surprised by my desires.

I'm also surprised by your anticipation on your desires :)

 And resolution is inconsistent with the png function, and less precise.  I 
 don't know what units I have with the resolution argument.  One of my high 
 ranking complaints about pymol has been certain inconsistencies in the api, 
 so that's actually what I care about more.  (Maybe I should write those up, 
 but fixing these things is always hard because backwards compatibility kind 
 of matters).

Please indicate the API inconsistencies. Solving inconsistencies
should be on everyone's wish list.

 Also, it would be nice to have this in the png function as well.

It's not possible to set both size and resolution as the png argument
merely writes out the image there is. You could either control the
resolution, adapting the size, or control the size, adapting the
resolution.

Cheers,

Tsjerk

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Computational Chemist
Medicinal Chemist
Neuropharmacologist

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Re: [PyMOL] New Feature Ideas

[Tsjerk Wassenaar]

Hi Sean e.a.,

In reply to your messages, first an overview as I picked up from the
other mails:

1. eMovie integration (Simon Kolstoe)
2. Powerpoint plugin (Roger Rowlett)
3. Enhanced morphing (ibid)
4. Foolproof download (David Hall)
5. DynoPlot integration (ibid)
6. Improved undo/redo (ibid)
7. Ray/png size/resolution (Georg Steinkeller)
8. Set mirrors for downloading (Adrian Schreyer)
9. WebGL output (ibid)
10. Vector graphics support (Sean Law)
11. PDF support (ibid)
12. Trajectory support (ibid)
13. CG object GUI (ibid)

As noted 2 and 3 are available in the incentive version. 4, 7 and 8
seem relatively straightforward to implement. For 5 steps should
probably be taken by the DynoPlot crew, or at least it should be done
in collaboration.

6 is indeed problematic but highly desirable. Undoing operations on
states would require to store the differences between states, which
can be huge, e.g. in the case of splitting accidentally. On the other
hand, using wild cards makes it trivial to remove the splitted states
again, so I don't think that particular point is worth the trouble. On
the other hand, a view is not memory demanding, and it would be easy
to keep a stack of those to allow undo/redo.

9. Yea :)

10. Yea. Not by any means trivial though. But I'd be happy to
brainstorm on that one.

11. Would be cool.

12. Definite yea. I fear that this requires some serious changes
inside though to allow efficient viewing of a trajectory, such as VMD
and Yasara offer. The lack of trajectory support is a reason for many
working on MD to use VMD rather than Pymol. On the other hand, for the
open source/freeware version, the gromacs trajectory API could be
interesting to aid in realization of it.
In relation to this I'd really like to have support added for reading
topology information, and to use this to set bonds, atom types, masses
and charges, rather than the internal databases. Especially with the
momentum of coarse grained simulations these days, it would be
required to keep Pymol favoured over VMD.

13. Errm, yea, but... This would almost come down to integration of
Pymol with Blender. Oh, please do, yea, yea! :D

In relation to the last point, I would (14.) really like to see
improved POV-Ray output. The mesh that is output currently is a mess,
and highly inefficient. A correct mesh would require for each mesh
object (cartoon, surface, ... per object) to be written as a set of
nodes, with a set of pigments and a set of triangles, referring to the
node list. Now each triangle is its own mesh2 object, which is
terrible. In addition, I would also like to write POV-Ray include
files on a per object basis, maybe as a setting split_povray_output.
That makes it much more easy to modify the scene. The master file
would only contain the global settings (camera, light, etc.) and a
number of include statements for the other objects. Actually, this is
what I'm now usually doing by hand, enabling/writing/disabling each
object and each representation... O, it's also almost trivial to
include all views in the master file, so that a complete scene can be
written out as a set of POV-Ray files. I'd be happy to streamline and
contribute my POV-Ray code for that.

Another thing on my mind is the desire to (15.) read in images as
objects, or, better, as pigment/texture on an object. That will make
it easy to overlay a structure on a graph for instance.

Finally, unless I think of more later, I would like to be able to
(16.) read and change coordinates quicker. Now, iterating over states
to fiddle with coordinates is painstakingly slow. I'm afraid though
that this is heavily tied in with the internal structure of Pymol,
regarding objects and states. But if that were streamlined, probably
together with 12, then probably Pymol would be able to become a true
platform for analysis of trajectories.

Cheers,

Tsjerk

On Wed, Jan 20, 2010 at 5:26 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
 PyMOLers,

 We need to move forward on PyMOL development, so I'm collecting ideas
 from all our users on what they most want in future versions of PyMOL.
  We already have a page on the PyMOL wiki for this
 (http://pymolwiki.org/index.php/Ideas) from 2008/2009.  We can discuss
 the ideas here and on the wiki; this list is more for two-way
 communication and the wiki for one-way.  If you have a specific
 request for an enhancement you can also email it directly to
 h...@schrodinger.com; please put PyMOL in the subject so I can get
 them easily.  Each request submitted will be considered for
 implementation.

 Last, you're particularly passionate about your feature request, email
 me directly and we can chat about it via phone/skype.

 Thanks,

 -- Jason

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

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120

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Re: [PyMOL] New Feature Ideas

[Tsjerk Wassenaar]

On Thu, Jan 21, 2010 at 10:47 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
 Hi Sean e.a.,

I really meant Jason e.a. :$

T.

-- 
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Computational Chemist
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Neuropharmacologist

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[PyMOL] Dynoplot/Get residues was:[Re: New Feature Ideas]

[David Hall]

 You would have to work with the DynoPlot author to improve this.


So, I figured it would be nicer if I sent the author a patch instead of just 
complaining, so I went to look at the code.
Right now, it uses integer math to try to find the residues before and after, 
but I know from my mistakes that is generally a bad idea as it ignores 
insertion codes (eg 82A, 82B in chain H of 1bgx).
I think I can get a list of residues in a chain in order by doing iterate.

For example:
iterate 1bgx and chain h and name CA, print resi
seems to give me the residues in the correct sequence.  With the correct 
syntax, this would give me a list in python.

Is this guaranteed to be the correct order?  Should we have a get_residues 
method in addition to get_chains that is guaranteed to produce residues in the 
correct sequence?

-David


  

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[PyMOL] New Feature Ideas

[Schubert, Carsten [PRDUS]]

Jason,

here are my feature requests, only slightly biased by the fact that some
of them would be useful for my paper now (-:

1) arbitrary clipping planes bound to an object with an intelligent gui
to place them. Something akin to be found in Maestro or semi-transparent
CGO objects which can be manipulated freely in space and then used to
define clipping planes

2) Implementation of bounding planes in raytracing to avoid showing the
inside of clipped surfaces, raster3D has this option. I know one can
fumble around in Povray to get the same effect, but I'd rather spend my
time on something more productive.

3) If 2) is not an easy option, how about raster3D output in addition to
povray? Pymol can read raster3d, why not have the output as well. 

4) A better density wizard, let's just copy coot and be done with it.
Ability to dynamically bind density levels or some other properties to
the scroll-wheel for that matter.

5) Updated documentation. One thing that always irritated me as a paying
subscriber was the fact that the documentation never kept up with
development and the search capabilities were not that great. Don't get
me wrong the Wiki and BB are great resources, but I'd expect a bit more
of the docs. Also having the internal help functionality for functions
and the API up to date would be great. Some functions don't seem to have
a doc-string.

6) Integration/bundling of wxPython as an alternative to TCL/Tk??

7) Internal FFT routines to be able to read map-coefficients

8) A CGO library for commonly used objects like arrows and such

Cheers,

Carsten

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[PyMOL] New Feature Ideas

[Adrian Schreyer]

I think a page where features ideas can be posted and voted up or down
would be very helpful (like Google product ideas) to collect feature
requests and see which ones are the most demanded.

Adrian

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Re: [PyMOL] PyMOL on the Mac

[David Hall]

Alright, here's a feature request that might convince people who still don't 
believe, despite your first commit to pymol trunk post-acquisition including 
Fixed a GL build bug on OSX (see 
http://pymol.svn.sourceforge.net/viewvc/pymol?view=revrevision=3887 )

A Pymol Quicklook plugin.  My primary purpose would be for pses, but you might 
as well pick up pdbs and other formats supported by pymol along the way.
For pdb files, I wouldn't want the default pymol view of lines colored by atom 
with green carbons being what I quicklook to, so either reading .pymolrc to get 
a default view or some variant ( .pymolqlrc ?) would be nice to allow users to 
customize their views.  Also, maybe default to a cartoon representation colored 
by chains with het atoms as sticks and metals as spheres, but that's probably 
just forcing the view I want on others when I could just stick that in my 
personal .pymolqlrc type file.

Hopefully I'm out of ideas nows,
David



- Original Message 
 From: Jason Vertrees jason.vertr...@schrodinger.com
 To: pymol-users@lists.sourceforge.net
 Sent: Wed, January 20, 2010 4:07:45 PM
 Subject: [PyMOL] PyMOL on the Mac
 
 PyMOLers,
 
 I just want to quickly reiterate: PyMOL will still be supported on the
 Mac--no need to worry.  Even though other Schrodinger software doesn't
 run on the Mac, PyMOL will.
 
 MacPyMOL will live on.
 
 Best,
 
 -- Jason
 
 -- 
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC
 
 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120
 
 --
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 attendees to learn about information security's most important issues through
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

[Tsjerk Wassenaar]

Hi David,

 Doesn't png already take a size and resolution argument?
 cmd.png(string filename, int width, int height, float dpi, int ray, int
 quiet)

 so, now I do cmd.png('1acb.png', 5,4,units=in, dpi=300) ?

Errm, that only makes sense if the viewport itself is resampled
somehow when you don't do raytracing, but I don't think it is. More
probable, one of both, size or resolution, will be disregarded.
Consider that your viewport has a fixed number of pixels on x and on y
(the same goes for a raytraced image). Now to write that to an image,
you can say I want to have so many pixels per inch and see what size
you end up with, or you can say, I want to have it this large and
see what resolution you get. If you are demanding a specific size and
resolution, there's no other option than to construct the image again
(adapt viewport/raytrace).

I hope this makes it clear.

Cheers,

Tsjerk

-- 
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Computational Chemist
Medicinal Chemist
Neuropharmacologist

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Re: [PyMOL] Feature Request/Ideas

[David A. Horita]

Hi,
I would definitely not like to see a default representation to be any
more than lines (as it is now).  Opening one of my 100,000 atom MD
trajectory frames would take far longer than it's worth.

Regarding png output, I think this is in there already (but don't
remember) - I'd like to be able to specify one dimension (usually width)
and have the other automatically calculated.  If I'm trying to frame a
molecule and adjust the size of the screen window I'll want output to
keep the same aspect ratio.

Also, I see a major slowdown when running remotely as compared to VMD,
especially with regards to using the menus (top and right).  I get an
unable to create direct context rendering message, and while I don't
expect it to perform as well as when running locally, I get very
adequate performance running VMD over the same connection.  This is
useful when checking of MD or NMR calculations on a remote cluster from
my lab machines.  The slowdown (especially the view descriptor menu on
the right side) is apparent even over a gigE lan.

I'll add another voice for a better undo function.  In my specific case
I can think of a number of times where I've highlighted a collection of
residues as spheres and then accidentally added spheres to the whole
molecule instead of the next selection.  Being able to get back from
that (even one step) would be a time-saver.

Dave

- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm

-Original Message-
From: David Hall [mailto:dwash59_2...@yahoo.com] 
Sent: Thursday, January 21, 2010 9:20 AM
To: Jason Vertrees; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] PyMOL on the Mac

Alright, here's a feature request that might convince people who still
don't believe, despite your first commit to pymol trunk post-acquisition
including Fixed a GL build bug on OSX (see
http://pymol.svn.sourceforge.net/viewvc/pymol?view=revrevision=3887 )

A Pymol Quicklook plugin.  My primary purpose would be for pses, but you
might as well pick up pdbs and other formats supported by pymol along
the way.
For pdb files, I wouldn't want the default pymol view of lines colored
by atom with green carbons being what I quicklook to, so either reading
.pymolrc to get a default view or some variant ( .pymolqlrc ?) would be
nice to allow users to customize their views.  Also, maybe default to a
cartoon representation colored by chains with het atoms as sticks and
metals as spheres, but that's probably just forcing the view I want on
others when I could just stick that in my personal .pymolqlrc type file.

Hopefully I'm out of ideas nows,
David




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Re: [PyMOL] Feature Requests Hint

[Jason Vertrees]

On Thu, Jan 21, 2010 at 5:33 AM, mjvanraaij mark.vanra...@usc.es wrote:
 yea to extending the ray feature to write pngs of specific size and
 resolution.

 it would additionally be nice to be able to specify only the width (or the
 height) of a picture.

 I.e. I have a pymol window open with the size adjusted to just see the
 picture right, but I want a png with a certain width (say that of a single
 journal column) and resolution - but I don't necessarily know the aspect
 ratio of the window. Or I have a panel A with height X (for example a
 picture of a crystal or something else unpymolrelated) and want to make a
 panel B with the structure with the same height, again not necessarily
 knowing the width to choose.


Mark,

This is an issue I've run into, too.  If the aspect ratio of the
viewport doesn't match that of the final image the view is changed
(atoms clipped, etc).  One solution might be to setup the viewport
using those same height/width commands we're talking about for ray.
(Maybe also adding global settings: image_height, image_width.)
Usage might be:
  # setup the viewport; DPI must be specified/assumed.
  viewport w=22.5cm, h=10cm, dpi=300

  # ... setup your image.

  # ray trace the
  png imageName.png ,22.5cm, 10cm, dpi=300

Food for thought,

-- Jason

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

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] New Feature Ideas

[Luca Varani]

- It would be nice if pymol could deal with/generate viral surfaces 
similar to this one:


http://www.pnas.org/content/100/12/6899/F2.medium.gif

I make all my images with pymol but have to switch to chimera for the 
viral surface.


- I would also find useful if pymol could easily export a list of 
residues/atoms/whatever with given properties, e.g. all the surface 
residues or all the charged residues in an interface.

Maybe it's just my ignorance but I don't know how to do this right now.


Thanks,
Luca
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Re: [PyMOL] Dynoplot/Get residues was:[Re: New Feature Ideas]

[Jason Vertrees]

This is one of the reasons I love open-source:

On Thu, Jan 21, 2010 at 7:58 AM, David Hall dwash59_2...@yahoo.com wrote:
 So, I figured it would be nicer if I sent the author a patch instead of just 
 complaining, so I went to look at the code.

To answer your question, iterate and alter scan over the residues in
order.  (If you make updates to the sequence or IDs in the sequence
don't forget to issue the sort command.)   I ran into this exact
problem when I wrote CEalign--missing residues.  Using iterate/alter
over a selection should solve your problem.

Good luck, let me know if I can help you out.

-- Jason

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

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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[PyMOL] Rendering plugin

[Michael Lerner]

With all of the recent discussion about extensions to the ray command, I
thought I'd mention a little plugin I wrote several years ago. You can find
it at the bottom of

http://sitemaker.umich.edu/carlsonlab/resources.html

It's not quite as full-featured as some of the proposed ray extensions, but
it does provide a really easy way for you to say I want a 4in x 3in figure
at 600dpi.

The Ray button raytraces, and the Draw button just draws the image
without raytracing (a fast way to see that the height/width look good).

It warns you not to have the plugin window on top of your main PyMOL window
when you click Ray. That doesn't seem to be necessary anymore, at least on
my MacBook Pro.

[image:
?ui=2view=attth=12651b51d47cc010attid=0.1disp=attdrealattid=ii_12651b51d47cc010zw]

Cheers,

-Michael

-- 
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)
ishot-10.png--
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Re: [PyMOL] New Feature Ideas

[Jason Vertrees]

On Thu, Jan 21, 2010 at 9:19 AM, Adrian Schreyer ams...@cam.ac.uk wrote:
 I think a page where features ideas can be posted and voted up or down
 would be very helpful (like Google product ideas) to collect feature
 requests and see which ones are the most demanded.

 Adrian

Let's do this.  Head over to http://pymolwiki.org/index.php/Ideas and
find the idea you like.  If it's not there, add it in the format on
the page.  If you want to vote for a feature you like, simply edit the
page, find the yea () associated with your feature and inside the
parentheses put ~~~.  In the wiki if you insert the text ~~~ it
expands to your user name.  This will make a list of usernames for
each feature.  I don't want to do vote counting and we'd have to
search the history if someone double voted.

-- Jason

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

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

[David Hall]

On Thu, Jan 21, 2010 at 9:46 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Errm, that only makes sense if the viewport itself is resampled
 somehow when you don't do raytracing, but I don't think it is.


I'm pretty sure it is resampled when you specify a width or height.  All
this below is with 1.2r1 incentive executable, but I'm pretty sure this also
occurs on my trunk builds as well.  Maybe this is some new behavior?

I do:
viewport 600,400
png out.png, 800,800

The viewport now looks the way it does if I did ray 800,800 (except not ray
traced) and I get an 800x800 picture.

Another example:
png out.png, 1,1
Scene-Warning: Maximum OpenGL viewport dimension exceeded. ScenePNG: wrote
8192x8192 pixel image to file out.png.

PyMol seems to be saying to me, I'm sampling an OpenGL viewport with the
dimensions you specified to create this png

-David
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

[Tsjerk Wassenaar]

Hi,

So what happens if you try it after ray-tracing?

T.

On Thu, Jan 21, 2010 at 5:17 PM, David Hall li...@cowsandmilk.net wrote:
 On Thu, Jan 21, 2010 at 9:46 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Errm, that only makes sense if the viewport itself is resampled
 somehow when you don't do raytracing, but I don't think it is.

 I'm pretty sure it is resampled when you specify a width or height.  All
 this below is with 1.2r1 incentive executable, but I'm pretty sure this also
 occurs on my trunk builds as well.  Maybe this is some new behavior?

 I do:
 viewport 600,400
 png out.png, 800,800

 The viewport now looks the way it does if I did ray 800,800 (except not ray
 traced) and I get an 800x800 picture.

 Another example:
 png out.png, 1,1
 Scene-Warning: Maximum OpenGL viewport dimension exceeded. ScenePNG: wrote
 8192x8192 pixel image to file out.png.

 PyMol seems to be saying to me, I'm sampling an OpenGL viewport with the
 dimensions you specified to create this png

 -David




-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist

--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

[Jason Vertrees]

Don't forget the PNG command also takes a ray argument:

 png fileName, height=X, width=Y, ray=1, dpi=300

PyMOL will resample in that case.  You always get a ray traced file
from that command.

If you do:
  ray 300, 300
  png fileName.ong, height=1000, width=1000

You get a 1000,1000 non-ray traced image.

-- J

On Thu, Jan 21, 2010 at 11:32 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
 Hi,

 So what happens if you try it after ray-tracing?

 T.

 On Thu, Jan 21, 2010 at 5:17 PM, David Hall li...@cowsandmilk.net wrote:
 On Thu, Jan 21, 2010 at 9:46 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Errm, that only makes sense if the viewport itself is resampled
 somehow when you don't do raytracing, but I don't think it is.

 I'm pretty sure it is resampled when you specify a width or height.  All
 this below is with 1.2r1 incentive executable, but I'm pretty sure this also
 occurs on my trunk builds as well.  Maybe this is some new behavior?

 I do:
 viewport 600,400
 png out.png, 800,800

 The viewport now looks the way it does if I did ray 800,800 (except not ray
 traced) and I get an 800x800 picture.

 Another example:
 png out.png, 1,1
 Scene-Warning: Maximum OpenGL viewport dimension exceeded. ScenePNG: wrote
 8192x8192 pixel image to file out.png.

 PyMol seems to be saying to me, I'm sampling an OpenGL viewport with the
 dimensions you specified to create this png

 -David




 --
 Tsjerk A. Wassenaar, Ph.D.

 Computational Chemist
 Medicinal Chemist
 Neuropharmacologist

 --
 Throughout its 18-year history, RSA Conference consistently attracts the
 world's best and brightest in the field, creating opportunities for Conference
 attendees to learn about information security's most important issues through
 interactions with peers, luminaries and emerging and established companies.
 http://p.sf.net/sfu/rsaconf-dev2dev
 ___
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 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Throughout its 18-year history, RSA Conference consistently attracts the
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Re: [PyMOL] New Feature Ideas

[Nathaniel Echols]

On Thu, Jan 21, 2010 at 6:10 AM, Schubert, Carsten [PRDUS] 
cschu...@its.jnj.com wrote:

 4) A better density wizard, let's just copy coot and be done with it.
 Ability to dynamically bind density levels or some other properties to
 the scroll-wheel for that matter.


+1


 6) Integration/bundling of wxPython as an alternative to TCL/Tk??


Also +1.  Warren mentioned this last year as a possibility for integrating
PyMOL with the Phenix GUI, and in theory support for embedding a PyMOL view
in wxPython is already present.  However, that code appears to be very old
and not maintained - I couldn't get it to work even after updating it to use
the newer wx modules.  I suspect there is not much work to do in order to
resurrect it, but I don't know enough about PyMOL internals, or have time to
learn.  Note that this feature (if it were open-source) would allow anyone
to make a native Mac PyMOL GUI and distribute that, so it isn't something
I'd ask Schrodinger to subsidize.  (If anyone else is interested in helping
figure this out, however, let me know.)

7) Internal FFT routines to be able to read map-coefficients


+2.  I believe the CCP4 libraries for this are open-source, so those are one
option.  CCTBX is another (I have tried this and it works), but this will be
a lot more overhead.
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

[Michael Lerner]

The ray command bugs me, so I'll take a stab at improving it this afternoon.

Can someone tell me how to get the size of the current viewport?

This solution:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html

width,height = cmd.get_session()['main'][0:2]


doesn't seem to work for me:

PyMOLprint sorted(cmd.get_session().keys())
['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
'version', 'view', 'view_dict', 'wizard']

-Michael

On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi,

  ray 10cm, 20cm, dpi=300?
  ray 2.5in, 5in, dpi=300?

 I'd slightly modify that to read:

 ray 10,10,units=cm,resolution=300

 where units can be pixels (default), cm, inches, meters, yards,
 lightyears...

 Cheers,

 Tsjerk


 --
 Tsjerk A. Wassenaar, Ph.D.

 Computational Chemist
 Medicinal Chemist
 Neuropharmacologist


 --
 Throughout its 18-year history, RSA Conference consistently attracts the
 world's best and brightest in the field, creating opportunities for
 Conference
 attendees to learn about information security's most important issues
 through
 interactions with peers, luminaries and emerging and established companies.
 http://p.sf.net/sfu/rsaconf-dev2dev
 ___
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-- 
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)
--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

[Michael Lerner]

I think this works. It handles different units (in and cm). If you leave out
width or height, it gets scaled correctly. If you  leave them both out, you
get whatever the current viewport size is (is there something better?).

#!/usr/bin/env pymol

from pymol import cmd

def rayy(width=-1,height=-1,dpi=300,units='in',**kwargs):

Slightly better version of the ray command.
You can specify width and height in the units of your choice, e.g.

rayy 3,2,units=in,dpi=300
rayy 3in,2in
rayy 1in, 2 cm, dpi=600

Extra keyword arguments get passed on to the normal ray command.

if type(dpi) in [type('')]: dpi = int(dpi)
in_per_cm = 0.393700787
def todots(x,units,dpi):
if type(x) in [type('')]:
x = x.lower()
if 'in' in x:   units = 'in'
elif 'cm' in x: units = 'cm'
x = float(x.replace(units,'').strip())
if units ==   'cm':   x = x * in_per_cm
elif units == 'in': pass
else: raise ValueError('Unknown units (%s)'%units)
print x,units,dpi
return int(x * dpi)
# How do we get current width/height of viewport? MainSceneGetSize
perhaps
# But it doesn't matter, as PyMOL will autoscale internally for us.
try:
height,width = todots(height,units,dpi),todots(width,units,dpi)
except ValueError:
print Unknown units
return
print 'width',width,'height',height
cmd.ray(width=width,height=height,**kwargs)
#cmd.png(self.filename.getvalue(), dpi=int(self.dpi.getvalue()))
cmd.extend('rayy',rayy)

On Thu, Jan 21, 2010 at 11:52 AM, Michael Lerner 
mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote:

 The ray command bugs me, so I'll take a stab at improving it this
 afternoon.

 Can someone tell me how to get the size of the current viewport?

 This solution:
 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html

 width,height = cmd.get_session()['main'][0:2]


 doesn't seem to work for me:

 PyMOLprint sorted(cmd.get_session().keys())
 ['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
 'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
 'version', 'view', 'view_dict', 'wizard']

 -Michael

 On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hi,

  ray 10cm, 20cm, dpi=300?
  ray 2.5in, 5in, dpi=300?

 I'd slightly modify that to read:

 ray 10,10,units=cm,resolution=300

 where units can be pixels (default), cm, inches, meters, yards,
 lightyears...

 Cheers,

 Tsjerk


 --
 Tsjerk A. Wassenaar, Ph.D.

 Computational Chemist
 Medicinal Chemist
 Neuropharmacologist


 --
 Throughout its 18-year history, RSA Conference consistently attracts the
 world's best and brightest in the field, creating opportunities for
 Conference
 attendees to learn about information security's most important issues
 through
 interactions with peers, luminaries and emerging and established
 companies.
 http://p.sf.net/sfu/rsaconf-dev2dev
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net




 --
 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)




-- 
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)
--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
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Re: [PyMOL] Feature Requests/Ideas (Sean Law)

[Michael Lerner]

Here's a slightly improved version. It only kicks in if dpi is specified. I
think that you could make the obvious modifications to the help message and
argument list and use it as a replacement for cmd.ray (as long as you're
aware of the fact that the argument list will be different).

#!/usr/bin/env pymol

from pymol import cmd

def rayy(width=-1,height=-1,dpi=-1,units='in',**kwargs):

Slightly better version of the ray command.
You can specify width and height in the units of your choice, e.g.

rayy 3,2,units=in,dpi=300
rayy 3in,2in
rayy 1in, 2 cm, dpi=600

Extra keyword arguments get passed on to the normal ray command.

Units can be 'in' or 'cm'.

For backwards compatibility, the conversion to dpi (or dots per
centimeter) is only performed when dpi is specified.

if type(dpi) in [type('')]: dpi = int(dpi)
in_per_cm = 0.393700787
def todots(x,units,dpi):
if type(x) in [type('')]:
x = x.lower()
if 'in' in x:
units = 'in'
elif 'cm' in x:
units = 'cm'
x = float(x.replace(units,'').strip())
if (dpi == -1):
return x
if units ==   'cm':   x = x * in_per_cm
elif units == 'in': pass
else: raise ValueError('Unknown units (%s)'%units)
print '%s%s at %sdpi'%(x,units,dpi)
return int(x * dpi)
# How do we get current width/height of viewport? MainSceneGetSize
perhaps
# But it doesn't matter, as PyMOL will autoscale internally for us when
given -1.
try:
width,height = todots(width,units,dpi),todots(height,units,dpi)
except ValueError:
print Unknown units
return
print 'width',width,'height',height
cmd.ray(width=width,height=height,**kwargs)
cmd.extend('rayy',rayy)


On Thu, Jan 21, 2010 at 2:39 PM, Michael Lerner 
mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote:

 I think this works. It handles different units (in and cm). If you leave
 out width or height, it gets scaled correctly. If you  leave them both out,
 you get whatever the current viewport size is (is there something better?).

 #!/usr/bin/env pymol

 from pymol import cmd

 def rayy(width=-1,height=-1,dpi=300,units='in',**kwargs):
 
 Slightly better version of the ray command.
 You can specify width and height in the units of your choice, e.g.

 rayy 3,2,units=in,dpi=300
 rayy 3in,2in
 rayy 1in, 2 cm, dpi=600

 Extra keyword arguments get passed on to the normal ray command.
 
 if type(dpi) in [type('')]: dpi = int(dpi)
 in_per_cm = 0.393700787
 def todots(x,units,dpi):
 if type(x) in [type('')]:
 x = x.lower()
 if 'in' in x:   units = 'in'
 elif 'cm' in x: units = 'cm'
 x = float(x.replace(units,'').strip())
 if units ==   'cm':   x = x * in_per_cm
 elif units == 'in': pass
 else: raise ValueError('Unknown units (%s)'%units)
 print x,units,dpi
 return int(x * dpi)
 # How do we get current width/height of viewport? MainSceneGetSize
 perhaps
 # But it doesn't matter, as PyMOL will autoscale internally for us.
 try:
 height,width = todots(height,units,dpi),todots(width,units,dpi)
 except ValueError:
 print Unknown units
 return
 print 'width',width,'height',height
 cmd.ray(width=width,height=height,**kwargs)
 #cmd.png(self.filename.getvalue(), dpi=int(self.dpi.getvalue()))
 cmd.extend('rayy',rayy)

 On Thu, Jan 21, 2010 at 11:52 AM, Michael Lerner 
 mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote:

 The ray command bugs me, so I'll take a stab at improving it this
 afternoon.

 Can someone tell me how to get the size of the current viewport?

 This solution:

 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html

 width,height = cmd.get_session()['main'][0:2]


 doesn't seem to work for me:

 PyMOLprint sorted(cmd.get_session().keys())
 ['cache', 'color_ext', 'colors', 'editor', 'movie', 'names', 'scene_dict',
 'scene_order', 'selector_secrets', 'session', 'settings', 'unique_settings',
 'version', 'view', 'view_dict', 'wizard']

 -Michael

 On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hi,

  ray 10cm, 20cm, dpi=300?
  ray 2.5in, 5in, dpi=300?

 I'd slightly modify that to read:

 ray 10,10,units=cm,resolution=300

 where units can be pixels (default), cm, inches, meters, yards,
 lightyears...

 Cheers,

 Tsjerk


 --
 Tsjerk A. Wassenaar, Ph.D.

 Computational Chemist
 Medicinal Chemist
 Neuropharmacologist


 --
 Throughout its 18-year history, RSA Conference consistently attracts the
 world's best and brightest in the field, creating opportunities for
 Conference
 attendees to learn about information security's most important issues
 

Re: [PyMOL] Rendering plugin

[Michael Lerner]

In keeping with the modern way of doing things, I've

1. put the rendering plugin up on the wiki (
http://pymolwiki.org/index.php/Rendering_Plugin )
2. put a metric version of the plugin on the same page
3. put the rayy code on my userpage on the wiki ( see my .pymolrc here:
http://pymolwiki.org/index.php/User:Mglerner ). If you add it to your
.pymolrc, you will be able to type rayy 3 in, 2 in, dpi=300 from the PyMOL
command line
4. Followed Luca Jovine's suggestion to change the order of rayy's
arguments.

Cheers,

-Michael

On Thu, Jan 21, 2010 at 11:29 AM, Michael Lerner mgler...@gmail.com wrote:

 With all of the recent discussion about extensions to the ray command, I
 thought I'd mention a little plugin I wrote several years ago. You can find
 it at the bottom of

 http://sitemaker.umich.edu/carlsonlab/resources.html

 It's not quite as full-featured as some of the proposed ray extensions, but
 it does provide a really easy way for you to say I want a 4in x 3in figure
 at 600dpi.

 The Ray button raytraces, and the Draw button just draws the image
 without raytracing (a fast way to see that the height/width look good).

 It warns you not to have the plugin window on top of your main PyMOL window
 when you click Ray. That doesn't seem to be necessary anymore, at least on
 my MacBook Pro.

 [image:
 ?ui=2view=attth=12651b51d47cc010attid=0.1disp=attdrealattid=ii_12651b51d47cc010zw]

 Cheers,

 -Michael

 --
 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)




-- 
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)
ishot-10.png--
Throughout its 18-year history, RSA Conference consistently attracts the
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attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
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[PyMOL] Fwd: [ccp4bb] Memorial Service for Warren DeLano

[Jason Vertrees]

PyMOLers,

If any of you want to pay respects to Warren, there is a memorial
service planned for Feb. 7th.  Details copied below.

See you there,

-- Jason


-- Forwarded message --
From: Axel Brunger brun...@stanford.edu
Date: Thu, Jan 21, 2010 at 6:32 PM
Subject: [ccp4bb] Memorial Service for Warren DeLano
To: ccp...@jiscmail.ac.uk



Begin forwarded message:

From: Charles Wolfus cwol...@gmail.com
Subject: Memorial Service for Warren DeLano
In case you have not already heard, the DeLano family is having a
memorial service for Warren:

Sunday, February 7th @ 10am
The Lucie Stern Center
1305 Middlefield Road
Palo Alto, 94301

Please join us in remembering Warren, his special gifts, and accomplishments.

Also, please freely forward this message to any others who may want to join us.

Best Regards,

Friends and Family of Warren DeLano


Axel T. Brunger
Investigator,  Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web:    http://atbweb.stanford.edu
Email:  brun...@stanford.edu
Phone:  +1 650-736-1031
Fax:    +1 650-745-1463


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

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
___
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