pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Using Numeric on Windows

[Warren L. D. <wa...@su...>]

I've folded Numeric Python 20.0.0 into the Windows binaries for PyMOL 0.68
(released today).  This is the most recent version of Numeric which works
with both 1.5.2 and Python 2.1.   

For those with an insatiable hunger for eye candy, PyMOL 0.68 also 
contains transparent surfaces. 8-)

Cheers,
Warren

On Fri, 26 Oct 2001, Paul Sherwood wrote:

> All,
> 
> I would like to try and use parts of PyMOL that use Numeric
> on the Windows platform. The "out-of-the-box" install
> procedures for PyMOL, Python (2.1.1) and Numeric lead to
> problems importing the Numeric module as follows.
> 
> ImportError: No module named Numeric
> 
> Is there a way to fix this?
> 
> thanks
> 
> Paul
> 

[PyMOL] Using Numeric on Windows

[Paul S. <p.s...@dl...>]

All,

I would like to try and use parts of PyMOL that use Numeric
on the Windows platform. The "out-of-the-box" install
procedures for PyMOL, Python (2.1.1) and Numeric lead to
problems importing the Numeric module as follows.

ImportError: No module named Numeric

Is there a way to fix this?

thanks

Paul
-- 
======================================================================
Dr Paul Sherwood,         email:  p.s...@da...
CLRC Daresbury Lab,       tel:    +44-1925-603553
Warrington,               fax:    +44-1925-603634
WA4 4AD,  UK.             http:   http://www.cse.clrc.ac.uk
======================================================================

RE: [PyMOL] Re: PyMOL-users digest, Vol 1 #2 - 2 msgs

[DeLano, W. <wa...@su...>]

> From: Peter Haebel [mailto:p.h...@au...]

> anyway, playing around I realised that it would be nice to be=20
> able to read
> out the pymol settings, such as 'bg_color', 'antialias' and any other
> variables. is there such a pymol function?

For well defined settings, this can be easily done, although the API is
somewhat incomplete.

(in python)

from pymol import cmd

print cmd.get_setting_tuple('bg_rgb')
my_variable =3D cmd.get_setting_tuple('antialias')

etc.

You will get a tuple of length 2.  The first field is a type identifier,
and the second is the value corresponding to the setting. =20

Current type identifiers: 3 for a float, 4 for a nested tuple of three
floats.  In the future, 1 will be a boolean, and 2 will be an int. =20

Settings are still in the process of being de-homogenized from being
pure floating point values.  Eventually we will supplement this function
with something more descriptive and user-friendly -- it only exists this
early because I needed it to support the first external GUI.

Please contribute your extension for inclusion in util.py when it is
done.

Note that you can use cmd.extend to bind it to a command for maximum
convenience.=20

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501

> -----Original Message-----
> From: Peter Haebel [mailto:p.h...@au...]
> Sent: Wednesday, October 24, 2001 1:12 PM
> To: pym...@li...
> Subject: [PyMOL] Re: PyMOL-users digest, Vol 1 #2 - 2 msgs
>=20
>=20
> Hi Warren,
>=20
> I have a related question. just wrote a little extension for=20
> pymol that
> generates stereo figures and merges the right and left stereo image to
> complete the figure.
>=20
> util.stpng(["filename"]).
>=20
> the extension is written in python and uses PIL (the python=20
> image library)
> to manipulate the images. It can output the merged figures in=20
> all standard
> image formats (png, tiff, jpeg, ps, pdf, etc only depends on=20
> the libraries
> you have installed) and derives the format from the extension of the=20
> output filename.
>=20
> anyway, playing around I realised that it would be nice to be=20
> able to read
> out the pymol settings, such as 'bg_color', 'antialias' and any other
> variables. is there such a pymol function?
>=20
> cheers
>=20

[PyMOL] Re: PyMOL-users digest, Vol 1 #2 - 2 msgs

[Peter H. <p.h...@au...>]

Hi Warren,

I have a related question. just wrote a little extension for pymol that
generates stereo figures and merges the right and left stereo image to
complete the figure.

util.stpng(["filename"]).

the extension is written in python and uses PIL (the python image library)
to manipulate the images. It can output the merged figures in all standard
image formats (png, tiff, jpeg, ps, pdf, etc only depends on the libraries
you have installed) and derives the format from the extension of the 
output filename.

anyway, playing around I realised that it would be nice to be able to read
out the pymol settings, such as 'bg_color', 'antialias' and any other
variables. is there such a pymol function?

cheers

peter


 :)__________________________________________

  Peter Haebel

  Laboratory of Structural Biology,   Phone: +64-9-373 7599 ext. 7237
  School of Biological Sciences,      Fax:   +64-9-373 7414
  University of Auckland              Email: p.h...@au...
  New Zealand                         http://www.netcolony.com/life/phaebel

  Meet LISA at http://lisa.sbs.auckland.ac.nz

On Wed, 24 Oct 2001 pym...@li... wrote:

> Send PyMOL-users mailing list submissions to
> 	pym...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
> 
> You can reach the person managing the list at
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
>    1. getting image sizes (Ben Cornett)
>    2. RE: getting image sizes (DeLano, Warren)
> 
> --__--__--
> 
> Message: 1
> To: pym...@li...
> From: Ben Cornett <ac...@em...>
> Date: 24 Oct 2001 09:09:18 -0400
> Subject: [PyMOL] getting image sizes
> 
> Does anyone know how to get the size (pixels) of the viewer?  I'd like
> to be able to write a python script that orients and colors a molecule
> and then renders it at whatever dpi I provide as a command-line
> argument.
> 
> Best,
> 
> Ben
> 
> 
> 
> --__--__--
> 
> Message: 2
> Subject: RE: [PyMOL] getting image sizes
> Date: Wed, 24 Oct 2001 09:06:42 -0700
> From: "DeLano, Warren" <wa...@su...>
> To: "Ben Cornett" <ac...@em...>,
> 	<pym...@li...>
> 
> Welcome everybody to the PyMOL mailing list.  There are over 30
> subscribers.  I am very pleased that so many people want to use (and
> thereby improve) the package.
> 
> > From: Ben Cornett=20
> 
> > Does anyone know how to get the size (pixels) of the viewer?  I'd like
> > to be able to write a python script that orients and colors a molecule
> > and then renders it at whatever dpi I provide as a command-line
> > argument.
> 
> Ben,
> 
> Hmm, not all of those features may exist yet, but the following will
> help.
> 
> The "viewport" command can be used to change the window size.
> Alternatively, the "ray" command can take width and height arguments.
> 
> Remember that two options exist for scripting: PyMOL commands and
> Python.   The former is easier for quick-and-dirty tasks.
> 
> # SCRIPT fig1.pml (PyMOL command language)
> # RUN AS "pymol -c fig1.pml"
> viewport 1024,768
> load example.pdb
> color marine
> orient
> ray=20
> png fig1.png
> # END
> 
> versus=20
> 
> # SCRIPT fig2.py (Python)
> # RUN AS "pymol -c fig2.py"
> from pymol import cmd
> cmd.viewport(1024,768)
> cmd.load("example.pdb")
> cmd.color("marine")
> cmd.orient()
> cmd.ray()
> cmd.png("fig2.png")
> # END
> 
> also equivalent to=20
> # SCRIPT fig3.pml (PyMOL)
> # RUN AS "pymol -c fig3.pml"
> load example.pdb
> color marine
> orient
> ray 1024,768
> png fig3.png
> # END
> 
> Passing additional command arguments can't yet be done reliably, but you
> might try playing around with -d (at least on unix). Note single quotes
> and no spaces within the quote.
> 
> pymol -d 'w=3D1024;h=3D768'
> 
> should define "w" and "h" in the interpreter namespace.
> 
> Thus, the following works...
> 
> # SCRIPT fig3.py (Python)
> # RUN AS "pymol -c -d 'w=3D1024;h=3D768' fig3.py "
> from pymol import cmd
> cmd.load("example.pdb")
> cmd.color("marine")
> cmd.orient()
> cmd.ray(w,h)
> cmd.png("fig3.png")
> # END
> 
> You might even be able to pass in the input and output filenames:
> 
> pymol -c -d 'w=3D1024;h=3D768;i=3Dexample.pdb;o=3Dfig4.png' fig4.py
> 
> # SCRIPT fig4.py (Python)
> from pymol import cmd
> cmd.load(i)
> cmd.color("marine")
> cmd.orient()
> cmd.ray(w,h)
> cmd.png(o)
> # END
> 
> - Warren
> 
> 
> 
> --__--__--
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> End of PyMOL-users Digest
> 

RE: [PyMOL] NMR models

[DeLano, W. <wa...@su...>]

> From: Ezequiel Panepucci [mailto:za...@SL...]

> Hi There,
> How would I go about selecting a specific model from a
> PDB file which includes several NMR conformations?

Zac,

load 1NGR.pdb

create mod6,1NGR,6,1 =20
# takes state/model 6 of 1NGR and puts it in frame 1
# of a new object called "mod6"

save mod8.pdb,1NGR,8
# saves state/model 8 of 1NGR to a new PDB file.

See "help create" and "help save"

- Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
>=20

[PyMOL] NMR models

[Ezequiel P. <za...@SL...>]

Hi There,
How would I go about selecting a specific model from a
PDB file which includes several NMR conformations?

Thanks,
	Zac

RE: [PyMOL] getting image sizes

[DeLano, W. <wa...@su...>]

Welcome everybody to the PyMOL mailing list.  There are over 30
subscribers.  I am very pleased that so many people want to use (and
thereby improve) the package.

> From: Ben Cornett=20

> Does anyone know how to get the size (pixels) of the viewer?  I'd like
> to be able to write a python script that orients and colors a molecule
> and then renders it at whatever dpi I provide as a command-line
> argument.

Ben,

Hmm, not all of those features may exist yet, but the following will
help.

The "viewport" command can be used to change the window size.
Alternatively, the "ray" command can take width and height arguments.

Remember that two options exist for scripting: PyMOL commands and
Python.   The former is easier for quick-and-dirty tasks.

# SCRIPT fig1.pml (PyMOL command language)
# RUN AS "pymol -c fig1.pml"
viewport 1024,768
load example.pdb
color marine
orient
ray=20
png fig1.png
# END

versus=20

# SCRIPT fig2.py (Python)
# RUN AS "pymol -c fig2.py"
from pymol import cmd
cmd.viewport(1024,768)
cmd.load("example.pdb")
cmd.color("marine")
cmd.orient()
cmd.ray()
cmd.png("fig2.png")
# END

also equivalent to=20
# SCRIPT fig3.pml (PyMOL)
# RUN AS "pymol -c fig3.pml"
load example.pdb
color marine
orient
ray 1024,768
png fig3.png
# END

Passing additional command arguments can't yet be done reliably, but you
might try playing around with -d (at least on unix). Note single quotes
and no spaces within the quote.

pymol -d 'w=3D1024;h=3D768'

should define "w" and "h" in the interpreter namespace.

Thus, the following works...

# SCRIPT fig3.py (Python)
# RUN AS "pymol -c -d 'w=3D1024;h=3D768' fig3.py "
from pymol import cmd
cmd.load("example.pdb")
cmd.color("marine")
cmd.orient()
cmd.ray(w,h)
cmd.png("fig3.png")
# END

You might even be able to pass in the input and output filenames:

pymol -c -d 'w=3D1024;h=3D768;i=3Dexample.pdb;o=3Dfig4.png' fig4.py

# SCRIPT fig4.py (Python)
from pymol import cmd
cmd.load(i)
cmd.color("marine")
cmd.orient()
cmd.ray(w,h)
cmd.png(o)
# END

- Warren

[PyMOL] getting image sizes

[Ben C. <ac...@em...>]

Does anyone know how to get the size (pixels) of the viewer?  I'd like
to be able to write a python script that orients and colors a molecule
and then renders it at whatever dpi I provide as a command-line
argument.

Best,

Ben

RE: [PyMOL] atom picking hooks

[DeLano, W. <wa...@su...>]

Ben,=20

   If all you have is a single structure loaded, then you can get
unambiguous identifiers corresponding to the atom positions in the
macromodel file by cmd.identify.

For example, if the user put some atoms into the "lb" selection using
the mouse, then you could get a Python list of their indices as follows:

print cmd.identify("(lb)")

[1,4,7,8,4,50]

(one based atom indices from the macromodel file).

Example usage with a Python function...

from pymol import cmd

def color_sele_red(sele):
   lst =3D cmd.identify(sele)
   cmd.color("white")
   for a in lst:
      cmd.color("red","(id %d)"%a)

color_sele_red("lb")
     =20
Note that if you have multiple objects loaded, you will need some way of
determining which identifiers correspond in which object.  Right now
that is complicated.  In version 0.67, you can pass a mode argument to
"identify" which will give you the object names and identifiers as a
list of tuples...

print cmd.identify("(lb)")

[('pept',2),('pept',6),('pept',11)]

It is also possible to grab user selections directly with the Wizard
capabilities.  That interface isn't documented, but several working
examples exist:

pymol/modules/pymol/wizard/*.py

Cheers,
Warren

Ben Wrote:

>Let me help break the new mailing list in.  I haven't been using pymol
>for very long, but I've been impressed with some of its features and
>with its potential.  At the moment, I'm working on a program that
>could benefit by integrating pymol.  Specifically, I need to be able
>to read in a molecule (macromodel format) and allow the user to select
>various atoms.  Does pymol provide a way for my code to access these
>selections? Thanks.

--=20
mailto:wa...@su...=20
Warren L. DeLano, Ph.D.=20
Informatics Scientist=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 fax: (650)-266-3501=20

[PyMOL] atom picking hooks

[Ben C. <ac...@em...>]

Let me help break the new mailing list in.  I haven't been using pymol
for very long, but I've been impressed with some of its features and
with its potential.  At the moment, I'm working on a program that
could benefit by integrating pymol.  Specifically, I need to be able
to read in a molecule (macromodel format) and allow the user to select
various atoms.  Does pymol provide a way for my code to access these
selections? Thanks.

Best,

Ben