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
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
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
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.
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.
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
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
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
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
--
Throughout its
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
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
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
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
- 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
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
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,
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
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
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
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
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
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
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
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).
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:
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]
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