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
Date: Thu, Jan 21, 2010 at 6:32 PM
Subject: [ccp4bb] Memorial Service for Warren
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/in
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/e
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,
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
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/bu
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 tra
Hi,
So what happens if you try it after ray-tracing?
T.
On Thu, Jan 21, 2010 at 5:17 PM, David Hall wrote:
> On Thu, Jan 21, 2010 at 9:46 AM, Tsjerk Wassenaar wrote:
>>
>> Errm, that only makes sense if the viewport itself is resampled
>> somehow when you don't do raytracing, but I don't think
On Thu, Jan 21, 2010 at 9:46 AM, Tsjerk Wassenaar 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 incentiv
On Thu, Jan 21, 2010 at 9:19 AM, Adrian Schreyer 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
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
This is one of the reasons I love open-source:
On Thu, Jan 21, 2010 at 7:58 AM, David Hall 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
ord
- 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 o
On Thu, Jan 21, 2010 at 5:33 AM, mjvanraaij 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
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
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 do
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=rev&revision=3887 )
A Pymol Quicklook plugin. My prima
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 18-ye
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 ma
> 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 t
On Thu, Jan 21, 2010 at 10:47 AM, Tsjerk Wassenaar wrote:
> Hi Sean e.a.,
I really meant Jason e.a. :$
T.
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
Throughout its 18
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.
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, o
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 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 at
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