Thanks,
it seems that Ubuntu has a quite updated pymol version in its repositories.
I will install a new version by hand.
John
On 02/18/2011 05:43 PM, Jason Vertrees wrote:
> Hi John,
>
>> I'm running version Version 1.2r2.
> This is probably why. I don't recall the exact version in which th
Hi John,
> I'm running version Version 1.2r2.
This is probably why. I don't recall the exact version in which this
became doable, but it's now available in the latest version.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(
Hi,
your program looks exactly like mine, but I don't get the
png image if I don't raytrace it before. I think everything
else is working because if I run interectively the molecule
is loaded properly, and by just adding the cmd.ray command
gives me a correct image (but raytraced).
I'm running ver
Hi John,
You don't actually need to ray trace before saying any more. That was
an older "feature".
Here's what worked for me:
# save this to examply.py
from pymol import cmd
cmd.load(sys.argv[1])
cmd.hide()
cmd.show("spheres")
cmd.set('sphere_scale',0.3)
cmd.set('orthoscopic',1)
cmd.png("print
Thanks for the reply (and the welcome). With your suggestion I can get a
raytraced image.
Is there a way to get a normal/OpenGL image staying in batch mode? All
those shades are quite disturbing,
since real molecules don't have a shade! :-)
On 02/18/2011 04:52 PM, Tsjerk Wassenaar wrote:
> Hi
Hi John,
It's what we're here for. If we care not to be bothered, we can unsubscribe.
Anyway, you have to raytrace the image if you don't have an OpenGL
window. Add cmd.ray(xresolution,yresolution) before, or add it to the
cmd.png command directly.
Cheers,
Tsjerk
On Fri, Feb 18, 2011 at 8:46 AM
I'm sorry to bother this mailing list so much but it
seems that I cannot save images.
This is the script examply.py
from pymol import cmd
cmd.load(sys.argv[1])
cmd.hide()
cmd.show("spheres")
cmd.set('sphere_scale',0.3)
cmd.set('orthoscopic',1)
cmd.png("printme
Thank you,
this indeed solves the problem! Now everything seems to work smoothely.
I also set an alias to mypymol="pyplot -r script.py -- " so now
everything is
very simple.
Thanks to all for the help.
John
On 02/17/2011 07:30 PM, David Hall wrote:
> No idea if this will fix your problem,
No idea if this will fix your problem, but what I've found is portable
across binaries from Delano Scientific/Schroedinger and
OS/self-compiled versions of pymol is to instead run:
pymol -r examply.py -- mymolecule.xyz
(or if I'm making pngs, usually pymol -qrck examply.py -- mymolecule.xyz )
Th
Hi John, Folmer,
First, in reply to Folmer's comment, it did cross my mind whether it
was necessary to call Pymol from a script, rather than the reverse.
But John gave an example with the file to load as command line
argument (./examply.py mymolecule.xyz). If the filename is required
internally in
Dear John
2011/2/17 John Russo :
> Hi,
> I'm sorry for making such beginner's questions but searching the manual,
> google
> or the wiki didn't help me.
>
You're welcome to ask here.
> I know how to extend pymol by writing python functions (through the
> extend command).
> But is it possible to
Thanks, that is what I was looking for! I just made a simple
script out of it which looks like this
#!/usr/bin/env python
import pymol
from pymol import cmd
import mymodule
pymol.finish_launching()
cmd.load("mymolecule.xyz")
cmd.hide()
cmd.show("spheres")
mymodule.dosomething()
I've noticed s
Hi John,
Is this what you're looking for?:
http://www.pymolwiki.org/index.php/Launching_From_a_Script
Cheers,
Tsjerk
On Thu, Feb 17, 2011 at 8:19 AM, John Russo wrote:
> Hi,
> I'm sorry for making such beginner's questions but searching the manual,
> google
> or the wiki didn't help me.
>
> I
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