The problem with animated gif is the color limitation to 254 + one
transparent colors, whereas PyMOL generated png's have millions of colors +
alpha channel...
-Original Message-
From: Karsten Seidel [mailto:k...@nmr.mpibpc.mpg.de]
Sent: jeudi, 6. juillet 2006 18:15
To: pymol-users@lists
For this purpose I've been using mencoder (http://www.mplayerhq.hu) which is
open source and gives access to a wide range of codecs (mpeg-1, mpeg-2,
mpeg-4 (divx), realmedia, mov, avi, asf, flash etc). Here is the batch file
I used to encode a video in two-pass divx encoding (the frames were in the
Terry,
You can also embed the transparency (ALPHA) value into your cgo file like
this:
from pymol.cgo import *
obj = [
BEGIN, LINES,
LINEWIDTH, 15,
ALPHA, 0.6,
VERTEX, 0.56, -0.88, 5.75,
VERTEX, -1.18, -0.99, -6.88,
END
]
Cheers,
Greg
even add these "new" definitions in your pymolrc file.
Hope it helped!
Cheers,
Greg
-Original Message-
From: Michael Weber [mailto:web...@mailer.uni-marburg.de]
Sent: samedi, 1. juillet 2006 20:02
To: Grégori Gerebtzoff
Subject: Re: [PyMOL] spheres representation and atomic /
Dear Michael,
I do not agree with you; I never observed any variation between sphere
representation and experimental data.
But to test the accuracy of the sphere size, I did the following sequence:
1) I created a molecule composed of one hydrogen and one oxygen, with a
"fake" distance of 1.52 A
Dear Liu Shiyong,
Please have a look to the nice page of Gareth Stockwell,
http://www.ebi.ac.uk/~gareth/, you will find under the section -pymol- some
nice pymol scripts, and in particular wall.py
The script is commented so have a look inside to find how you shall use
it... You might also change t
Hi Jon,
I don't know if this is possible, but Warren posted some weeks ago two
scripts you can run on two PyMOL sessions, in order to synchronize the view
on both visualization windows.
Have a look at these two links:
http://sourceforge.net/mailarchive/message.php?msg_id=14392630
and
http://source
Try the
set ribbon_width, 4.0
command
Cherrs,
Greg
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jose
Borreguero
Sent: jeudi, 16. février 2006 15:47
To: pymol mailing list
Subject: [PyMOL] thic
Hi Joel,
Have you tried the frame control commands at the lower right corner of your
main PyMOL window?
Cheers,
Greg
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Joel Tyndall
Sent: jeudi, 16. février 2006
Dear Milton,
This question has been answered several times; please search the archives of
the PyMOL mailing list
(http://sourceforge.net/search/index.php?type_of_search=mlists&group_id=4546
&forum_id=60) or have a look at pymolwiki
(http://www.pymolwiki.org/index.php/Category:FAQ)
Regards,
Grégo
Have you tried to simply use your mouse wheel? This will change the clipping
view.
Hi Jim,
I am not aware of such functionality, but I posted some time ago a script to
generate cgo objects to render DNA molecules; maybe you can adapt this
script for your needs... Have a look here:
http://sourceforge.net/mailarchive/message.php?msg_id=12611100
Regards,
Greg
-Original Mes
Hi Simon,
Before I start I have to say that I never ever used neither cctbx nor
draw_cell.py.
I installed Python 2.4.1 and cctbx 2005_08_18_0201 on my WinXP machine. I
then had a look to the Roger Dodd's Solution and found out that I cannot
work properly since the file c:\cctbx_source\libtbx\libt
Hi Daniel,
This problem has been tackled several times, maybe have a look at the
following URLs, it might help you getting started:
http://www.rubor.de/bioinf/tips_python.html#msdist
http://sourceforge.net/mailarchive/message.php?msg_id=2914266
And also dont forget the search feature o
Same script, but with hydrogen bonds between nucleotides.
Load the pdb file 127D, run the script and type DrawNT in PyMol command
line
I have a question, maybe Warren you can answer:
I wanted to use the set_color command to define a new color for the Hydrogen
bonds (MyRGBColor = [x,y,z]
Hello List,
Maybe useful, maybe not
Here is a small py script for filling nucleotides
with colored CGO objects. I just tried it on the pdb file 127D.
Of course not as efficient as Nuccyl!!! But I couldnt find out how to run
perl scripts on my Windows-running PC, and this is exactly (and only
Hi Brian,
I had exactly the same problem while installing this version of Pymol on
WinXP SP2; I could fix this problem by replacing this file from the folder
c:\windows\repair to the folder c:\windows\system32. However if it doesn't
work (or if the file is absent from this repair folder), you shou
Hi,
I'm on WinXP and I use Skype for a long time, and the sound quality is
amazing; I just discovered vSkype, a video plugin for Skype. It can handle
up to 200 users simultaneously, and you can also share your desktop or just
a part of your desktop (i.e. a window). Skype is available for multiple
Hi Warren!
I tried the new features of PyMOL, my OS is WinXP Pro SP2 and my graphic
card an ATI Radeon 9700.
The "draw" command runs without any problem, of course I tried to go above
4096 pixels :-) and PyMOL rescale the values to fit 4096. It's really fast
and I love the white frame around the s
Simply type
show surface
set transparency=0.5, my_object
This syntax is true for most Pymol commands...
Greg
color of
your object within Pymol!
Many thanks for your answer(s)!
Grégori Gerebtzoff
Division of Biophysical Chemistry
Biozentrum, University of Basel
Klingelbergstrasse 70
CH-4056 Basel / Switzerland
Tel: +41 61 267 21 92
Fax: +41 61 267 21 89
e-mail: gregori.gerebtz
Hi Sara,
I don't think this is directly possible, since the centers of the aromatic
rings are not declared per se. But I see another way to obtain the result
you want, maybe this can be written as a small Python script (sorry I never
wrote any Python scripts, so I can't translate my idea!!).
The i
Dave,
Try the move command;
move x, value and move y, value for the translation
move z, value for zoom in and zoom out
Greg
Have you tried the "select resi" function? This allows you to specify the
identification numbers of the amino-acids you want to select (and color).
Have a look here for the complete description:
http://pymol.sourceforge.net/newman/user/S0220commands.html
Regards,
Grégori Gerebtzoff
D
**PROBLEM FIXED**
I found yesterday a way to avoid the problem.
First I launch PyMol, then I change the viewport to the one I have in my
script; and finally I run the pml script. This gives full, uncutted png
images.
Btw, does anybody know if there is a python command to wait until a
proc
Hi Kristoffer,
Your suggestion is interesting, but is not in accordance with the various
size of the black part that I get when changing the resolution (viewport),
as the progress bar of PyMol has always the same size, regardless of the
resolution (i.e. 240x60 pixels).
Hi Jacob,
Many thanks for your answer. Here is the follow-up:
I tried to exclude the "load" commands from my script, to pre-load the
structures, display them, be sure that no other windows were overlapping the
PyMol display window (I even placed the PyMol window on another location on
my screen!),
black lines).
Many thanks for your help! Of course I can send script and files if one
wants to try it out
Regards,
Grégori Gerebtzoff
Division of Biophysical Chemistry
Biozentrum, University of Basel
Klingelbergstrasse 70
CH-4056 Basel / Switzerland
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