Dear PyMolers,
Recently, we have had a spate of spammers hitting our beloved wiki; some
30+ attackes in the last few days.
Due to this unfortunate change, I have turned off new user registration
so that we can curb this abuse. New users can still be added by
administrators/sysops, in the meanti
Dear PyMol Users,
Due to the increasing popularity of the PyMol Wiki, and the fact that
I'll be hard to reach until Dec. 2nd, we need some people to do very
simple, daily, checks on the PyMol Wiki to make sure that no spammers
have attacked the Wiki.
Recently, we have had attempts to seed the P
Oliver,
I know it'll sound crazy but -- "get". :-)
For example,
get two_sided_lighting
or
get bg_rgb
I think this is covered on the Wiki somewhere, too.
(http://www.pymolwiki.org/)
HTH,
-- Jason
On Wed, 2005-10-19 at 20:24 -0700,
pymol-users-requ...@lists.sourceforge.net wrote:
> Message:
I just rebuilt from CVS on my SuSe x86-64 box. Anyone know why keyboard
input isn't working in the Pmw command line? The internal GUI command
line still works. One quirk though, if I select
Setting -> Edit All
I can edit entries in there using the keyboard/mouse.
I have python2.4 now & used t
Jie,
The PyMolWiki can help you here!
First, the PyMol tricks, that you need, for aligning are described here
http://www.pymolwiki.org/index.php/Intra_Rms
But, if you already know what you want to align, the Kabsch algorithm
can do the job (optimally well)
http://www.pymolwiki.org/index.php/
Anbang Li,
9 out of 10 new PyMol users find the PyMolWiki very helpful*. Check out
http://www.pymolwiki.org/
There are images, tutorials and scripts to automate some harder tasks.
HTH,
-- Jason
* -- Statistics purely made up.
On Thu, 2005-10-06 at 20:07 -0700,
pymol-users-requ...@lists.sou
Nat,
I'm working on a 'smart' alignment program, hence the rotation and
translation part is a subset of the work. (The part that's written thus
far is the Kabsch algorithm for optimal alignment of two sets of points
of vectors).
I've uploaded the complete script, but what you want is the part to
Sreekala,
You want to 'split_states'. Load the biological unit into Pymol then
run 'split_states'.
Check out the PyMolWiki: http://www.pymolwiki.org/index.php/Split_States
where it's described more fully.
-- Jason
On Mon, 2005-08-01 at 20:22 -0700,
pymol-users-requ...@lists.sourceforge.net wr
Sebastien,
That doesn't sound normal. I have a Dell Latitude w/Radeon Mobility
9000 and I get 30+ FPS for larger proteins. I don't however use, FC4.
If you need specs, I can get them for you when I'm near my laptop (later
today) -- just let me know.
-- Jason
On Wed, 2005-07-06 at 06:29 -0700,
Andre,
The Wiki (http://www.pymolwiki.org/) has some information about this.
It also shows you how to change some properties to make things easier to
fit.
Intra_Rms (http://www.pymolwiki.org/index.php/Intra_Rms), and Fit
(http://www.pymolwiki.org/index.php/Fit) on the wiki may help.
HTH,
-- Jas
Alejandro,
Someone a while back wrote a beautiful script to do this for us. I
posted it on the wiki. Check out
http://www.pymolwiki.org/index.php/Stereo_Ray
It should have all the information you'll need.
HTH,
-- Jason
On Fri, 2005-06-10 at 20:19 -0700,
pymol-users-requ...@lists.sourceforge.
PyMolers,
The docs leave me stranded here. The wiki page
(http://www.pymolwiki.org/index.php/Rms_Cur) is the same as the docs.
I'm trying to rms_cur two selections. I keep getting an
ExecutiveRMS-Error: No atoms selected.
error.
I load two proteins, 1gh2 and 1kao. I then, created two easy s
PyMolWiki'ers,
If you're interested in the future of the PyMolWiki or would like to
comment on its design, please check out the site, more directly
(http://www.pymolwiki.org/index.php/Talk:Main_Page) to add your concepts
of what needs to be changed or fixed or left alone.
As a side note, the Py
I saw a black and white representation that either MolScript or Ribbons
did. It looked real neat and I wondered if PyMol could do it. Well, I
found a REAL simple way to do it, and with the trick for creating 300DPI
images, you could do it for printing or publication.
The steps are now on the PyM
NVidia:
I just got the 7174 driver (for 64-bit Linux). PyMol works fine, no
crashes. What do other folks see with 7174? My openGL apps run
nominally faster on 7174 than they do on 6629.
Nuccyl:
As there was little response from the PyMol audience, I will go ahead an
add Nuccyl to the PyMol wiki
Howdy,
This is a request to see if someone familiar with Nuccyl would please
add some documentation and comments to the PyMolWiki, possibly with
example images.
I've setup the page on the wiki and put a little introduction to it
(copied from the Nuccyl page). I'm happy to do it myself, but I'd
r
Shameless PyMolWiki plug time:
We PyMol frequenters have setup a PyMolWiki and you can get lots of
information and newbie hints/tips there. Already over 100 pages; topics
varying from simple commands & scripts to more complicated 3D
information. (Feel free to add what you know!)
Your specific q
PyMolers & PyMolWiki Editors,
After reaping stacks of suggestions from users & wiki gurus I have
devised the first pseudo-structure of the wiki. I say
"pseudo-structure" because: MediaWiki has no built-in hierarchy; and,
because as the wiki grows it'll take on its own structure regardless of
what
PyMolers,
The new PyMol wiki is up for use! The site is still new and rough. We
need volunteers to populate data and organize the site. We're using
MediaWiki.
I've already taken all the suggestions I've received and put them into
the Initial Wiki Layout.
Please make suggestions and changes to
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