[Chimera-users] Dockprep and WriteMol2

Eric Pettersen pett at cgl.ucsf.edu
Sat Feb 4 19:28:14 PST 2006

Hi Steve,
	Your Googling hit our development documentation, which includes  
features not in the latest production release and in some cases  
features that aren't in any release yet.  Dock Prep is one of those.   
We are preparing a release candidate that we anticipate being on the  
web early next week that will include Dock Prep -- though I can't  
absolutely guarantee that there won't be an unforeseen hangup that  
delays it a few days.  If you want to use Dock Prep ASAP, I could send  
you the relevant Python files to drop into your 1.2186 distribution --  
let me know.  As you noticed, the WriteMol2 module got mistakenly left  
out of the 1.2186 snapshot, so I would be sending you the files for  
that as well.  The files I'd send you would include one small feature  
that won't be making it into the release candidate:  structures with  
alternate atom locations will have them pruned to the locations with  
highest occupancy.

	Eric Pettersen
	UCSF Computer Graphics Lab

On Feb 4, 2006, at 4:13 PM, Steven Finckbeiner wrote:

> I have Chimera beta version 1 build 2186.  I think it's the latest  
> beta available.  I'm trying to clean up some structures to run in  
> Dock.  When I do a google search, the following page comes up:
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ 
> dockprep.html
> I can't find Dockprep under the Surface/Binding Analysis menu.  Is  
> this something that will come out in future versions but the web page  
> is already built?  Or is it in later versions?  If so which?  My  
> particular situation makes it hard to get to SYBYL to assign charges  
> and define rigid and anchor sets.  I was thrilled to see that  
> something like Dockprep has at least been concieved of. 
> Also, when I try to save as mol2, I ! get the following error:
> "Import Error: No module named WriteMol2."
> I apologize ahead of time if this marks me as a hopeless novice.  Any  
> help would be much appreciated. 
> Steve
> "Sometimes, life hits you in the head with a brick."
> Steve Jobs
> ----------------------------------------------------------------
> Steve Finckbeiner
> 132 Grace Cancer Drug Center
> Roswell Park Cancer Institute
> Elm and Carlton Streets
> Buffalo, NY 14263-0001
> (716)845-5818
> Yahoo! Mail - Helps protect you from nasty  
> viruses._______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 2558 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20060204/f0dff345/attachment.bin>

More information about the Chimera-users mailing list