[chimera-dev] again Chimera and Dock

[Eric Pettersen]

On Friday, October 3, 2003, at 07:52 AM, Roberto Sanavio wrote:

> Greetings to all,
>  
> I'm a novice user of Chimera, and I downloaded it recently with the 
> intention to use it also for calculating molecular surfaces as input 
> for UCSF DOCK.From the documentation I haven't understood if the 
> latest version of Chimera is able to do that. 
>  
> on Thu, 19 Dec 2002 Eric Pettersen wrote, answering to Eckhart 
> Guthöhrlein , same date:
>  
> "The current version of Chimera (12/02; build 1602) doesn't have the
> capability to prepare an ms file suitable for DOCK, though we
> anticipate that capability being in the next release (~ 3/03).  "
>  
> If, as I suspect, it's still not possible this use of Chimera, could 
> you tell me if and when it will be?Do you perhaps know of alternatives 
> still functioning on WindowsXP systems ( I'm a novice even about SGI ) 
> or the better choice for me is still to study how to run old DMS on 
> Irix?

As you suspect, saving an MS-format file is not in the 1700 release 
(3/03) nor will it be in the the next release, available in about two 
weeks (though ironically you will be able to read and display an MS 
file!).  Although we have made a lot of improvements in Chimera, we 
just have not made as much progress on this issue as we would like.

Instead of promising a specific date or release for this feature, I 
will email you and this list when it becomes available.

In the interim, I'd like to make the same suggestion that was in a 
later part of the email you quoted:  download the DMS source code from 
http://www.cgl.ucsf.edu/Overview/software.html and compile it.  You 
will also have to download and compile the C-languange PDB library from 
the same place since DMS depends on that.  There is a freely-available 
Unix-like command line environment and compilation tools for XP at 
http://www.cygwin.com/ .

For DMS and the PDB library, you will have to follow the instructions 
in the README files and at the top of the Makefiles.  Also, you will 
have to copy pdb.h from the PDB library into /usr/local/include, since 
that doesn't get installed by default.

Hope to have better news on this front for you soon.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu
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