Subject: Re: R: [nmr_sparky] Chimera and Sparky
From: Tom Goddard
Date: Oct 6, 2009

Previous: 610

Hi Marco,

The Sparky manual only describes which versions of Chimera are compatible up to Sparky 3.112.

http://www.cgl.ucsf.edu/home/sparky/manual/extensions.html#Chimera

There may be a Chimera version that will work with Sparky 3.113 or there may not be one. Your best bet is to try the Chimera that worked with 3.112 which the manual says is Chimera 1.2154. That Chimera is from August 2005 and is on the old releases page.

http://www.cgl.ucsf.edu/chimera/olddownload.html

Chimera has changed immensely since that time. If you want to try a newer Chimera here are some ideas. One requirement is that they must use the same Python version. Sparky 3.113 uses Python 2.4. Chimera switched from Python 2.4 to 2.5 in February of 2008. (Sparky 3.115 uses Python 2.5.) So you would need Chimera 1.2470 or older. But the Sparky / Chimera interface was last modified in 2004 and Chimera has changed dramatically since then. So you probably need a circa-2004 version of Chimera to make this work.

Tom

-------- Original Message --------
Subject: R: [nmr_sparky] Chimera and Sparky
From: Marco
To: nmr_sparky
Date: 10/5/09 2:13 PM

Hi,

it seems it is possible but perhaps I have not the right combination of Sparky (I have version 3.113) and Chimera (version1.2422).

Marco

--- Lun 5/10/09, Marco ha scritto:

Da: Marco
Oggetto: [nmr_sparky] Chimera and Sparky
A: nmr_sparky
Data: Luned 5 ottobre 2009, 22:54

Hi all,

Im using Sparky with a NOESY map of a protein and I have a preliminary structure.

Now for some cross peaks Im usingthis preliminary structureto solve for ambiguitiesin cross peaks assignments. Thus every time I have more possibilities in a croos peak assignment I check distances in Chimera. Since Sparky and Chimera have some connection is there a way to do this more easily or I have to check by hand every time?

Thanks,

Marco

Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, Tor Vergata
via della Ricerca Scientifica, 00133, Rome, Italy