[Chimera-users] Fwd: chimera to rebuild crystal

Brady Bernard bradyb at u.washington.edu
Thu Jan 11 19:53:47 PST 2007

hi tom ...

multiscale modeling would be too restrictive - your 5x5x5 example (or any 
other number that i can modify in a chimera script) is more adequate.  i 
would like to make the n x n x n structure, save it to a PDB, and use perl 
or some other program separately to process the pdb file and perform the 
statistics.  so chimera would take the single molecule with cryst1 data, 
make the larger crystal, and write it out to a pdb.

hope that helps - let me know if you have any other questions.


----- Original Message ----- 
From: "Thomas Goddard" <goddard at cgl.ucsf.edu>
To: <bradyb at u.washington.edu>
Cc: <pett at cgl.ucsf.edu>; <goddard at cgl.ucsf.edu>
Sent: Thursday, January 11, 2007 7:48 PM
Subject: Re: Fwd: chimera to rebuild crystal

> Hi Brady,
>  When you say "rebuild a crystal" do you mean you want to open many
> copies of the asymmetric unit to form a 5x5x5 (for example) block of
> unit cells?  Or do you mean you want the Chimera "multiscale model"
> where just one copy of the asym unit is opened but surfaces can be
> shown for the others?  Both are possible using Chimera scripts.
>  What sort of "distance-dependent statistics" are you talking about?
> Are they going to be calculated within Chimera? or is Chimera just
> used for displaying some result?  Perhaps I missed some previous email
> to Eric Pettersen that would help me understand what you need.
> Tom 

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