[Chimera-users] Fwd: chimera to rebuild crystal

Brady Bernard bradyb at u.washington.edu
Thu Jan 11 20:19:39 PST 2007


hi tom ...

>The different copies could be written to separate files
>with names based on which unit cell and symmetry operator was used.

i think that sounds like a good solution.

thanks,
brady


----- Original Message ----- 
From: "Thomas Goddard" <goddard at cgl.ucsf.edu>
To: <bradyb at u.washington.edu>
Cc: <goddard at cgl.ucsf.edu>
Sent: Thursday, January 11, 2007 8:06 PM
Subject: Re: Fwd: chimera to rebuild crystal


> Hi Brady,
> 
>  Ok, that helps.  Might be easiest to not open all those copies of
> the PDB asym unit in Chimera but instead open one and then use Chimera
> routines to output many transformed copies.  Would you want all the
> copies in a single PDB file?  That presents the problem that you'll
> have many copies with the same chain ID's and residue numbers and how
> will you know which unit cell and symmetry each atom belongs to.
> Maybe that isn't needed for your statistics?  Do the statistics
> involve interface interactions?  Also you may exceed the PDB format
> 100,000 atom limit (serial number can only be 5 digits) if they all go
> in one file.  The different copies could be written to separate files
> with names based on which unit cell and symmetry operator was used.
> 
>  If I know exactly what you need I might be able to send a script
> your way tomorrow.
> 
> Tom





More information about the Chimera-users mailing list