> I am trying to measure the distance between four aromatic rings of two
> non-standard residues, each residue has two aromatic rings. I'd be
> happy just to get the distance between the centers of each ring and the
> 'distance' command seems appropriate for this but I'm having difficulty
> with the mask.
>
> The residues are call FLP and DAP. The atoms that comprise the rings
> of FLP are C1-C6 and C7-C12 (and there are three additional carbons).
> In DAP, the numbers are not contiguous in one ring and run C1, C2, C9,
> C10, C11, C12. The are contiguous in the other ring (C3-C8).
>
> What :mask could I use to define each of these rings. Thanks.
The checkmask command is very useful to try out atom selections...
But, I think the following will work:
distance d1 out d1.out :FLP.C1-C6,C7-C12 :DAP.C1,C2,C9,C10,C11,C12
Let me know if you are still stuck.
--tom
\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3.utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A
http://www.chpc.utah.edu/~cheatham
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Received on Wed Nov 02 2005 - 17:53:00 PST
