Re: Using CARNAL to compute per-residue RMSD between PDB files

From: Bill Ross <>
Date: Thu 2 Nov 2000 13:35:08 -0800 (PST)

The RMS residues question:

I think this is what you want - I should have a pointer to it in
the RMS section if I don't already:

          TABLE tbid { column_list } ;
              At least one column must be specified. Columns are
              printed in their order in the list. Column_list may
              include ids, classes of measurement (e.g. DIST) which
              print in the order declared, MEAS which prints all
              scalar measurements, or ALL which prints everything.
              AXIS ids result in vectors, PLANE ids in normals, and
              GROUP ids default to center of geometry unless
              attributes are specified, such as grpid%cmass. RMS
              ids default to the rms of the group, while
              rmsid%residues and rmsid%atoms give per-residue and
              per-atom rms respectively. For per-residue rms, the
              group must not have any partially-included residues.
              If either per-residue or per-atom options are used,
              the statistics are printed in the summary with the
              residue and atom names.

You can also fit on 1 group and measure on another, which gives
the ability to get rms for partial residues, although tediously.


From 3 Nov 2000 11:33:47 -0500
Message-id: <>
Date: 3 Nov 2000 11:33:47 -0500
From: Boyd <>
To: AMBER list <>
Subject: Emerging Technologies/COMP 2001
In-Reply-to: < Using CARNAL to compute per-residue RMSD between PDB files>

Computational Chemists,

(Apologies for multiple-list posting.)

Next summer, the Computers in Chemistry Division (COMP) will be
holding the second annual Symposium on Emerging Technologies.
The symposium will be at the American Chemical Society National
Meeting, Chicago, Illinois, USA, August 26-30, 2001.

A $1000 prize, kindly sponsored by Schrodinger, Inc., will be
to be presented for the best talk at the symposium.

You are invited to participate. The talks will be evaluated by
a Panel of Experts based on the impact the research will have on
the future of computational chemistry and allied sciences. The
symposium will be ideal for presenting your latest and best
methodological advances.

To participate, e-mail a 1000-word (text-only) abstract to me
no later than March 1, 2001. The talks must be original and not
be repeats of talks at other ACS symposia.

Sincerely, Don

Donald B. Boyd, Ph.D.
Organizer, COMP's Symposium on Emerging Technologies
Editor, Journal of Molecular Graphics and Modelling
        (publication of the ACS COMP division and MGMS)
Editor, Reviews in Computational Chemistry

Department of Chemistry
Indiana University-Purdue University at Indianapolis
402 North Blackford Street
Indianapolis, Indiana 46202-3274, U.S.A.
Telephone 317-274-6891, FAX 317-274-4701

Schrodinger, Inc.
Received on Thu Nov 02 2000 - 13:35:08 PST
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