Nope - LSQMAN would still be looking for stretches of sequentially ordered
residues and would only match atoms with identical names (" CB " with " CB ",
for instance).
--G
PS: Brownie points for the non-phenix solution, though!
On Fri, 26 Feb 2010, J?rgen Bosch wrote:
How about LSQMAN ?
with ATOM_types Side_chain ?
That should do the trick.
J?rgen
P.S. sorry it's not really a CCP4 related program, but I use it very
frequently in conjunction with the CCP4 suite :-)
On Feb 26, 2010, at 11:22 AM, Ed Pozharski wrote:
On Fri, 2010-02-26 at 16:50 +0100, Gerard DVD Kleywegt wrote:
But it still won't solve Miri's problem. I think what she is asking
for is a
program that detects which atoms should be matched to which,
irrespective of
their names (i.e., not assuming they are called " CA ") and order
(i.e., not
nicely sequential such as amino-acid residues), and then applies the
operator
that follows from that.
How about FM option in molrep?
http://www.msg.ucsf.edu/local/programs/ccp4-6.0.2/html/molrep.html#FM
Other MR programs can be used as well, just generate FC from one model
in a suitable cell and run search with another.
HTH,
Ed.
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
-
J?rgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se
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