CCL: Help with Mercury / defining a plane

 Sent to CCL by: "Wayne Steinmetz" [WES04747(0)pomona.edu]
 Before I answer the question, I'll first summarize the task as I
 understand it.  Given the three-dimensional structure of a molecule, one
 wishes to fit a set of atoms to a plane.  For this purpose, I use a
 module in Tripos' SYBYL.  SYBYL allows one to select the atoms by
 point-and-click or via a script written in SBYL Program language.  The
 module generates an equation for the plane and the rms deviation of the
 atoms selected for the operation from the plane.  The equation for the
 plane is added to the SYBYL mol2 file.  One can in later operations
 calculate the distance of any atom in the structure from the plane.
 SYBYL uses a least-squares function to find the best plane for n atoms.
 Obviously, n must be at least 3.
 So the good news is the existence of the required functionality.  The
 bad news is the price.  Tripos has a budget program, Alchemy, which
 might have the required module.
 Wayne E. Steinmetz
 Carnegie Professor of Chemistry
 Woodbadge Course Director
 Chemistry Department
 Pomona College
 645 North College Avenue
 Claremont, California 91711-6338
 USA
 phone: 1-909-621-8447
 FAX: 1-909-607-7726
 Email: wsteinmetz,pomona.edu
 WWW: pages.pomona.edu/~wsteinmetz
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 > From: owner-chemistry,ccl.net [mailto:owner-chemistry,ccl.net]
 Sent: Monday, May 22, 2006 12:00 PM
 To: Wayne Steinmetz
 Subject: CCL: Help with Mercury / defining a plane
 Sent to CCL by: Charles McCallum [mmccallum|,|pacific.edu]
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 A colleague of mine is using the program Mercury (http-:-//
 www.ccdc.cam.ac.uk/products/csd_system/mercury/downloads/) to define
 some planes in her crystal structure, and while it is doing what she
 wants, it is not reporting an error/sum of residuals (or any other
 uncertainty).  I know it is a long shot with this crowd, but does
 anyone have any experience with this?  Either a way to extract this
 information from the program, or another program that would allow us
 to define planes including some atom selections, and give residuals
 would be most appreciated.
 Cheers,
 Mike
 --
 C. Michael McCallum           http://www.pacific.edu/college/
 chemistry/McCallum/cmccallum.html
 Associate Professor
 Department of Chemistry, UOP
 mmccallum .at. pacific .dot. edu                (209) 946-2636 v  /
 (209) 946-2607 fax
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 <HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode:
 space; =
 -khtml-line-break: after-white-space; ">A colleague of mine is using the
 =
 program Mercury (<A =
 href=3D"http://www.ccdc.cam.ac.uk/products/csd_system/mercury/downloads/
 ">=
 http://www.ccdc.cam.ac.uk/products/csd_system/mercury/downloads/</A>)
 to
 =
 define some planes in her crystal structure, and while it is doing what
 =
 she wants, it is not reporting an error/sum of residuals (or any other =
 uncertainty).=A0 I know it is a long shot with this crowd, but does =
 anyone have any experience with this?=A0 Either a way to extract this =
 information from the program, or another program that would allow us to
 =
 define planes including some atom selections, and give residuals would =
 be most appreciated.<DIV><BR =
 class=3D"khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR
 =
 class=3D"khtml-block-placeholder"></DIV><DIV>Mike</DIV><DIV><BR><DIV>
 =
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