From owner-chemistry@ccl.net Mon May 22 20:41:01 2006 From: "Wayne Steinmetz WES04747^pomona.edu" To: CCL Subject: CCL: Help with Mercury / defining a plane Message-Id: <-31810-060522202719-9831-NHcid933ixUI3bG/c5mWig]-[server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 22 May 2006 17:26:57 -0700 MIME-Version: 1.0 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 -----Original Message----- > 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] --Apple-Mail-1-366570671 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed 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 --Apple-Mail-1-366570671 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 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).=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.

Cheers,

Mike

C. Michael McCallum = =A0 =A0 =A0 = =A0 =A0 = http://www.pacific.edu/college/chemistry/McCallum/cmccallum.html

Associate Professor = =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0

=A0 = =A0

mmccallum .at. pacific .dot. = edu=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 (209) 946-2636 v=A0 / (209) = 946-2607 fax

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