From owner-chemistry@ccl.net Fri Jul 19 13:07:01 2013 From: "Guilherme Arantes garantes###gmail.com" To: CCL Subject: CCL: pDynamo Workshop & Molecular Simulation symposia - 2013 Message-Id: <-48973-130719085123-20373-R6cEZOo9VJ6BOkPShslaeg(0)server.ccl.net> X-Original-From: "Guilherme Arantes" Date: Fri, 19 Jul 2013 08:51:22 -0400 Sent to CCL by: "Guilherme Arantes" [garantes[-]gmail.com] pDynamo Workshop & Molecular Simulation symposia - 2013 http://gaznevada.iq.usp.br/cursos/ms2013/ We would like to announce that a pDynamo workshop and a Molecular Simulation symposia will be held in So Paulo, Brazil, from the 21st to the 23rd November 2013 at the Chemistry Institute, Universidade de So Paulo (USP). Both events will consist of a number of presentations by invited speakers and members of the pDynamo community, together with a number of practical sessions using pDynamo. Students and those new to pDynamo are especially welcome. A poster session open to all participants will also be held. Support for both events is being provided by FAPESP. Additional information can be found at: http://gaznevada.iq.usp.br/cursos/ms2013/ A provisional list of confirmed speakers is: Fernando Bachega (USP, Brazil) Ramon Crehuet (IQAC, Spain) Martin Field (IBS, France) Gerhard Hummer (NIH, USA) Luis Rego (UFSC, Brazil) Pengyu Ren (Texas at Austin, USA) Marius Retegan (MPI-CEC, Germany) Gerd Rocha (UFPE, Brazil) Troy Wymore (ORNL, USA) Daniel Zuckerman (Pittsburgh, USA) Organizing comitee: Guilherme Menegon Arantes (USP, Brazil) Martin Field (IBS, France) Troy Wymore (ORNL, USA) From owner-chemistry@ccl.net Fri Jul 19 21:29:01 2013 From: "Bradley Welch bwelch5===slu.edu" To: CCL Subject: CCL: Generating neighboring molecule Message-Id: <-48974-130719212739-11197-XQgbHFkI4CAcusvWbDmiOg-#-server.ccl.net> X-Original-From: Bradley Welch Content-Type: multipart/alternative; boundary=20cf3036401fd3058104e1e758a6 Date: Fri, 19 Jul 2013 20:27:30 -0500 MIME-Version: 1.0 Sent to CCL by: Bradley Welch [bwelch5---slu.edu] --20cf3036401fd3058104e1e758a6 Content-Type: text/plain; charset=ISO-8859-1 This is probably the simplest (in terms of getting what I want done quickly) graphics program I've used in awhile. Thanks for the help. On Thu, Jul 18, 2013 at 1:52 AM, Jacco van de Streek jacco.vandestreek*o* sund.ku.dk wrote: > > Sent to CCL by: Jacco van de Streek [jacco.vandestreek{}sund.ku.dk] > > I have a .cif of a molecule from the literature. I want to do a > calculation on > > its dimer. The authors give the transformation to generate the > neighboring > > molecule (the .cif does not include the dimer). What software could I > use to > > help me generate the molecule? I have chemcraft and jmol but any other > program > > suggested works would be fine as well. > > The program that Brad Rose suggests is indeed one of the best programs for > visualising and analysing crystallographic files. The program is called > Mercury: > > http://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx > > It is free and it is available for multiple operating systems. It is > distributed by the Cambridge Crystallographic Data Centre (CCDC). > > Read the cif into Mercury and either: > 1. switch on "Packing" and delete the excess molecules or > 2. switch on "H-bond" and click on the hydrogen bond you are interested in > to expand the contact into a full molecule and generate the dimer (if the > dimer is hydrogen-bonded). If the dimer is not hydrogen bonded, you may try > the same trick with "Short Contact". > > Mercury can export the atoms that you see on the screen to a .xyz file. > > Best wishes, > -- > Dr Jacco van de Streek > Department of Pharmacy > University of Copenhagen> > > -- Bradley Welch Saint Louis University Monsanto Hall Room 218 --20cf3036401fd3058104e1e758a6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
This is probably the simplest (in terms of getting what I = want done quickly) graphics program I've used in awhile. Thanks for the= help.=A0


On Thu,= Jul 18, 2013 at 1:52 AM, Jacco van de Streek jacco.vandestreek*o*sund.ku.dk <owner-chemistry*ccl.net&g= t; wrote:

Sent to CCL by: Jacco van de Streek [jacco.vandestreek{}sund.ku.dk]
> I have a .cif of a molecule from the literature. I w= ant to do a calculation on
> its dimer. The authors give the transformation to generate the neighbo= ring
> molecule (the .cif does not include the dimer). What software could I = use to
> help me generate the molecule? I have chemcraft and jmol but any other= program
> suggested works would be fine as well.

The program that Brad Rose suggests is indeed one of the best program= s for visualising and analysing crystallographic files. The program is call= ed Mercury:

http://www.ccdc.cam.ac.uk/Solutions/FreeSoftware= /Pages/FreeMercury.aspx

It is free and it is available for multiple operating systems. It is distri= buted by the Cambridge Crystallographic Data Centre (CCDC).

Read the cif into Mercury and either:
1. switch on "Packing" and delete the excess molecules or
2. switch on "H-bond" and click on the hydrogen bond you are inte= rested in to expand the contact into a full molecule and generate the dimer= (if the dimer is hydrogen-bonded). If the dimer is not hydrogen bonded, yo= u may try the same trick with "Short Contact".

Mercury can export the atoms that you see on the screen to a .xyz file.

Best wishes,
--
Dr Jacco van de Streek
Department of Pharmacy
University of Copenhagen



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--
= Bradley Welch
Saint Louis University
Monsanto Hall Room 218
--20cf3036401fd3058104e1e758a6--