From owner-chemistry@ccl.net Sat Jan 7 09:58:01 2006 From: "NielsJohan Christensen njc-,-kvl.dk" To: CCL Subject: CCL: QSAR: TSAR problem with reading PDB connectivity Message-Id: <-30440-060107083848-21350-RuevA3fbAOXR1V3c5MO9Hg#server.ccl.net> X-Original-From: "NielsJohan Christensen" Sent to CCL by: "NielsJohan Christensen" [njc###kvl.dk] Dear CCL'ers. I am trying to establish a QSAR for disaccharides. To this end I am employing the TSAR package from Oxford Molecular (Version 3.3, trial edition). I have generated various disaccharide models with the SWEET II program (http://www.dkfz-heidelberg.de/spec/sweet2/doc/index.php). These structures (PDB files) display correctly when loaded into e.g. Arguslab (http://www.planaria-software.com/arguslab40.htm). However, when loading the PDB files into TSAR, the integrated Tsar Visualizer displays erroneous connectivity. For example, in the model of sucrose, the pyranose ring is collapsed into a four carbon ring. (The furanose ring of the disaccharide, however, is represented correctly.) The outcome is not improved by including explicit connectivity (CONECT) in the PDB file. Apparently TSAR ignores the CONECT info. Any suggestions on how to tackle this problem is highly appreciated. Thanks in advance. Best regards, Niels Johan Christensen From owner-chemistry@ccl.net Sat Jan 7 16:08:00 2006 From: "Alex Allardyce aa[*]chemaxon.hu" To: CCL Subject: CCL: ChemAxon's 2006 User Group Meeting - May 30-31: First call for papers Message-Id: <-30441-060106111213-1234-yfnLzkMyPVPsN0S3uqm50Q::server.ccl.net> X-Original-From: Alex Allardyce Date: Fri, 06 Jan 2006 14:15:59 +0100 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa*o*chemaxon.hu] Hi - please excuse cross postings ChemAxons 2006 User Group Meeting will be held on Tuesday May 30th and Wednesday 31st, 2006 at the Gellert Hotel, Budapest, Hungary. The meeting will include oral and poster presentations from ChemAxon users and developers and a separate track on day 2, for developer issues and hacking. We are requesting those interested in presenting at the meeting to submit abstracts for review. The deadline for reciept of abstracts is March 3rd. To review the submission guidelines please visit http://www.chemaxon.com/forum/ftopic295.html . To review the full presentations from the 2005 meeting archive please visit http://www.chemaxon.com/UGM/05/index.html I you have any questions please feel free to contact us. Hope to see you there. Alex -- Alex Allardyce Communications Director Chemaxon Ltd Tel.: +361 4532658 e-mail: aa|,|chemaxon.com