From chemistry-request:~at~:server.ccl.net Thu Jul 19 08:00:23 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6JC0N512990 for ; Thu, 19 Jul 2001 08:00:23 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id OAA06390 ; Thu, 19 Jul 2001 14:00:04 +0200 (MET DST) Received: (from hinsen -x- at -x- localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id NAA06302; Thu, 19 Jul 2001 13:58:09 +0200 Date: Thu, 19 Jul 2001 13:58:09 +0200 Message-Id: <200107191158.NAA06302 #at# chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen ^%at%^ cnrs-orleans.fr using -f From: Konrad Hinsen To: vani;at;reef.phys.lsu.edu CC: chemistry |-at-| ccl.net In-reply-to: (message from Vemparala Satyavani on Wed, 18 Jul 2001 10:32:08 -0500 (CDT)) Subject: Re: CCL:atom names in PDB files References: > ATOM 1 N GLN A 1 63.870 -23.035 -4.001 1.00 2.09 > MCP1 N > ATOM 2 CA GLN A 1 65.000 -22.112 -3.695 1.00 1.89 > MCP1 C > ATOM 3 C GLN A 1 64.534 -20.647 -3.880 1.00 1.67 > MCP1 C > > my question is there are 2 Nitrogens, 5 carbons etc.,..in Glutamine > residue. how would i know which corresponds to what? Each atom has a unique name, for example, the "CA" is the alpha carbon, and "C" is the carbon in the peptide group. Check the PDB specification for details. However, some programs use their own naming rules instead of those defined by the PDB, including widespread codes such as CHARMM and XPlor. And for hydrogens, the chaos is almost perfect. Moreover, not all programs respect the rules for atom name justification (right justification for the element symbol, left justification for the unique identification part). Alpha-carbons thus are frequently labelled as calcium atoms. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen: at :cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais -------------------------------------------------------------------------------