From chemistry-request@ccl.net Sun Oct 5 11:38:14 2003 Received: from kafka.net.nih.gov (mailfwd.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h95Fbf59012685 for ; Sun, 5 Oct 2003 11:37:41 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.10/8.12.9) with ESMTP id h95FbfcD019263; Sun, 5 Oct 2003 11:37:41 -0400 (EDT) Date: Sun, 5 Oct 2003 10:50:09 -0400 From: Rick Venable To: Ru-Zhen Li cc: chemistry~at~ccl.net Subject: Re: CCL:question about the output file babel In-Reply-To: <008001c38b4e$780158d0$432b258a@lucylaptop> Message-ID: References: <008001c38b4e$780158d0$432b258a@lucylaptop> ReplyTo: Rick_Venable~at~nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_NJABL,REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_PINE, X_NJABL_OPEN_PROXY version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I've observed the same thing for other conversions to PDB using various versions of Babel, in that most of the identifying info is lost, esp. atom and residue name. I've stopped using Babel, largely for this reason. It was easier to write a quick conversion program specific to the task at hand. On Sun, 5 Oct 2003, Ru-Zhen Li wrote: > I converted one Accelrys .car file into .pdb file with babel16, but > the output file is quite strange, it is not the same as the pdb file > from Protein Data Bank, for eg: > > 1. the atom name is just one character > 2. the forth column of the coordinate of the atoms should be the > residue the atom belongs to, but all the name of the residue in the > output file is UNK. > > can anyone tell me why? =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable~at~nih.gov ALT email: rvenable~at~speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=