Hi Mischa, It has to do with pdb format v2.3 vs v3.0 -- coot wants v2.3 but it looks like your input file is v3.0.
A previous suggestion on the ccp4bb was to use the Richardson lab's pdb remediator (used by molprobity to handle both formats) and convert to v2.3 before using coot and then convert back to 3.0 if you need a 3.0 formatted file. http://kinemage.biochem.duke.edu/software/remediator.php Here is the original ccp4bb post suggesting it... http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0806&L=ccp4bb&D=0&T=0&P=30760 Regards, Mitch -----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:[EMAIL PROTECTED] On Behalf Of Mischa Machius Sent: Friday, August 01, 2008 10:18 AM To: [email protected] Subject: [COOT] Problem with writing PDB files containing hydrogens I am using coot-0.5-pre-1 on Mac OS X 10.5.4. When I write PDB files containing hydrogens, the names of the hydrogen atoms end up being misformatted in the resulting file: original file: ... ATOM 10 HG11 VAL A 357 21.109 3.615 9.285 0.91 43.58 H ATOM 11 HG12 VAL A 357 21.030 4.075 7.783 0.91 43.58 H ATOM 12 HG13 VAL A 357 19.879 4.458 8.785 0.91 43.58 H ... written file: ... ATOM 10 HG1 VAL A 357 21.109 3.615 9.285 0.91 43.58 H ATOM 11 HG1 VAL A 357 21.030 4.075 7.783 0.91 43.58 H ATOM 12 HG1 VAL A 357 19.879 4.458 8.785 0.91 43.58 H ... Is this a "feature" of the version I am using, or is this a general bug? Sorry if that question has been answered before. Thanks so much. Best - MM -------------------------------------------------------------------------------- Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
