Bugs item #869549, was opened at 2004-01-02 21:28 Message generated for change (Settings changed) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=869549&group_id=23629
Category: File Input/Output Group: v8 Status: Closed Resolution: Fixed Priority: 5 Submitted By: Nick Greeves (ngreeves84) >Assigned to: Miguel (migueljmol) Summary: Lanthanide complexes as PDB - problems Initial Comment: Certain X-ray stuctures as PDB files display well under Chime but poorly under Jmol. I have created a web page to demonstrate the problems which range from incorrectly sizing the structure in the frame, failing to display the central lanthanide ion, and introducing spurious bonds to nearby lithium ions. http://www.liv.ac.uk/Chemistry/jmol/test2.html There is a wide variety of software that claims to export PDB files but the resulting files are not all the same! It would be useful if Jmol was as forgiving as possible. This represents a significant problem for anyone seeking to convert a Chime based site as every structure would require careful individual checking. ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2004-05-14 21:38 Message: Logged In: YES user_id=608250 ---------------------------- Original Message ---------------------------- Subject: Re: [ jmol-Bugs-869549 ] Lanthanide complexes as PDB - problems From: "Nick Greeves" <[EMAIL PROTECTED]> Date: Fri, May 14, 2004 21:12 To: "Miguel Howard" <[EMAIL PROTECTED]> -------------------------------------------------------------------------- Hi Miguel, Yes, this can safely be closed. It works well with our lanthanide structures now. ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2004-05-14 20:30 Message: Logged In: YES user_id=608250 Nick, I would like to try to close this bug report ... again :-) Are the outstanding issues resolved with the current version of Jmol v10 pre ? Miguel ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2004-01-03 03:08 Message: Logged In: YES user_id=608250 Glad that v10 works better. The hot pink color was chosen to make it easily visible ... I guess it worked. When things show up in pink it is generally because the atomic symbol is not recognized. Please send me the file that is causing you trouble ... directly to [EMAIL PROTECTED] I am not a chemist ... a two sentence explanation of the molecule you are trying to work with would be helpful. Miguel ---------------------------------------------------------------------- Comment By: Nick Greeves (ngreeves84) Date: 2004-01-03 00:56 Message: Logged In: YES user_id=941641 Indeed I was using Jmol v8 but switching to v10pre4 improves things tremendously (and the applet is so much smaller which is great for slower connections) - great job! The only PDB that still has any problems is the first one which fails to colour the atoms correctly - Barbie pink!! The freestanding application has the same problem. An unrelated query: Chime allowed "spin" to be set and the structure would turn forever which i liked for many of our examples. Can this be set in Jmol (and the speed controlled)? Nick ---------------------------------------------------------------------- Comment By: Miguel (michaelthoward) Date: 2004-01-02 22:12 Message: Logged In: YES user_id=608250 It looks like you are using Jmol v8 ... the current official release of Jmol. If you are converting existing Chime applications, I strongly suggest that you switch to Jmol v10 ... currently in Beta test. Goto http://jmol.sf.net/betatest Jmol v10 has significantly enhanced .pdb support with an explicit goal of being a Chime replacement. It may still have troubles with these .pdb files, so please let me know how files work with v10. Miguel ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=869549&group_id=23629 ------------------------------------------------------- This SF.Net email is sponsored by: Oracle 10g Get certified on the hottest thing ever to hit the market... Oracle 10g. Take an Oracle 10g class now, and we'll give you the exam FREE. http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
