Well, Bill, looks like my contribution is the one that ignited the flames here. I'm completely satisified with Miguel and Egon's analyses. On the one hand, you guys are correct that we can't just ignore HTML codes. I see your point. On the other hand analysis of the first four lines of a file certainly doesn't give Jmol anything more than an educated "guess" at the actual file format, and there are plenty of things that might be in a file that are not "to code" and yet Jmol would ignore and still read the file just fine. For example, the first record of a PDB file is HEADER. It must be the first record and it is mandatory. But Jmol, Chime, and Rasmol are all more flexible than that. If you really say you want to limit yourself to "precisely" PDB format, then I think all you have to look for is HEADER, not all the other possible records listed in the reader code. My point is simply that Jmol -- rightfully so IMHO -- errs on the lenient side of file formats. This is good, IMHO. The number 4 here is totally arbitrary, of course. If it were six lines being read, then Jmol would have successfully read Bill's file. Would changing 4 to 6 break something, or would it simply make the Jmol applet a little more flexible regarding header info?
Bob
William Reusch wrote:
Jaime, Miguel and others,
I'm sorry my inquiry about incompatible pdb files initiated this fuss. Since for many years I have been using all kinds of pdb files with Chime, I was surprised to find that some of the older files did not work with Jmol. Your explanations clearly indicate the nature of the problem, and it is easy to correct. Unfortunately, time has passed and I can't tell you where I found the offending hemoglobin file. For Jmol use I have replaced it with 1A3N from the protein databank.
All of my past queries have come from an effort to translate my Chime based Virtual Text of Organic Chemistry to a Jmol version. I have almost finished, and I will post the url once I am convinced everything is functioning correctly. Incidently, I have restricted the Jmol displays to applet generated buttons to avoid the Javascript problems that have been prominently discussed here. I use both Wintel and Macintosh platforms, and I find the latter fails to function well with many of the fine sites referenced here, despite upgrades to OS10.3.5 and the most recent Java fixes.
Thanks for all your help.
Bill
Jaime Prilusky wrote:
Jaim wrote:
This file comes from OCA, and it's intended to be received by a web
A small correction. The 'incompatible' files headed with
<!-- send-pdb -->
are NOT generated by OCA, but for a script I wrote long time ago.
I will appreciate to know the full site URL so I can contact the administrator and suggest an update.
OCA does send fully compatible PDB files when requesting "Save to disk" from the browser, or when calling either .../oca-bin/save-pdb?id=XXXX or .../oca-bin/send-x-pdb?id=XXXX (compressed) at any of the OCA mirrors (http://bip.weizmann.ac.il/oca-docs/mirrors.html)
Jaim
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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