> > Annemarie, > > You probably picked up a development version of Jmol. Is that possible?
Probably, I just hit the green "Looking for the latest version? Download it now!" button on the sourceforge.net jmol download page (http://sourceforge.net/projects/jmol/files/Jmol/Version%2011.4/) last friday (file jmol-12.2.2.zip), and replaced the content of the jmol folder in my DARPin project intranet site, before testing a few newly added pages. It is definitely not the file. This was my first suspicion, because the new pages called pdb files that have not yet been deposited in the PDB and might have contained something strange. However, the problem also affected the older pages, which had worked previously and which called structures downloaded from the pdb. This morning, before I mailed you, i downloaded jmol-12.2.3.zip and found the same problem with all files tested, both within the intranet site and locally, with our own pdb files and with others freshly downloaded from the pdb. I checked the documentation for the command to make sure that there was no change in the time since I wrote the script I am using in the site, and tried the command with jmol.jar, and kept getting the same error for all pdb files tested. Therefore I replaced the content of the jmol folder in my site with those of jmol-11.9.6, and everything worked fine again, for all pages including the new one. using jmol-12.2.2: 'drag-and-drop' ing file on local jmol window: DE NOVO PROTEIN 14-MAY-10 2XEE STRUCTURAL DETERMINANTS FOR IMPROVED THERMAL STABILITY OF DESIGNED ANKYRIN REPEAT PROTEINS WITH A REDESIGNED C- CAPPING MODULE. 4,742 atoms selected 4,917 atoms selected => structure is displayed $ load "" {1 1 1} range -4 script ERROR: Unexpected end of file after line 5333: END for file file:/Users/ahonegger/Sites/DARPinSites/DarpinCrystalContacts/jmol/structures/raw/2XEE.pdb type Pdb ---- $ show version version = <not defined> => download file from the pdb, drag and drop on the jmol window: HYDROLASE 01-JUL-02 1M40 ULTRA HIGH RESOLUTION CRYSTAL STRUCTURE OF TEM-1 5,712 atoms selected 6,476 atoms selected $ load "" {1 1 1} range -4 script ERROR: Unexpected end of file after line 11055: END for file file:/Users/ahonegger/Downloads/1M40.pdb type Pdb ---- => load file using the "load" command" $ load file:/Users/ahonegger/Downloads/1M40.pdb {1 1 1} range -4 script ERROR: Unexpected end of file after line 11055: END for file file:/Users/ahonegger/Downloads/1M40.pdb type Pdb ---- $ load =file:/Users/ahonegger/Downloads/1M40.pdb {1 1 1} range -4 script ERROR: Unexpected end of file after line 11055: END for file http://www.rcsb.org/pdb/files/file:/Users/ahonegger/Downloads/1M40.pdb type Pdb ---- So the command definitely is broken in the versions currently downloaded with the sourceforge download button. The files used for the test shown above were freshly downloaded from www.rcsb.org. going back to the older version of jmol solved my immediate problem, but I thought you should know that there is a problem with the newest versions on sourceforge. (Working under Mac OS X Version 10.6.8, 2 x 2.66 GHz Dual Core Intel Xeon, 4 GB Memory) best regards and thank you for your help Annemarie Honegger > I've checked in a correction when you use FILTER "TLS" that might have been > causing this, but I'm not sure if that's really the problem. > > On Tue, Nov 1, 2011 at 8:42 AM, Robert Hanson <[email protected]> wrote: > That's not the range, that's the PDB file. What is the source of this file? > Does it do the same with the following? > > load =3NOC {1 1 1} range -6 > > > Here's what I see: > $ show _version > _version = 1202004 > $ load =3NOC {1 1 1} range -6 > TRANSPORT PROTEIN/PROTEIN BINDING 25-JUN-10 3NOC > DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) BINDERS TO ACRB: PLASTICITY > OF THE INTERFACE > > 2 atoms selected > 49,055 atoms selected > 1,165 atoms selected > 51,839 atoms selected > > So I think it's definitely working. Something else is odd with your file. Can > you send me that, if it is not the RCSB version? > > Bob ________________________________________________________ Dr. Annemarie Honegger, Ph.D. Zürich University, Dept. of Biochemistry Winterthurerstr.190 CH-8057 Zürich Switzerland e-mail: [email protected] Tel.: 41-44-635 55 62 Fax: 41-44-635 57 12 URL: http://www.bioc.uzh.ch/antibody URL: http://www.bioc.uzh.ch/nanowelt _______________________________________________________ ------------------------------------------------------------------------------ RSA® Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
