Hmm. OK, let's figure this out. First, could you send me an offending
file? here's what I see in Jmol 12.2.3:
$ load =2xee
DE NOVO PROTEIN 14-MAY-10 2XEE
STRUCTURAL DETERMINANTS FOR IMPROVED THERMAL STABILITY OF
DESIGNED ANKYRIN REPEAT PROTEINS WITH A REDESIGNED C-
CAPPING MODULE.
$ load "" {1 1 1} range -4
DE NOVO PROTEIN 14-MAY-10 2XEE
STRUCTURAL DETERMINANTS FOR IMPROVED THERMAL STABILITY OF
DESIGNED ANKYRIN REPEAT PROTEINS WITH A REDESIGNED C-
CAPPING MODULE.
1 atoms selected
14,916 atoms selected
Please take a look and see if there is an error message in the main Java
console.
Bob
On Tue, Nov 1, 2011 at 12:58 PM, Annemarie Honegger <[email protected]>wrote:
> >
> > 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
> _______________________________________________________
>
>
>
>
>
>
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>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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