Dear All,
Based on what Bob has done below for relative file paths I think we
(Bob?) can now make a compressed jmol save file, which is something I
was considering doing based on the jmolInstance used for web export.
Here's my idea:
1) Copy the data file, state script and any jvxl files associated with
view in a single directory with a user chosen name.
2) The state script would need to use the appropriate relative paths
(now easy, I think).
3) Zip this into one file with the name <directoryname>.jmol.
4) If I remember how Jmol opens things, I think we can open this file
directly and it could be passed from machine to machine without a
problem.
5) There are still some issues with updating. I like the safe update
method. a) Write updated file with a temporary name. b) Upon
successful write erase old file and rename new to the old file name.
I was going to use something like this for the multi-viewer we once
discussed, but haven't had time to work on that.
What do people think?
Jonathan
On Sep 3, 2009, at 5:19 PM, SourceForge.net wrote:
> Feature Requests item #2837721, was opened at 2009-08-14 10:40
> Message generated for change (Comment added) made by hansonr
> You can respond by visiting:
> https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2837721&group_id=23629
>
> Please note that this message will contain a full copy of the
> comment thread,
> including the initial issue submission, for this request,
> not just the latest update.
> Category: None
> Group: None
> Status: Closed
> Priority: 5
> Private: No
> Submitted By: Christopher King (popnose)
> Assigned to: Nobody/Anonymous (nobody)
> Summary: Use relative address in state files
>
> Initial Comment:
> On one computer, a file, 1edn.pdb, was opened. The state was saved
> as 1edn.spt in the same directory as 1edn.pdb. Both files were
> transferred to the same directory on another computer. On that
> computer, the state file gave an error because the directory
> structure was different than on the original computer. Can the
> state file be changed to use a relative address for the original
> file? Then, I could transfer state files from office to classroom
> and not have to worry as much about having the same directory
> structure.
>
> ----------------------------------------------------------------------
>
>> Comment By: Bob Hanson (hansonr)
> Date: 2009-09-03 17:19
>
> Message:
> one more comment. This works by finding
> /*file*/"http://rcsb.org/pdb/files/1crn.pdb"; in a state script. If
> you had
> your own script, you could do the same; just make sure you have /
> *file*/
> immediately preceding a double-quoted file name.
>
>
> ----------------------------------------------------------------------
>
> Comment By: Bob Hanson (hansonr)
> Date: 2009-09-03 17:15
>
> Message:
> OK, this is done. See Jmol 11.9.2
> (http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip and
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm)
>
> There are two new options for SCRIPT and WRITE STATE commands. These
> are
> LOCALPATH and REMOTEPATH. Each takes an argument in quotes. Setting
> the
> LOCALPATH replaces any file reference in the script, either on
> reading or
> writing, to that path; setting REMOTEPATH does the same for anything
> with
> an "http" "https" or "ftp" prefix. So, for example, if you have a
> state
> that refers to files on a local file system and now you want to run
> it but
> load files from a different system, you would do something like this:
>
> script LOCALPATH "" "myfile.spt"
>
> That says, "whatever the local file path to a file accessed by this
> script
> command, (in LOAD or SCRIPT commands, for example), make them come
> from the
> current directory. (This might be on a web host or another local
> machine.)
>
>
> script LOCALPATH "data" "myfile.spt"
>
> would set all local file references to data/....
>
> If the file reference already contains .../data/... in its path,
> then it
> is simply truncated to data/....
>
> Same for REMOTEPATH, but here we are changing only the remote file
> references. So, for example, if you had used
>
> load =1crn
>
> and then saved the script as "myfile.spt", that script will have in
> it:
>
> load "http://rcsb.org/pdb/files/1crn.pdb";
>
> So, say now I have that file on disk and don't want to go back to the
> server for it. Then I just say:
>
> script REMOTEPATH "" "myfile.spt"
>
> This will now read 1crn.pdb from the local drive but otherwise run the
> same.
>
> Bob Hanson
>
>
Dr. Jonathan H. Gutow
Chemistry Department [email protected]
UW-Oshkosh Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/faculty_staff/gutow/
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