Re: [Jmol-users] codebaseDirectory from CGI scripts.

2005-03-12 Thread Brian Salter-Duke 
On Thu, Mar 10, 2005 at 06:31:45PM -0500, Miguel wrote:
> Brian,
> 
> > When using jmol.js in web pages it tells you to make the
> > codebaseDirectory relative to the calling page not the web server root.
> > Fine. If you do make it relative to the web server root it gives a pop
> > up window to discourage you from doing this. Again, fine.
> >
> > However, I am constructing the web page including the  ..
> >  code in a CGI perl script, so I am in the cgi tree not the
> > htdocs tree. These trees should be kept separate. How can I avoid using
> > a path relative to the htdocs server root and avoid this popup window
> > coming up?
> 
> You should still be able to use a relative path ...
> 
> Look at the path from the perspective of a user of your http server.
> 
> Let's say that your is in your /cgi-bin directory. Then the root of your
> server is at .., and the contents of your htdocs directory is accessible
> from there.
> 
> www.example.com/cgi-bin/foo.pl
> www.example.com/brian/jmol/Jmol.js
> 
> In foo.pl you should say that the codebaseDirectory is
> 
>  ../brian/jmol
> 
> That is the relative path from the perspective of a user of your web
> server, even though it is not the relative path within your local file
> system.

After a struggle I did get this to work, but I do not know why it works.
I just followed what the error messages in the log were saying it could
not find and finished with ../../../jmol which does not make sense to me
at present but I guess I'll figure it out some time. The installation I
am working on (not my own machine) has so many links to the different
web directories that it is difficult to follow some times. The cgi
script is also writing scripts to later run in different directories and
changing the current directory in the script.
 
> 
> Separately ...
> 
> Let me know if you encounter problems when configuring this using a cgi
> directory. A few months ago someone contacted me and they had many
> problems. I don't rememeber exactly what was going on, but I have the
> impression that the java plugin was doing something strange. In that case,
> he ended up fixing the problem by using .htaccess to allow cgis to execute
> from within his htdocs tree.
> 
> I don't remember exactly what happened, but I have this feeling that I
> tried out a simple applet and saw that the codebase was messed up when the
> applet was served out of a cgi-bin directory.

I did not have to do anything special. It works fine. Essentially
htdocs, cgi-bin abd cgi-data directories are all in /var/www. The third
is where data is written in sub-directories. One application for example
does the following in the cgi script:-

Read a Z-matrix and other data to construct a Gaussian input com file.
Set up data to run Gaussian for this file.
Uses babel to translate the com file to a pdb file.
Queues the gaussian job.
Uses jmol to display the molecule on the page that reports what has been
done.
E-mails the Gaussian run to the user when it finishes.

One small concern is that each run gives many error messages in the web
error log where it is searching for stuff in org/openscience. I found a
message in the archives explaining this and suggesting they can be
ignored, but I'll have to ask the administrator to rotate the log file
to stop it getting very large.

Cheers, Brian.
 
> Miguel
> 
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-- 
Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED]  
 Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia
  Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/


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Re: [Jmol-users] No bonds drawn to metals from shelxl .res file

2005-03-12 Thread Miguel 
>>Perfect. Yes, this should be implemented. Very easy:
>>
>>SFAC C H O LI EU
>>  1 2 3 4  5
>>
>>
> with the one caveat that not all elements are encoded in shelx via that
> form of the SFAC. There is also the general form
>
> SFAC [with scattering factor curve coefficients]
>
> for this form the zeroth element of the equation would need to be
> calculated so the Z value of the element could be determined (and hence
> the element identity derived).

Rich,

Can you send me a file that has this *issue*?

I could use another 2 or 3 shelx files anyway ... we only have 1 or 2 in
the source code repository for testing.


Miguel



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Re: [Jmol-users] Re: 'set measurements ...' to update *all* labels

2005-03-12 Thread Miguel 
Chris wrote:
>>That is what we will do unless someone comes up with some good
>> objections.
>
> Excellent - have logged an RFE
> 
> to track the issue.

Thank you *very* much for filing the bug report.


Miguel



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Re: [Jmol-users] No bonds drawn to metals from shelxl .res file

2005-03-12 Thread Rich 
On 3/11/05 15:26, Bob Hanson wrote:
[EMAIL PROTECTED] wrote:
 

Perfect. Yes, this should be implemented. Very easy:
SFAC C H O LI EU
 1 2 3 4  5
 

with the one caveat that not all elements are encoded in shelx via that 
form of the SFAC. There is also the general form

SFAC [with scattering factor curve coefficients]
for this form the zeroth element of the equation would need to be 
calculated so the Z value of the element could be determined (and hence 
the element identity derived).

Rich
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