[sharp-discuss] - peak list from residual map

[Venkataraman Kabaleeswaran]

Dear Clemens,
 
Yes, I viewed the residual map using O without any problem. 
But  I could not view it through SHARP because it  was searching for the 
menu, startup files for O  in the wrong dir. "/usr/local/O/data/menu.odb" 
instead of right dir "/usr/pgm/08.0/menu.odb."

I am using the perl5 (revision 5.0 version 6 subversion 0) version.

Yes I changed the rms limits for peak picking.

After the crash ../tmp/XXXX.dir  is survived with following files  
peaks.log, peaks.pdb,  RESID.1.map, peaks.out.  
Peaks.log file has full list of peaks end up with normal termination.

I ran checkBDG.sh script  , it gave one warning as 

" NOTE    003 : your Perl version is 5.6.0 - is this the latest
               stable from www.cpan.org?


 WARNING 001 : I'm not quite sure - but it doesn't look like your httpd is
               running! You can start it using the 'restart_server' command

               Continue [y]/n ? y

 -----------------------------------------------------------------------------
-
 SUMMARY     : a total of 1 warnings were given"


thanks

venkataraman



On Tuesday 12 March 2002 11:54 am, you wrote:
> Dear venkataraman,
>
> according to your log file (which is $BDG_home/sushi/logs/error_log
>
> btw) it seems that the file down't exist:
> > Unable to determine CCP4 version from file /tmp/6961.dir/peaks.log
> > (No such file or directory)
>
> I'm not quite sure why this could happen. But some hints:
>
>   - can you actually view this residual map (using e.g. O)?
>
>   - what Perl version are you running (see BDG_perl variable in
>     $BDG_home/machines/*/host.setup)? See notes in the installation
>     manual ..
>
>   - have you changed the RMS limits for the peak picking? The defaults
>     usually work fine ...
>
>   - just after it crashes: is the /tmp/XXXX.dir still there? What's in
>     it? What does the peaks.log file (if present) contain?
>
> You can always run the checkBDG.sh script (from
> http://www.globalphasing.com/sharp/installation/index.html#trouble).
>
> Hope that helps.
>
> Cheers
>
> Clemens
>
> PS: it runs without problems on our various RedHat 7.x machines - so I
> don't think it is related to that.
>
> On Tue, Mar 12, 2002 at 10:25:07AM -0500, Venkataraman Kabaleeswaran wrote:
> > I got the following error messages when I tried to pick peaks on a
> > residual map in autosharp. (sharp 3.0.2 &  ccp4 4.1.1 in redhat 7.2). The
> > peak.log file was created in the tmp directory by CCP4, but it didnot
> > display on the Sharp windows, this worked properly in sharp (2.0).
> >
> > any suggestions
> >
> > thanks
> > venkataraman
> >