[sharp-discuss] Problem with NCS detection

[Claus Flensburg]

Hi Alejandro,

On Sat, Mar 04, 2006 at 10:53:27AM +0100, Alejandro Buschiazzo wrote:
> On 04/03/2006, Claus Flensburg <claus at globalphasing.com> wrote:
> > Hi James,
> > 
> > On Fri, Mar 03, 2006 at 02:37:32PM -0500, James M. Vergis wrote:
> > > I am having a problem with the NCS detection using SHARP.  When I press
> > > "START" in the Phase Improvement and Interpretation Control Planel, the log
> > > file created for NCS detection is blank and I get the following error
> > > reported in the STDERR file:
> > > 
> > > Scalar found where operator expected at
> > > /srv/local/programs/sharp/2.2.0/bin/sharp/getax.pl line 233, near "$section"
> > > 	(Missing semicolon on previous line?)
> > > syntax error at /srv/local/programs/sharp/2.2.0/bin/sharp/getax.pl line 233,
> > > near "$section"
> > > Execution of /srv/local/programs/sharp/2.2.0/bin/sharp/getax.pl aborted due
> > > to compilation errors.
> > > 
> > > At 1st glance I don't see any problem with that perl script but I may be
> > > missing something.
> > > Any help would be appreciated.  Thanks,
> > 
> > add a semicolon at line 303 of /srv/local/programs/sharp/2.2.0/bin/sharp/getax.pl
> > to read:
> > 
> > print "</td></tr>\n";
> > 
> > See also: https://www.globalphasing.com/pipermail/sharp-discuss/2006-February/001724.html
> > 
> > Regards,
> > 
> > ClAuS
> > 
> > _______________________________________________
> > sharp-discuss mailing list
> > sharp-discuss at globalphasing.com
> > http://www.globalphasing.com/mailman/listinfo/sharp-discuss
> 
> Hi, since I was the user involved in that February discussion, I just wanted to add  that although that semicolon did indeed fix the perl script, unfortunately the subsequent obstacle was DM getting confused with the column labels ... (when performing the second, I believe automask, job)

would you send the error message with information about the job to
sharp-develop at globalphasing.com

> 
> even after applying the suggested patch to the ccp4-5.0.2 cmtzlib_f library, I couldn't get this getax task to work properly inside SHARP (does work if I do it outside)
> ...so, I gave up, but I'll surely appreciate knowing if this works for you

not sure what patch you've applied.

I've just run the following test:

(fresh install of SHARP2.2.0;apply the attached patch to fixup getax.pl;set preference 'User level' to Expert)

1) start SHARP using IF3-C.1
2) goto the 'Phase improvement panel'
3) run one 'Density Modification' (Solvent-flattening) job
4) one finished return to the Phase improvement panel and run
   the NCS-detection using the solo_50.0pc results

This job did finish. I'm using CCP4 version 5.0.2 patched
with the patchset of Clemens available from:
https://www.globalphasing.com/people/vonrhein/ccp4/index.html
(In this case: ccp4-5.0.2-cv11).

Could you try running the same test? Thanks.

With best wishes,

ClAuS
-------------- next part --------------
--- getax.pl~	2005-11-08 12:13:28.000000000 +0100
+++ getax.pl	2006-03-04 11:48:30.000000000 +0100
@@ -300,7 +300,7 @@
 	$NCSdetect{nmono} = 1;
     }
 }
-print "</td></tr>\n"
+print "</td></tr>\n";
 #
 $section++;
 if ( ! -e "selfrot.lis" ) {