[sharp-discuss] Re: SHARP user with getax error

[Clemens Vonrhein]

Dear all,

there are a few issues with this part (NCS-detection with GETAX) that
I'm looking into. Unfortunatley they show up only under various
(random?) conditions.

Anyway, if the DM step (automasking) crashes: just run this one by
hand. The log file (with the error message) should contain all the
keywords you need to use (search for 'Data line' near the top). Just
add the SIZE keyword (see DM doc).

Also to clarify: if you have heavy atom sites and you assume they
follow the NCS (e.g. Se-MET or sulphur phasing) it might be better to
use programs that work from these (e.g. PROFESSS in CCp4 ... but there
are others). GETAX will work in cases where

 - there are no NCS-related heavy atom sites (most experiments apart
   from Se-MET and S-Cys/Met)

 - you have a Cn or Dn symmetry (i.e. a closed, proper local symmetry)

See

  Vonrhein C, Schulz GE. Locating proper non-crystallographic symmetry
  in low-resolution electron-density maps with the program GETAX.
  Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):225-9.

or something more recent:

  Pai R, Sacchettini J, Ioerger T. Identifying non-crystallographic
  symmetry in protein electron-density maps: a feature-based approach.
  Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1012-21.

Cheers

Clemens


On Wed, Sep 27, 2006 at 03:07:50PM -0300, Alejandro Buschiazzo wrote:
> artis at chemistry.montana.edu escribió:
> >Hello Alejandro,
> >I had posted an error about getax yesterday and while looking up the
> >archives I saw you had a somewhat similar experience and so decided to
> >write a direct note to you.
> >Did you get getax to work from within SHARP. Did you use CCP4 5.0 for this.
> >I have CCP4 6.0.1 and am thinking of configuring SHARP to version 5.0.
> >What is the patch that you talk about in your mail.
> >I shall be grateful for any help on this.
> >Thank you.
> >Sincerely
> >Arti Pandey
> >Chemistry and Biochemistry
> >Montana State University
> >Bozeman, MT USA 59717
> >
> >
> >  
> Hi Arti,
> 
> indeed I had that problem......unfortunately I was never able to solve 
> it from within SHARP (i.e. ended up doing more or less the same type of 
> work with the individual CCP4 programs)
> 
> At that time I was using CCP4 5.0; now I'm using CCP4 6.0.1, and it 
> doesn't work either. Misteriously enough, Claus Flensburg said that e.g. 
> the tutorial with the IF3-C.1 data worked just fine...which is 
> definitely not the case for me.
> 
> The error  (after adding that missing ';' at the end of line 303 on the 
> getax.pl perl script  in /whereverSHARP//bin/sharp/) is still the same: 
> as reported in STDERR
> 
> >CAD:   Fatal Error
> >Error in script /Applications/Crystallography/Sharp/bin/sharp/getax.pl 
> - File "getax_50.0pc/g_dm_34.3_14.3_180-1.2.mtz1" not found or not 
> readable at >/Applications/Crystallography/Sharp/lib/libhtml.pl line 1482
> 
> and indeed, that mtz is never written, because CAD crashes
> 
> Last, that patch that was mentioned on those mails refers to a possible 
> problem with the cmtzlib_f library, that could've been the reason 
> affecting column assignment in CAD (as suggested on the ccp4 Problems 
> page for v5.0.2); but that didn't (nor doesn't) improve this particular 
> problem.
> 
> Sorry for not being helpful...
> 
> 
> -- 
> Alejandro Buschiazzo, PhD
> Research Scientist
> Laboratory of Structural Biology
> Pasteur Institute of Montevideo
> Mataojo 2020
> Montevideo 11400
> URUGUAY
> 
> Phone: +5982 5258049 int. 126
> Fax:   +5982 5252813 int. 111
> 
> 
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/sharp-discuss
> 

-- 

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