[sharp-discuss] SHARP CCP4 arp_waters ??

[Clemens Vonrhein]

Dear Doug,

On Tue, May 06, 2008 at 08:06:52AM -0400, Doug Bailey wrote:
> Hello Everyone,
> 
> We have a SHARP job that terminates with the following error that 
> seems to be related to arp_waters

Not quite: this is related to ARP/wARP (i.e. the separate software
from EMBL-HH/NKI). arp_waters is just a water-updating code in CCP4
(and as far as I can tell it will be withdrawn in one of the enxt
releases).

> 
> "Too many sections - increase dimensions in S/R ARPDN2"
> 
> SHARP 2.2.0 /SUSHI Version 3.4.0
> 
> CCP4 5.x and 6.0.2
> 
> If we take the results from SHARP at the point of failure and run 
> from CCP4i the job seems to finish properly. I understand this may 
> not be a valid comparison since we may be setting up the job 
> differently in CCP4i then the original job as run from SHARP.
> 
> Does arp_waters.f need to be modified and rebuilt ?

No.

If you can run ARP/wARP outside of SHARP/autoSHARP (i.e. through the
normal CCP4i interface) I would stick with that. Make sure to use the
right columns from the eden_flat_XY.Zpc.mtz file though! And maybe
there is a way in the CCP4i interface to tell ARP/wARP about possible
heavy atoms present in your structure (e.g. if you did a Fe SAD
phasing, if it is a Se-MET or something similar). I would also make
use of the SHARP HLA-D during the REFMAC refinement step (as phase
restraint). All that is done automatically in our interface to
ARP/wARP 6.X though.

Important: SHARP/autoSHARP will currently not work with the latest
ARP/wARP 7.0.X release! We're trying to get this organised though. So
in the meantime I would recommend keeping an installation of ARP/wARP
6.X around (for use in SHARP/autoSHARP) and otherwise running version
7.0.X through the official interface.

Hope that helps ...

Cheers

Clemens

> 
> 
> Any help would be appreciated.
> 
> 
> Thanks,
> Doug
> 
> 
> 
> 
> Douglas Bailey                  Ph: 301-846-5328
> NCI-Frederick                           Fax: 
> 301-846-6322
> 1050 Boyles Street                  E-mail: baileyd at ncifcrf.gov
> Frederick, Maryland 21702
> 
> 
> 
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