[sharp-discuss] error of SHARP-ARP/wARP

[Clemens Vonrhein]

Dear Cholien,

your sequence file looks fine to me - 2 molecules in there. I can't
see anything wrong with this. Things you might want to check:

  1. does the wARP_XX.Ypc/seq.pir file look the same as the original
     file? This is the file finally used by ARP/wARP (you should have
     a link from the wARP_XX.Ypc.log.html file).

  2. what version of ARP/wARP are you running?

  3. maybe the ':' or '_' character at the top confuses side_trace:
     try simplifying the file, e.g. using

>AmiF

     as first line (but this would be weird ...)

  4. it is possible, that my hacks for older versions of ARP/wARP (to
     be able to dock even when NCS is present) aren't working. I
     recommend trying the latest ARP/wARP 6.1.1 in stand-alone mode
     (i.e. not through the SHARP/autoSHARP interface). You can use the
     generated warp.par from the SHARP/autoSHARP interface as a guide
     on how to fill in the official ARP/wARP interface (i.e. the CCP4i
     task).

     These hacks always worked fine for me (but who knows?). Are you
     sure you have 2 molecules in the asymmetric unit? What does the
     Matthews parameter analysis show? Have you specified the correct
     number of residues in the interface (i.e. the number of residues
     in the asymmetric unit ... _NOT_ the number of residues in the
     monomer): 334

Hope that helps.

Cheers

Clemens

On Thu, Nov 11, 2004 at 02:25:22PM +0800, ???? wrote:
> Dear Sir,
> 
> I used autoSHARP, the ARP/wARP program is terminated finally. The error show: ERROR : program terminated in SIDE_TRACE (see side_trace.log), the log file show: ***** ERROR *****
> PIR file second line must be blank ! 
> The additional file is PIR file, please check , I have no idea where/what is wrong?
> 
> 
> Thanks in advanced. 
> 
> cholien
> 
> 

> [-- octet-filter file type: "ASCII text" --]
> 
> >HP1238:_AmiF
> 
> MGSIGSMGKPIEGFLVAAIQFPVPIVNSRKDIDHNIESIIRTLHATKAGYPGVELIIFPE
> YSTQGLNTAKWLSEEFLLDVPGKETELYAKACKEAKVYGVFSIMERNPDSNKNPYNTAII
> IDPQGEIILKYRKLFPWNPIEPWYPGDLGMPVCEGPGGSKLAVCICHDGMIPELAREAAY
> KGCNVYIRISGYSTQVNDQWILTNRSNAWHNLMYTVSVNLAGYDNVFYYFGEGQICNFDG
> TTLVQGHRNPWEIVTGEIYPKMADNARLSWGLENNIYNLGHRGYVAKPGGEHDAGLTYIK
> DLAAGKYKLPWEDHMKIKDGSIYGYPTTGGRFGKMGSIGSMGKPIEGFLVAAIQFPVPIV
> NSRKDIDHNIESIIRTLHATKAGYPGVELIIFPEYSTQGLNTAKWLSEEFLLDVPGKETE
> LYAKACKEAKVYGVFSIMERNPDSNKNPYNTAIIIDPQGEIILKYRKLFPWNPIEPWYPG
> DLGMPVCEGPGGSKLAVCICHDGMIPELAREAAYKGCNVYIRISGYSTQVNDQWILTNRS
> NAWHNLMYTVSVNLAGYDNVFYYFGEGQICNFDGTTLVQGHRNPWEIVTGEIYPKMADNA
> RLSWGLENNIYNLGHRGYVAKPGGEHDAGLTYIKDLAAGKYKLPWEDHMKIKDGSIYGYP
> TTGGRFGK*

-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
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