Re: [ccp4bb]: arp/warp in ccp4i

[Huiying Li <hli@bragg.bio.uci.edu>]

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Thanks for all the suggestions. Indeed there was an error "bad system
call" in the arp-warp log file, arp-warp quitted first leaving an empty
arp_0.pdb, which confused refmac. We found, as Petrus Hendrik Zwart
pointed out, that the program could not run at all on an Alpha machine
under OSF v4.0, but it ran smoothly on an SGI or another Alpha under OSF
V5.0. I don't know if authors of program were aware of this problem.

The test run on the data set I mentioned was a success. After 15 cycles of
autobuilding with fast mode, 95% of residues of a small 12kDa protein were
built with connectivity index 0.97. I did not provide the sequence for
docking during the arp-warp run, but ran guiSIDE afterward. There are two
molecules per ASU, autobuilding assembled all the residues into 3
chains(A,B,C). However, guiSIDE could fix the sidechains for only one
molecule at a time. I tested two running modes, residue number or chain
ID, but could not get both molecules docked in simultaneously. Am I
missing something here to get it work?

Thanks in advance,

Huiying

On Fri, 2 Aug 2002, Anastassis Perrakis wrote:

> 
> 
> Garib N Murshudov wrote:
> 
> > ***  For details on how to be removed from this list visit the  ***
> > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >
> > It usually means either there is no atom in the input file or all atom names
> > are so tht they can not be converted to element names.
> >
> 
> Indeed. That occurs usually because of an earlier failure to the building stage
> of arp/warp.
> arp_0.pdb HAS to have atoms - namely free atoms from the building stage.
> 
> If you look carefully in the log file, I think there is an error message BEFORE
> the one
> from refmac. The program should had stopped then but it goes on due to a bug.
> You should try to correct the earlier error or mail me if you can not figure it
> out yourself.
> 
>     Tassos
> 
> >
> > Regards
> > Garib
> >
> > On Wednesday 31 Jul 2002 12:06 am, Huiying Li wrote:
> > > ***  For details on how to be removed from this list visit the  ***
> > > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> > >
> > >
> > > I got the following error while testing the new version of apr/warp
> > > using all the default setting under CCP4i:
> > >
> > >  Input file :arp_0.pdb
> > >   ERROR: reading title of input file
> > > ===> Error: No Scatterers
> > >  Refmac_5.1.24:  No Scatterers
> > >
> > > My input MTZ is a SHARP/Solomon refined phase set at 1.75A. Running mode
> > > "automated model building starting from experimental phases" was
> > > chosen. The arp_0.pdb file is empty since I wanted to test auto-building
> > > from scratch. I don't know why REFMAC seems to expect some coordinates
> > > from it. The same set of data had been successfully used for automated
> > > model building with older version of arp/warp interfaced with old REFMAC.
> > >
> > > Any help would be appreciated.
> > >
> > > Huiying
> > > --------------------------------------------------
> > > Huiying Li, Ph. D
> > > Department of Molecular Biology and Biochemistry
> > > University of California at Irvine
> > > Irvine, CA 92697, USA
> > > Tel: 949-824-4322(or -1797);  Fax: 949-824-3280
> > > email: hli@bragg.bio.uci.edu
> > > --------------------------------------------------
> >
> > --
> > Garib N. Murshudov, Chemistr Department, University of York
> > Tel: (01904) 328252
> 
> --
> NKI, Department of Molecular Carcinogenesis
> Plesmanlaan 121 1066 CX Amsterdam NL
> Phone +31-20-512-1951 Fax +31-20-512-1954
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> 
>