Re: [ccp4bb]: stuck R and arp and refmac problems

[Anastassis Perrakis <perrakis@nki.nl>]

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> Somebody suggested using arp/warp to generate a super map but the refmac
> step
> seems to get stuck with the following error
>  Refmac_4.0.6:   *** Error in GAUSSJ - called from SCALING ***
> 
> Seems to be a bulk solvent scaling error, but I don't know how to fix it.
> 

This usually means that no atoms were read in refmac.
If you look a few lines up you will see that 0 atoms were read in. 
That, in turn, means that 'reshuffle' which prepares you input
pdb file for warpNtrace produced an error (look at
logs/1st_reshuffle.log).
My guess for that is that you PDB had no proper CRYST/SCALE cards.

> One more question, the molrep option in arp/warp requires a .brk file and
> a protin output file. How could these be generated?

...brk is a normal pdb file (from pdb at BRooKhaven days).
(?? for warpNtrace from a model you also needed a .brk file ...!)
As for protin, it is INput that is needed.
A bit of RTFM or look at the example file distributed 
with arp/warp can help.



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