Re: [ccp4bb]: ccp4bb- Warp-Arp

[Anastassis Perrakis <perrakis@nki.nl>]

Dear Syed,

I would recommend two things:

1. Try 'Autobuilding starting from a model'. Make sure you use the 'Slow' protocol. Run at least 15(big)x10(small) == 150 total cycles.
2. Try ' Improve model ...'. Run 20-30 'small' cycles (there's no big cycle here since there's no autobuilding)

I would also suggest to try DM or ReSolve density modification to try and remove bias and then use Arp/wARp from
'Autobuilding from experimental phases'. Dm can be run just by clicking on the CCP4i ARP/wARP interface
under 'ARp/wARP flow parameters'. Resolve will do a better job I think. It will also produce a PDB file
from its own autobuilding routines. That can be used as is, but atthat resolution if its used as 'new' input
for ARP/wARP I believe that ARP/wARP might deliver an (even) better model for you to continue.

Tassos

PS A small note: I always use 1000-1500 reflections for Rfree instead of the more 'standard' 10%.
Saving on a few reflections sometimes for me simply does the trick.
<flamewar>

PS2  If I use DM first and THEN autobuilding I would be tempted to switch OFF Rfree. If you get nothing built,
Rfree was still high ... If you DO get 80-90% of the structure though, well, the Rfree must have dropped.
In a way I am saying that the 'autobuilding quality/connectivity index' is a validation of your refinement
protocole as well. Thus, in cases where autobuilding is not used and resolution is marginal I always tend
to have a try with Rfree off. of course, NEVER switch off Rfree if you dotn use autobuilding, ie 'DISCARDING' the
model evry few cycles and buildign it from free atoms again.



On Tuesday, Feb 4, 2003, at 17:33 Europe/Amsterdam, syed ibrahim wrote:

> Dear All,
>
> I am trying to solve my structure of 2.3 A resolution data using Warp- Arp program. But never I got strucutre build automatically. I used starting model of R-factor with 41% and Rfree -47%, given was 10 cycles. After program completion I end up with higher rfree value! and the model was not built. The resulting *pdb file containing dummy atoms.
>
> Please suggest me to reduce rfree value and to continue refinement.
>
> Thank you
>
> syed
>
> -------------------------------------------------------------------------------------------------------------------------
>
> B. Syed Ibrahim,
>
> Dept Of Crystallography and Biophysics, University of Madras, India
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