Re: [ccp4bb] Phaser MR pairwise percent packing criterion

[Randy Read]

Hi,

The old approach of counting the number of clashes was changed to the 
percentage of trace atoms (typically CA atoms) involved in clashes largely 
because, as people like Eleanor pointed out to us, the number of clashes grows 
with the size of the problem and solutions can be rejected when the fraction of 
the structure involved in clashes is still very small.  The default now is to 
accept up to 10% of the trace atoms being involved in clashes.  So increasing 
that to a larger number should have the same basic effect as increasing the 
number of allowed clashes did in the old version.

If you want to get sophisticated, there's even another new feature, where you 
can use the ENSEMBLE…TRACE command to define a TRACE molecule.  That will be 
carried along with the actual search model and used to check for clashes.  This 
might be useful if, for instance, you think a domain might change  conformation 
slightly so you don't want it in the search model, but you want to exclude 
solutions that would create clashes with that domain.

Best wishes,

Randy Read

> On 17 Feb 2017, at 08:28, Xiao Lei  wrote:
> 
> Dear CCP4bb members,
> 
> I found in the newer CCP4 Phaser MR version (I use CCP4 7.0.0 in Win7), there 
> is no "allow maximal clash..." option anymore. There are only two options 
> "pairwise percent packing" and "accept all solutions".  I used to increase 
> the number in the "allow maximal clash" (let's say from 100 to 200) to do MR 
> and this works fine in a couple of cases.
> 
> With the new Phaser version, I could not do this anymore, can I understand 
> that I just need to increase the pairwise percent packing cutoff (let's say 
> from 5% to 10%) to loose the tight packing criteria and allow more clashes in 
> finding solutions? 
> 
> 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

[ccp4bb] Phaser MR pairwise percent packing criterion

[Xiao Lei]

Dear CCP4bb members,

I found in the newer CCP4 Phaser MR version (I use CCP4 7.0.0 in Win7),
there is no "allow maximal clash..." option anymore. There are only two
options "pairwise percent packing" and "accept all solutions".  I used to
increase the number in the "allow maximal clash" (let's say from 100 to
200) to do MR and this works fine in a couple of cases.

With the new Phaser version, I could not do this anymore, can I understand
that I just need to increase the pairwise percent packing cutoff (let's say
from 5% to 10%) to loose the tight packing criteria and allow more clashes
in finding solutions?