You can do it in phenix.refine. The prototype is:
for trial in trials:
phenix.refine model.pdb data.mtz main.random_seed=random_value
modify_start_model.adp.shake=true output.prefix=str(random_value)
where each refinement will start with the original B-factors that are
shaken by a certain value.
Pavel.
PS> You can use phenix.pdbtools to do any manipulations on your model,
such as shaking, setting, shifting of coordinates, b-factors,
occupancies, etc.
On 12/3/09 4:05 AM, MARTYN SYMMONS wrote:
Discussing with Fred Vellieux offlist I suggested the following: would
it be useful to have a sort of 'simulated annealing' of the B-factor
values? - in refinement I often try resetting them to higher values
(Moleman has a function for this I think) and then see which ones
refine back down nicely - but it would be good to have some sort of
randomization method - that would be a test of how much the values are
inherited from the modelling early on - say from the MR probe model
for example.
We could do multiple B-factor refinements with different starting
kicks to the values and look for the best final Rfree or some measure
of map quality?
Martyn
Martyn F. Symmons
Cambridge
'Chan fhiosrach mur feòraich.' Gaelic proverb - Nothing asked, nothing
learned.
------------------------------------------------------------------------
*From:* Pavel Afonine <pafon...@lbl.gov>
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Wednesday, 2 December, 2009 22:52:45
*Subject:* Re: [ccp4bb] Refining residues as rigid bodies
Hi,
you can do similar thing (that is resulting in similar outcome) in
phenix.refine by increasing the weight on ADP restraints term.
Example: increase "wu" or decrease "wxu_scale". Although I believe a
regular refinement of individual isotropic ADPs should normally work
just fine at 3A resolution in phenix.refine.
Pavel.
On 12/1/09 11:18 PM, Frederic VELLIEUX wrote:
If the problem is B-factor refinement, you can do that easily at low resolution
with CNS. You just give tight restraints.
You modify the file bindividual.inp
This section:
{* target sigma values for restrained B-factor refinement *}
{* mainchain bonds *}
{===>} bsig_main=1.5;
{* mainchain angles *}
{===>} asig_main=2.0;
{* sidechain bonds *}
{===>} bsig_side=2.0;
{* sidechain angles *}
{===>} asig_side=2.5;
I cannot remember in which direction the values have to go. I think up. I have
done this with a very low resolution structures (4.5 A?) a few years ago, you
get smoothly varying B values, very tightly restrained. I do not think we
published that structure, we obtained a higher resolution structure later (I
don't think the referees would have been very happy seeing B factor refinement
at low resolution). But it worked.
Fred.
Message du 01/12/09 23:51
De : "Jason C Porta"
A : CCP4BB@JISCMAIL.AC.UK
Copie à :
Objet : Re: [ccp4bb] Refining residues as rigid bodies
Basically my reasoning for doing this is a low data-to-parameter ratio, which
makes B-factor refinement unfeasible. So far I have had nice results with
breaking the complex into rigid subdomains. So i was basically just thinking of
a way I could refine the structure best, without using too many parameters.
I see now how this can be done in Phenix. I will give it a try.
Thanks for all of your suggestions!
