Hi Alex,
if you want Phaser to select the best of a set of alternative models,
you need to use the "Add ensemble" button below the one you found,
define all six models (they do not have to be superimposed), and then
turn on "Allow search with alternative ensembles for a single component
of ASU" in "Additional search parameters", and specify all ensembles you
defined in the search window. Phaser will automatically search with each
model, and select the best based on the LLG-score.
Although it is not relevant to your problem, you can use Ensembler
(available through the "Model generation" submenu of "Molecular
replacement") to create a set of superposed models. Ensembler has an
iterative procedure to automatically weight up structurally conserved
regions in your models, which often improves model quality compared to
an unweighted superposition.
BW, Gabor
On 2016-04-22 08:06, Alex Lee wrote:
> Hi All,
>
> I am using Phaser MR to solve structure with a single protein chain
> (around 70 amino acid length). There are 6 homolog candidate models
> with sequence identity from 90% to 70%. I could run 6 jobs separately
> with each model as an ensemble to see which model gives best solution.
> But I am thinking is there a more convenient approach to put the 6
> candidate models in one job and let Phaser MR compare which one gives
> the best solution?
>
> After I did some Internet search, I do not know if this is called "add
> superimposed pdb file to the ensemble" in Phaser MR GUI (in CCP4),
> where I just add the six conadidate models (PDBs) before starting run.
> I also notice a program called Superpose in CCP4, I do not know if I
> need this program to superimpose my 6 models first and then add the
> superimposed pdb (in this case I guess it's the final one pdb output
> after superimposed 6 models) in to Phaser MR before starting run?
>
> Thanks in advance.
--
##################################################
Dr Gabor Bunkoczi
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
Addenbrooke's Hospital
Hills Road
Cambridge CB2 0XY
##################################################
|