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Dear Alex, in case you have other things to do and can wait for a few hours: just upload your mtz and paste your sequence into Balbes (one of the programs found at http://www.ccp4.ac.uk/ccp4online). Click 'check full space group' and 'run arp/warp' as needed. all the best, Stefan *Stefan T Arold, PhD* *Associate Professor* *Division of Biological and Environmental Sciences and Engineering* *Computational Bioscience Research Center (CBRC) King Abdullah University of Science and Technology (KAUST)* *Thuwal 23955-6900 Bldg 2, Level 4, Room 4275 Kingdom of Saudi Arabia* *Office: +966 (0)12 808 2557* *Mobile: +966 (0)5 4470 0432* *Em: **[log in to unmask]* <[log in to unmask]> On 23 April 2016 at 00:52, Alex Lee <[log in to unmask]> wrote: > Hi All, > > I really appreciate all of your suggestions! For my simple case, "allow > search with alternative ensembles for a single component of ASU" in Phaser > would work. For more difficult case, I have learned to generate > superimposed ensembles following your suggestions about using Ensembler or > MrBUMP. > > > > > > On Fri, Apr 22, 2016 at 2:30 AM, Gabor Bunkoczi <[log in to unmask]> wrote: > >> 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 >> ################################################## >> > >