[phenixbb] phenix.automr questions

Randy J. Read rjr27 at cam.ac.uk
Sun Aug 29 01:58:00 PDT 2010

Dear Kay,

We were thinking that AutoMR would be the interface for people with 
(relatively) straightforward problems, and that the Phaser-MR GUI would 
allow all of the fine control available from keyword (or indeed Python 
scripting) input. Of course, it might be a good idea to add a few more 
options to AutoMR and we're open to suggestions. If you don't like GUIs, 
there isn't a command-line equivalent to Phaser-MR, but you can always use 
a shell script.

>a) is there a way to make the program try all permutations for the 
>search order of my four search molecules, or do I have to write a script ?

This can be done from Phaser-MR

>b) how can I completely switch off the search in the alternative 
>spacegroups - I am under the impression that although the "effective 
>parameters" are
>     all_plausible_sg_list = None
>     use_all_plausible_sg = False
>the search is not only done in the spacegroup I specified (#92=P41212) 
>but also in #96=P43212 . I believe so because the output says:
>  ...
>    2 alternative spacegroups
>    SpaceGroup will be determined by highest LLG in search for FIRST 
>    Search order:
>      P 43 21 2
>      P 41 21 2
>  ...
>(I would rather run a second search "manually" in the other spacegroup!)

You can also do this in Phaser-MR. We changed the default from just testing 
the space group in the MTZ to testing the enantiomorph as well (if 
applicable) first because you don't usually know in advance which 
enantiomorph you want, and second because we found that many users forgot 
to add a search for the other enantiomorph.

>c) I have two occurrences of seq_file ("all.seq" and "all.dat"; the 
>latter is symlinked to the former). Am I right that I could just leave 
>out one of them? I did this after looking at 
>http://www.phenix-online.org/documentation/automr.htm#anch70 but I 
>wonder which of the specifications of sequences and masses overrides the 
>other one? or is the first specification used for editing the search 
>models, and the second for getting the likelihood terms right?

Tom answered this in his reply.

>d) what kind of editing is done? Is phenix.sculptor run internally? I 
>find {a,b,c,d}_edited.pdb but are they actually used?

At the moment you have to run sculptor as a separate step. At some point 
this will be integrated as an optional step in AutoMR.

Best wishes,


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