phenix.automr questions
Dear developers, I have four questions concerning phenix.automr (I'm using version 1.6.4): 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 ? 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 ensemble Search order: P 43 21 2 P 41 21 2 ... (I would rather run a second search "manually" in the other spacegroup!) 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? 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? thank you, Kay P.S. I run with "phenix.automr mr.eff" where mr.eff is automr { data = "m879_2_rg92.mtz" seq_file = all.dat ensemble { ensembleID = "mol1" copies_to_find = 1 coords = a.pdb identity = 80 } ensemble { ensembleID = "mol2" copies_to_find = 1 coords = b.pdb identity = 45 } ensemble { ensembleID = "mol3" copies_to_find = 1 coords = c.pdb identity = 45 } ensemble { ensembleID = "mol4" copies_to_find = 1 coords = d.pdb identity = 45 } component { component_type = *protein nucleic_acid seq_file = all.seq component_copies = 1 } autobuild_variables{ n_cycle_rebuild_max = 1 } }
Hi Kay, I'll answer what I can; perhaps Randy the others may have more comments.
Dear developers,
I have four questions concerning phenix.automr (I'm using version 1.6.4):
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 ?
It would be a good idea for me to put that in. For now, yes, you have to make a script to do that.
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 ensemble Search order: P 43 21 2 P 41 21 2 ... (I would rather run a second search "manually" in the other spacegroup!)
Yes, it runs the inverse hand even if you say "use_all_plausible_sg=False". However it should not run all the other space groups (all_plausible_sg_list : ['P 4 2 2', 'P 4 21 2', 'P 41 2 2', 'P 41 21 2', 'P 42 2 2', 'P 42 21 2', 'P 43 2 2', 'P 43 21 2']). I'll see if we can put in a flag so it doesn't run the inverse hand if you don't want it to.
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?
Looking at your parameters file, I see what you mean. If you supply two different files, then yes, the one you specified at the top of your file with "seq_file=all.dat" is going to be used for editing the file for autobuild, and the one you specified in the scope "component" is going to be used for getting the likelihood terms right. Normally (always?) these should be the same. So normally, just supply the first one "input_seq_file=seq.dat") and it will be used for both purposes. Or if you have several components, only specify them in the "component" scopes, and all of them will be put together into a single file and used as the input to autobuild.
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?
Only basic editing to make the model compatible with autobuild is done. No sculpting is done inside automr for now. All the best, Tom T
thank you,
Kay
P.S. I run with "phenix.automr mr.eff" where mr.eff is automr { data = "m879_2_rg92.mtz" seq_file = all.dat ensemble { ensembleID = "mol1" copies_to_find = 1 coords = a.pdb identity = 80 } ensemble { ensembleID = "mol2" copies_to_find = 1 coords = b.pdb identity = 45 } ensemble { ensembleID = "mol3" copies_to_find = 1 coords = c.pdb identity = 45 } ensemble { ensembleID = "mol4" copies_to_find = 1 coords = d.pdb identity = 45 } component { component_type = *protein nucleic_acid seq_file = all.seq component_copies = 1 } autobuild_variables{ n_cycle_rebuild_max = 1 } }
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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 ensemble 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, Randy
On Sun, Aug 29, 2010 at 1:58 AM, Randy J. Read
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.
Actually, there *is* a command-line equivalent to Phaser-MR, but it is undocumented because I didn't think anyone would use it. And as I just found out, it is somewhat difficult to figure out how to use. But if anyone is interested, the attached parameter file shows how to configure it - it was necessary to do this to get the GUI working but I also find this syntax easier to use than the old keyword input. So if you run this: phenix.phaser params.eff it will use the Phenix-style configuration file, but if you just run "phenix.phaser" with no arguments (or a shell redirect from a file), it will use the CCP4-style keyword input. -Nat
participants (4)
-
Kay Diederichs -
Nathaniel Echols -
Randy J. Read -
Thomas C. Terwilliger