[phenixbb] LABIN labels for Autosol/resolve NCS scores
schmitzberger at crystal.harvard.edu
Thu Sep 16 10:59:10 PDT 2010
Thank you very much for the prompt reply!
I think I understand. One more question, still being somewhat
unfamiliar with the Phenix GUI/command line concept; can I actually
specify the correct_aniso=True keyword within the GUI or do I have to
do that via an .eff file or via the command line. If the first
applies, where do I specify this in the GUI ("Refine eff file list" ?)
Would you also recommend to explicitly specify a range and ratio for
the anisotropy correction, such as "delta_b_for_auto_correct_aniso=20"
or let Phenix take care of that?
I am putting in heavy atom sites from ShelxD, so use Autosol primarily
for phasing and density modification right now; so I think including
slightly more noisy data should not make as big a difference.
On Sep 16, 2010, at 11:57 AM, Tom Terwilliger wrote:
> Dear Florian,
> Normally I would recommend letting AutoSol deal with the anisotropy
> of your data, as it already has the capability of anisotropy
> correction. It is usually best to keep your "data" uncorrected, so
> that the "data" are not changing as you develop new interpretations
> of them. You can control the application of anisotropy corrections
> in AutoSol as you noticed with correct_aniso=True. AutoSol will
> apply an anisotropy correction during structure solution and map
> generation, and will keep your uncorrected data for refinement (an
> anisotropy term is automatically applied as a parameter in
> refinement as well).
> There is a possible advantage to using the UCLA anisotropy server in
> that it throws away data that is weak, and it is possible that in
> some cases that weak data could interfere with structure solution.
> If you do use anisotropy-corrected data for AutoSol I would
> 1. Specify a "refinement file" explicitly, and supply a file that is
> not anisotropy-corrected (i.e., your original data).
> 2. Specify "correct_aniso=False" for AutoSol (it would probably do
> that anyway as your corrected-data would have no anisotropy left).
> AutoSol would not normally use FP or SIGFP from the data file, only F
> +SIGF+ F-SIGF-; however if you are supplying a "refinement file"
> then this file would need F and SIGFP (and you would would want to
> use uncorrected data there)
> The NCS overlap is not an absolute scale, so greater than one is
> ok. The NCS correlation goes from -1 to 1, and 0.5 is ok, but not
> that great.
> You can supply AutoBuild with a sharpened map with
> map_file=Mymap_coeffs.mtz and it will use this map in the first
> cycle of building (you might only run one cycle in this case). At
> 4.1 A, I would only use the helices_strands_only option in AutoBuild
> however, as model building at this resolution, particularly with a
> relatively difficult map, will not work well.
> I hope that helps!
> All the best,
> Tom T
> On Sep 16, 2010, at 8:23 AM, Florian Schmitzberger wrote:
>> Dear All,
>> I would have a number of Phenix related questions:
>> Firstly, I used the anisotropy server ( to anisotropically truncate
>> my mtz file with anomalous signal (SAD data). My question is if the
>> labels (for F+/F- and SIGF+/SIGF- are correctly recognized by
>> Phenix (Autosol).
>> The columns labels are: F_ref for FP; QSIGF_ref for SIGFP; GF(+)pk
>> for F(+); LSIGF(+)pk for SIGF(+), GF(-)pk for F(-); LSIGF(-)pk for
>> It seems QSIGF and GF(+)pk/LSIGF(+)pk etc. are , but I am uncertain
>> if it recognizes F_ref, because for the LABIN INPUT LABELS it says
>> "NONE" for"F".
>> Phenix does not seem to detect the anistropy ("Not using aniso-
>> corrected data files as the range of aniso b is only 19.52 and
>> 'correct_aniso' is not set); so I suppose I should use the
>> correct_aniso=True keyword.
>> Secondly, what are good values for the evaluation of the NCS mask
>> and NCS averaging Resolve is using in Phenix; NCS overlap values
>> (e.g. in my case 1.1) and NCS_CORR (in my case 0.52) in the
>> "resolve.scores" file. Does an NCS overlap value of greater than 1
>> make sense?
>> I am working with a (anisotropic) dataset with 4.1/4.5 A
>> resolution, 78 % solvent content, 2-fold NCS; Perhaps a naive
>> question: It is not possible to use B-factor sharpened maps for
>> autobuilding with Phenix Autobuild is it?
>> Thank you for any comments!
>> Florian Schmitzberger
>> Biological Chemistry and Molecular Pharmacology
>> Harvard Medical School
>> 250 Longwood Avenue, SGM 130
>> Boston, MA 02115, US
>> Tel: 001 617 432 5602
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
> Tel: 505-667-0072 email: terwilliger at LANL.gov
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Biological Chemistry and Molecular Pharmacology
Harvard Medical School
250 Longwood Avenue, SGM 130
Boston, MA 02115, US
Tel: 001 617 432 5602
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