[phenixbb] LABIN labels for Autosol/resolve NCS scores
Tom Terwilliger
terwilliger at lanl.gov
Thu Sep 16 11:23:05 PDT 2010
Hi Florian,
>
> 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" ?)
You can specify "correct_aniso=True" (or False) either via a parameters (.eff) file or via the command line or in the GUI.
In a parameters file, it would look like:
autosol {
scaling {
correct_aniso = true
}
}
on the command line, it would be one more keyword as:
correct_aniso=true
In the GUI you would click on "All parameters" and then "Advanced" and then "Scaling" and then you'll find "Apply anisotropy correction" with the default of "Auto" (which in this case means apply it if there is serious anisotropy).
>
> 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'd let Phenix take care of it usually, these parameters are set to apply it to significant anisotropy only. Note that sometimes it is worth trying both with and without the correction, however.
>
> 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.
Yes, not having to find the sites may make autosol a little less sensitive to the f' and f" values.
All the best,
Tom T
>
> Best regards,
>
> Florian
>
>
>
> 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 recommend:
>>
>> 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 SIGF(-).
>>>
>>> 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!
>>>
>>> Regards,
>>>
>>> Florian
>>> -----------------------------------------------------------
>>> 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
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>> Thomas C. Terwilliger
>> Mail Stop M888
>> Los Alamos National Laboratory
>> Los Alamos, NM 87545
>>
>> Tel: 505-667-0072 email: terwilliger at LANL.gov
>> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
>> PHENIX web site: http:www.phenix-online.org
>> ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
>> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
>> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
>>
>>
>>
>>
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>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
> -----------------------------------------------------------
> Florian Schmitzberger
> Biological Chemistry and Molecular Pharmacology
> Harvard Medical School
> 250 Longwood Avenue, SGM 130
> Boston, MA 02115, US
> Tel: 001 617 432 5602
>
>
>
>
>
>
>
>
>
>
Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: terwilliger at LANL.gov
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
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