[phenixbb] regarding ncs distance

[sbiswas2 at ncsu.edu]

Hi Pavel,

Whenever I run ncs using the default parameters I get the following:
  The current limit is:
    refinement.ncs.excessive_distance_limit=1.5
  The number of distances exceeding this limit is: 364
  Please correct your model or redefine the limit, e.g. with:
    refinement.ncs.excessive_distance_limit=3
  To disable this message completely define:
    refinement.ncs.excessive_distance_limit=None

It runs fine when you put refinement.ncs.excessive_distance_limit=None in
the command line. My question is what would be the best distance for the
program to run without this message.
thanks,
Shya






> Hi Raja,
>
> here are a few comments:
>
> - if you used TLS previously and then run a refinement without TLS (that
> is "strategy=..." does not include "tls"), the previous TLS refinement
> gets invalidated, because phenix.refine will automatically convert
> ANISOU into isotropic equivalent. It says it somewhere in .log file.
>
> - the "run 1" looks better than the others indeed (judging by the
> R-factors and bond/angles RMSDs at this resolution).
>
> - your original concern was the geometry problems, so using H in
> refinement, as well as optimizing weights, may help fixing them. So I
> would check the geometry too for all the runs below, and not only
> R-factors.
>
> - yesterday Kendall suggested a set of good ideas to try out regarding
> NCS.
>
> - I did not understand what you mean by "default extension of high
> resolution range in PHENIX". phenix.refine uses all reflections that it
> finds in your input data files, unless specified otherwise using
> high/low resolution cutoffs and sigma cutoffs. phenix.refine does not
> collect any additional data for you -:)
>
> - at 2.9A it is very likely that you still ok to refine individual ADPs
> and switching to group ADP can increase R-factors. So no surprises here.
> I doubt that using bulk-solvent correction and anisotropic scaling
> increases the R-factors; probably you tried it in combination with
> something else, and that "something else" was the cause of increased
> R-values.
>
> - are you using the latest version of PHENIX ?
>
> Pavel.
>
>
> On 11/18/09 8:47 AM, Raja Dey wrote:
>> Hi Pavel,
>>               I finished 4 runs as you suggested. See below:
>> run1.
>> phenix.refine 1205A-p21212.mtz nov138_001.pdb ncs_groups.params
>> main.ncs=true ncs.find_automatically=false
>> refinement.ncs.excessive_distance_limit=None
>> xray_data.high_resolution=2.9 refinement.main.number_of_macro_cycles=5
>> output.write_maps=true output.prefix=nov17
>> REMARK Start: r_work = 0.2803 r_free = 0.3036 bonds = 0.012 angles =
>> 1.488
>> REMARK Final: r_work = 0.2438 r_free = 0.2994 bonds = 0.009 angles =
>> 1.309
>> b_ave=70.09
>>
>> run2. with wxc and wxu optimization
>> phenix.refine 1205A-p21212.mtz nov138_001.pdb ncs_groups.params
>> main.ncs=true ncs.find_automatically=false
>> refinement.ncs.excessive_distance_limit=None
>> xray_data.high_resolution=2.9 refinement.main.number_of_macro_cycles=5
>> optimize_wxc=true optimize_wxu=true output.write_maps=true
>> output.prefix=nov17-opt
>> REMARK Start: r_work = 0.2803 r_free = 0.3036 bonds = 0.012 angles =
>> 1.488
>> REMARK Final: r_work = 0.2143 r_free = 0.2961 bonds = 0.032 angles =
>> 3.281
>> b_ave=64.71
>>
>> phenix.reduce may21_pdbset.pdb > may21_pdbset_h_added.pdb
>>
>> run3.  with hydrogen
>> phenix.refine 1205A-p21212.mtz nov138_001_h_added.pdb ncs_groups.params
>> main.ncs=true ncs.find_automatically=false
>> refinement.ncs.excessive_distance_limit=None
>> xray_data.high_resolution=2.9 refinement.main.number_of_macro_cycles=5
>> output.write_maps=true output.prefix=nov17-wh
>> REMARK Start: r_work = 0.2860 r_free = 0.3123 bonds = 0.085 angles =
>> 1.672
>> REMARK Final: r_work = 0.2381 r_free = 0.3029 bonds = 0.017 angles =
>> 1.685
>> b_ave=77.7
>>
>> run4. with both hydrogen and optimization
>> phenix.refine 1205A-p21212.mtz nov138_001_h_added.pdb ncs_groups.params
>> main.ncs=true ncs.find_automatically=false
>> refinement.ncs.excessive_distance_limit=None
>> xray_data.high_resolution=2.9 refinement.main.number_of_macro_cycles=5
>> optimize_wxc=true optimize_wxu=true output.write_maps=true
>> output.prefix=nov17-wh-opt
>> REMARK Start: r_work = 0.2860 r_free = 0.3123 bonds = 0.085 angles =
>> 1.672
>> REMARK Final: r_work = 0.2447 r_free = 0.3032 bonds = 0.020 angles =
>> 1.922
>> b_ave=80.75
>>
>> It looks output from run1 is the best, adding hydrogen and optimizing
>> wxc and wxu did not help much.
>> I have had little better Rfree and rmsd at the end of my last run.
>>
>>
>> You are right. the commands I used at the last stage looks weird. Before
>> that run I have used
>> "strategy=rigid_body+individual_sites+group_adp+tls" and also included
>> bulk_solvent and scaling. The map is pretty good. But, the number of
>> reflections used in the refinement was more than that in mtz file and
>> that was the warning in the pdb validation summary letter. I think
>> that's because default extension of high resolution range in PHENIX. So,
>> I needed to run 1 macro cycle with a little lower high resolution 2.9A
>> with the last refined pdb. I found those are the combination of commands
>> gives the best R, Rfree and rmsd for bonds and angles. As soon as I was
>> including bulk solven and scaling correction and/or b_group the values
>> were increasing. Although I don't have clear explanation, but that is
>> what I found. Any way these are very little differences and might not be
>> so important.
>>
>> I fixed the problem in dna. The problem was related with the occupancy
>> of the 2 alternate conformations of dna. But, I still have 8 amino
>> acids' (out of 400) phy, psy  out side Ramachandran plot. Probably this
>> does not mater much if I I deposite this co-ordinate in PDB.
>> Thanks for all your suggestions though.
>>
>> Regards...
>> Raja
>>
>>
>> ----- Original Message -----
>> From: Pavel Afonine <PAfonine at lbl.gov>
>> Date: Tuesday, November 17, 2009 12:20 pm
>> Subject: Re: [phenixbb] fixing geometry for deposition
>> To: PHENIX user mailing list <phenixbb at phenix-online.org>
>>
>>
>>> Hi Raja,
>>>
>>>
>>>>               I used the following commands at the last stage of
>>>>
>>> refinement:>
>>>
>>>> phenix.refine 1205A-p21212.mtz nov138_001.pdb
>>>>
>>> simulated_annealing=false ncs_groups.params main.ncs=true
>>> ncs.find_automatically=false
>>> refinement.ncs.excessive_distance_limit=None
>>> main.bulk_solvent_and_scale=false strategy=rigid_body+individual_sites
>>> xray_data.high_resolution=2.9 refinement.main.number_of_macro_cycles=1
>>> output.write_maps=true output.prefix=nov139 --overwrite
>>>
>>>>
>>>>
>>> The above command seems extremely weird to me for the following
>>> reasons:
>>> 1) Bulk-solvent correction and anisotropic scaling always has to be
>>> done
>>> (unless you are experimenting with fake data or these corrections
>>> have
>>> been already applied to Fobs, which is bad ideas anyway). By using
>>> "main.bulk_solvent_and_scale=false" you turn bulk-solvent
>>> correction and
>>> anisotropic scaling off.
>>>
>>> 2) By default, phenix.refine does 3 refinement macro-cycles, but
>>> often
>>> (depending how far you are from the final model) this is not enough
>>> for
>>> refinement to converge, so increasing it to 5 or so is a good idea.
>>> Doing just one macro-cycle
>>> (refinement.main.number_of_macro_cycles=1)
>>> does not make much sense to me. By the way, you can use shortcuts
>>> like
>>> "main.number_of_m=5".
>>>
>>> 3) You can drop this off the list since it is the default setting
>>> anyway: "simulated_annealing=false".
>>>
>>> 4) The refinement strategy: "strategy=rigid_body+individual_sites".
>>> Normally, you do the rigid body refinement at initial stages of
>>> refinement when your model is poor, and not at the final run. This
>>> is
>>> because the rigid-body refinement can be very rude on your model:
>>> bonds
>>> can be broken between rigid groups since no restraints is used, for
>>> example. Also, it's strange that the ADP refinement is turned off -
>>> it's
>>> always good to do, and at 2.8A you can still refined individual
>>> ADPs.
>>> Well, I'm not mention using TLS...
>>>
>>> So, I would modify the above command as following:
>>>
>>> phenix.refine 1205A-p21212.mtz nov138_001.pdb ncs_groups.params
>>> main.ncs=true ncs.find_automatically=false
>>> refinement.ncs.excessive_distance_limit=None
>>> xray_data.high_resolution=2.9 output.write_maps=true
>>> output.prefix=test
>>> --overwrite
>>>
>>> and try running it as is, and with adding keywords
>>> "optimize_wxc=true
>>> optimize_wxu=true", using a model with or w/o H riding H atoms,
>>> etc...
>>> what I wrote in my previous email.
>>>
>>>
>>>> Regarding amino acids phy, psy..... I tried real space
>>>>
>>> refinement/regularization in coot,
>>>
>>> This is not the same as what I suggested to try in my previous
>>> email.
>>> Anyway, I would first try the modified command above and only then
>>> try
>>> other suggested things.
>>>
>>> Good luck,
>>> Pavel.
>>>
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>>>
>>>
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