[phenixbb] regarding ncs distance - .geo file
Pavel Afonine
PAfonine at lbl.gov
Sat Nov 21 09:51:38 PST 2009
Hi Maia,
just looking at distances is not enough: in addition, one needs to look
at how those residues appear in maps. It's a part of planned
improvements of NCS refinement.
However, for the moment phenix.refine stops prompting the user to check
the NCS groups and problem residues. I saw a number of cases where this
helped to identify wrong NCS selections due to atom selection syntax errors.
Pavel.
On 11/21/09 8:56 AM, Maia Cherney wrote:
> Hi Pavel,
> I would like to make a suggestion about the use of
> excessive_distance_limit. Instead of shutting down the refinement due to
> excessive_distance over the limit why not use it for excluding only
> those residues from NCS refinement and do the ncs refinement for the
> rest of the residues.
>
> Maia
>
>
>
> Pavel Afonine wrote:
>
>> By the way, it may be worth of repeating that the .geo file contains
>> the list of all the geometry restraints used in phenix.refine
>> refinement (bonds, angles, planarities, chiralities, dihedrals,
>> non-bonded, NCS, custom defined restraints and edits), for each and
>> every atom, making it a complete foot-print of geometry restraints
>> used to obtain the final refined structure.
>>
>> Pavel.
>>
>> On 11/18/09 11:12 AM, Pavel Afonine wrote:
>>
>>> Hi Shya,
>>>
>>> inspect the .geo file for something like "EXCESSIVE DISTANCE" (or
>>> something similar, I don't remember exactly), and that will give you
>>> an idea by how much you exceed the default 1.5 value.
>>>
>>> It might be worth of looking at those atoms in NCS copies that have
>>> too large deviations between NCS copies, and if you find that it is
>>> for the reason, then you may want to exclude them from NCS.
>>>
>>> Good luck!
>>> Pavel.
>>>
>>>
>>> On 11/18/09 11:07 AM, sbiswas2 at ncsu.edu wrote:
>>>
>>>> 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.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> phenixbb mailing list
>>>>>>> phenixbb at phenix-online.org
>>>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
>>>>>>
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