[phenixbb] very weak reflections
chern
chern at ualberta.ca
Fri Dec 11 09:03:42 PST 2009
Thanks for the suggestion. My original question was that the phenix refines
the isoalloxazine ring as a flat plane whereas refmac refines it bent. (Same
cif file)
And the density fits the shape produced by each program. I guess, I should
tighten restraints in refmac and see if it can make the plane and look at
the difference map.
Maia
----- Original Message -----
From: "Dale Tronrud" <det102 at uoxray.uoregon.edu>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Thursday, December 10, 2009 4:10 PM
Subject: Re: [phenixbb] very weak reflections
>
> This is true for bond lengths and angles, but a bent isoalloxazine
> ring can be identified at much lower resolution because the shifts
> on the edges of the ring system will be large and correlated. I
> recommend that you try a null hypothesis test. Force the rings to
> be planar with a high weight. If the final difference map indicates
> that the edges need to be moved you have solid evidence that the
> ring system is bent. If the difference map is featureless then the
> bending is smaller than your data can detect.
>
> Dale Tronrud
>
> Paul Adams wrote:
>>
>> Yes, you need very high resolution data (at least 1.5A or better) to
>> determine small molecule geometry from a crystallographic experiment.
>>
>> On Dec 10, 2009, at 2:10 PM, chern wrote:
>>
>>> Thank you for you reply.
>>> My problem is that I want to determine the chemistry of my molecules.
>>> The isoalloxazine ring of the FAD cofactor can be planar or bent,
>>> depending on the oxidation state, the other ligands also can be both.
>>> But it looks like I don't have high enogh resolution to see that for
>>> sure.
>>>
>>> Maia
>>>
>>> ----- Original Message ----- From: "Paul Adams" <PDAdams at lbl.gov>
>>> To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
>>> Sent: Thursday, December 10, 2009 11:45 AM
>>> Subject: Re: [phenixbb] very weak reflections
>>>
>>>
>>>>
>>>> Phenix.refine includes weak reflections in refinement. If you have
>>>> negative intensities in our data I suggest using the Truncate
>>>> procedure (available in CCP4) to convert these to positive amplitudes.
>>>>
>>>> The issues you mention with regard to ligands and FAD are most
>>>> likely due to the geometry restraints used - you should look into
>>>> using phenix.elbow to create restraints if you are obtaining results
>>>> that don't fit what you know about the chemistry of the molecules.
>>>>
>>>> On Dec 10, 2009, at 10:38 AM, chern wrote:
>>>>
>>>>> Hi Pavel,
>>>>> Now that Randy sent you a reference about the effect of very weak
>>>>> reflections will you include the changes in the refiment procedure?
>>>>> I am wondering about that because I get different maps from the
>>>>> phenix refinement and from the refmac refinement. In one case I see
>>>>> the isoalloxazine ring of the FAD cofactor flat, in the other case
>>>>> this ring is bent. The same story with the densities for ligands.
>>>>> Is it about geometry restraints or effects of exclusion of very
>>>>> weak reflections?
>>>>>
>>>>> Maia
>>>>>
>>>>> ----- Original Message -----
>>>>> From: Pavel Afonine
>>>>> To: PHENIX user mailing list
>>>>> Sent: Thursday, December 10, 2009 9:31 AM
>>>>> Subject: Re: [phenixbb] refinement
>>>>>
>>>>> Hi Pei-Chun,
>>>>>
>>>>> the target function for coordinates refinement that is used in
>>>>> phenix.refine is following:
>>>>>
>>>>> T = wxc_scale * wxc * Txray + wc * Trestraints
>>>>>
>>>>> where: wxc is determined automatically, wc =1 by default, and
>>>>> wxc_scale = 0.5 by default. A user can adjust wxc_scale or wc.
>>>>>
>>>>> Responding your question about "put much more weight on geometry
>>>>> restraints": you can do it either by decreasing wxc_scale or by
>>>>> increasing wc. I would try an array of values for wxc_scale to see
>>>>> which one gives the best result.
>>>>>
>>>>> Please let me know if it's still not clear or if you have any other
>>>>> questions!
>>>>>
>>>>> Pavel.
>>>>>
>>>>>
>>>>> On 12/10/09 7:38 AM, Pei-Chun Lin wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> When talking about "put much more weight on geometry restraints to
>>>>>> avoid overfitting", what wxc and wxu value will you suggest to use
>>>>>> for a 4A structure?
>>>>>> I am working on a 3.5A structure and have no experience of
>>>>>> adjusting weight value before. Any suggestion will be very helpful
>>>>>> to me.
>>>>>>
>>>>>>
>>>>>> PC
>>>>>>
>>>>>>
>>>>>> Date: Tue, 8 Dec 2009 20:12:29 -0800
>>>>>> From: PAfonine at lbl.gov
>>>>>> To: phenixbb at phenix-online.org
>>>>>> Subject: Re: [phenixbb] refinement
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> although I've seen cases like yours when SA in Cartesian space did
>>>>>> miracles, in many of cases modeling at 4A resolution is a tough
>>>>>> problem.
>>>>>>
>>>>>> Since clearly SA didn't work out (given R/Rfree ~ 37/50% and the
>>>>>> starting 48/50), I would try splitting your model into rigid
>>>>>> domains and refine each as a rigid body. Plus, I would refine one
>>>>>> isotropic B per residue or per domain (try both). This is a few
>>>>>> minutes to try so why don't you do so.
>>>>>> Also, I would still combine it (rigid body and B-factor refinement)
>>>>>> with Cartesian SA, but I would put much more weight on geometry
>>>>>> restraints to avoid overfitting.
>>>>>>
>>>>>> As you probably aware of, in phenix.refine you can run combined
>>>>>> refinement jobs, for example, consisting of SA, rigid body, B-
>>>>>> factor refinement and so on. So I would recommend playing with the
>>>>>> above suggestions to see if it works. Plus, don't forget looking
>>>>>> at the maps - may be you manage to fit something manually.
>>>>>>
>>>>>> By the way, which R-factors you get if you run:
>>>>>>
>>>>>> phenix.model_vs_data data.mtz model.pdb
>>>>>>
>>>>>> (phenix.model_vs_data will account for twinning (if any) using
>>>>>> Xtriage automatically) ?
>>>>>>
>>>>>> Write us if you have questions.
>>>>>>
>>>>>> Good luck,
>>>>>> Pavel.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 12/8/09 7:02 PM, r n wrote:
>>>>>> Thanks a lot. I did download the new -dev249 and did cartesian SA,
>>>>>> R goes down to 37 but R-free (50) did not.
>>>>>> Any suggestions?
>>>>>>
>>>>>>
>>>>>>
>>>>>> From: Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov>
>>>>>> To: phenixbb at phenix-online.org
>>>>>> Sent: Tue, December 8, 2009 3:34:09 PM
>>>>>> Subject: Re: [phenixbb] refinement
>>>>>>
>>>>>> > I do have very low resolution data (around 4 ang), what are
>>>>>> > the efficient way of doing refinement, either rigid body alone or
>>>>>> > rigidbody and tls or individual with group_adp. I did both, but not
>>>>>> > much significant changes in Rfree stays around 48/50%.
>>>>>>
>>>>>> You could also try Cartesian or torsion-angle simulated annealing.
>>>>>> I'd try both. In my experience Cartesian SA often works better even
>>>>>> at low resolution.
>>>>>> If you get errors running torsion-angle annealing, please try
>>>>>> the latest nightly build (dev-249) since I've fixed several
>>>>>> problems since the 1.5-2 release.
>>>>>>
>>>>>> > Also I do have other questions
>>>>>> >
>>>>>> > 1. While doing rigid body refinement, phenix complaint about the
>>>>>> > special position and could not perform rigid body refinement,
>>>>>> > whereas individual site refinement is working fine. I do have to
>>>>>> > delete the atom in special position for rigid body refinement?
>>>>>>
>>>>>> You could use
>>>>>> sites.rigid_body = ...
>>>>>> to select the bodies you want to refine. The rest (including your
>>>>>> atom on the special position) will not move.
>>>>>>
>>>>>> Ralf
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>>>>>>
>>>>>>
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>>>>>
>>>>>
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>>>> --
>>>> Paul Adams
>>>> Acting Division Director, Physical Biosciences Division, Lawrence
>>>> Berkeley Lab
>>>> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
>>>> Vice President for Technology, the Joint BioEnergy Institute
>>>> Head, Berkeley Center for Structural Biology
>>>>
>>>> Building 64, Room 248
>>>> Tel: 1-510-486-4225, Fax: 1-510-486-5909
>>>> http://cci.lbl.gov/paul
>>>>
>>>> Lawrence Berkeley Laboratory
>>>> 1 Cyclotron Road
>>>> BLDG 64R0121
>>>> Berkeley, CA 94720, USA.
>>>>
>>>> Executive Assistant: Patty Jimenez [ PAJimenez at lbl.gov ] [
>>>> 1-510-486-7963 ]
>>>> --
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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