[phenixbb] very weak reflections

Thu Dec 10 14:10:30 PST 2009

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
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>> Keep your friends updated— even when you’re not signed in.
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
> -- 
> 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 ]
> --
>
>
>
>
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> 