[phenixbb] Simple Phaser Question (Ed Pozharski

Joseph Noel noel at salk.edu
Sat Dec 25 13:15:40 PST 2010


Hi Ed,

Yes, that is what I generally do but it sometimes is a slightly different so I wanted a more general approach. 

Joe
___________________________________________________________
Joseph P. Noel, Ph.D.
Investigator, Howard Hughes Medical Institute
Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
The Salk Institute for Biological Studies
10010 North Torrey Pines Road
La Jolla, CA  92037 USA

Phone: (858) 453-4100 extension 1442
Cell: (858) 349-4700
Fax: (858) 597-0855
E-mail: noel at salk.edu

Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
___________________________________________________________

On Dec 25, 2010, at 12:00 PM, phenixbb-request at phenix-online.org wrote:

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> Today's Topics:
> 
>   1. Simple Phaser Question (Joseph Noel)
>   2. Re: Simple Phaser Question (Ed Pozharski)
>   3. Questions about phenix.refine with twin_law (Keitaro Yamashita)
>   4. Re: Questions about phenix.refine with twin_law (Peter Zwart)
>   5. Re: Questions about phenix.refine with twin_law (Pavel Afonine)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 24 Dec 2010 17:11:37 -0800
> From: Joseph Noel <noel at salk.edu>
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] Simple Phaser Question
> Message-ID: <5E3B81ED-4C13-488E-8C28-33DB29263AEF at salk.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi All,
> 
> I am working with a protein that is a physiological dimer. On occasion I obtain a unit cell with one monomer in the asymmetric unit but most often I obtain an enantiomorphic space group with an expanded C axis that contains two molecules in the asymmetric unit. Anyway, that is all moot to some extent. I am wondering if for the case of my NCS dimer, is there a way using Phaser in Phenix to ensure that when both monomers are found, they are "close together" representative of the physiological dimer? When I search with individual monomers I often obtain a solution with two monomers but in different asymmetric units. Of course, I could easily do the transformation to form the physiological NCS dimer for later refinement but just wondering if I could avoid this from the get go with the appropriate Phaser keyword input (GUI if possible).
> 
> Thanks and Happy Holidays!
> 
> Joe
> ___________________________________________________________
> Joseph P. Noel, Ph.D.
> Investigator, Howard Hughes Medical Institute
> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
> The Salk Institute for Biological Studies
> 10010 North Torrey Pines Road
> La Jolla, CA  92037 USA
> 
> Phone: (858) 453-4100 extension 1442
> Cell: (858) 349-4700
> Fax: (858) 597-0855
> E-mail: noel at salk.edu
> 
> Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
> Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
> ___________________________________________________________
> 
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> ------------------------------
> 
> Message: 2
> Date: Fri, 24 Dec 2010 23:54:07 -0500
> From: Ed Pozharski <epozh001 at umaryland.edu>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Simple Phaser Question
> Message-ID: <1293252847.2206.15.camel at thunderclap>
> Content-Type: text/plain; charset="UTF-8"
> 
> You could search with the dimer...
> 
> On Fri, 2010-12-24 at 17:11 -0800, Joseph Noel wrote:
>> Hi All,
>> 
>> 
>> I am working with a protein that is a physiological dimer. On occasion
>> I obtain a unit cell with one monomer in the asymmetric unit but most
>> often I obtain an enantiomorphic space group with an expanded C axis
>> that contains two molecules in the asymmetric unit. Anyway, that is
>> all moot to some extent. I am wondering if for the case of my NCS
>> dimer, is there a way using Phaser in Phenix to ensure that when both
>> monomers are found, they are "close together" representative of the
>> physiological dimer? When I search with individual monomers I often
>> obtain a solution with two monomers but in different asymmetric units.
>> Of course, I could easily do the transformation to form the
>> physiological NCS dimer for later refinement but just wondering if I
>> could avoid this from the get go with the appropriate Phaser keyword
>> input (GUI if possible).
>> 
>> 
>> Thanks and Happy Holidays!
>> 
>> 
>> Joe
>> ___________________________________________________________
>> Joseph P. Noel, Ph.D.
>> Investigator, Howard Hughes Medical Institute
>> Professor, The Jack H. Skirball Center for Chemical Biology and
>> Proteomics
>> The Salk Institute for Biological Studies
>> 10010 North Torrey Pines Road
>> La Jolla, CA  92037 USA
>> 
>> Phone: (858) 453-4100 extension 1442
>> Cell: (858) 349-4700
>> Fax: (858) 597-0855
>> E-mail: noel at salk.edu
>> 
>> Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
>> Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
>> ___________________________________________________________
>> 
>> 
>> 
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Sat, 25 Dec 2010 14:21:43 +0900
> From: Keitaro Yamashita <yamashita at castor.sci.hokudai.ac.jp>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: [phenixbb] Questions about phenix.refine with twin_law
> Message-ID:
> 	<AANLkTik9hW40MJCqdcB3bic5fHC3UPoYGqrEetPseAg4 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Dear Phenix developers,
> 
> I'm working with pseudo-merohedrally twinned data (fraction 45%),
> using Phenix-dev-616.
> 
> I have three questions about phenix.refine with twin_law.
> (running on the command line)
> 
> During refinement with twin_law, the log file says x-ray target
> function is set to "twin_lsq_f".
> Does it mean, we cannot use maximum likelihood target for twinned data?
> If so, is it recommended to refine without twin_law at first several cycles?
> 
> 
> When I tried to refine using the model refined without twin_law,
> the target function was still ml, not twin_lsq_f although I specified twin_law.
> Is this a bug?
> 
> 
> When I used twin_law option, in the table "R-free likelihood based estimates",
> "Scale factor" were None in all resolution bins.
> Cannot scale factor be calculated during twin refinement?
> 
> 
> Thanks in advance and Wishing you the best holidays,
> 
> Keitaro
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Fri, 24 Dec 2010 21:43:11 -0800
> From: Peter Zwart <PHZwart at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Questions about phenix.refine with twin_law
> Message-ID:
> 	<AANLkTinY+-qJVcTowbr6cnp-B=FbabCFy1WC-40xtdG=@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Keitaro,
> 
>> 
>> During refinement with twin_law, the log file says x-ray target
>> function is set to "twin_lsq_f".
>> Does it mean, we cannot use maximum likelihood target for twinned data?
>> If so, is it recommended to refine without twin_law at first several cycles?
> 
> I have never done a systematic study to answer this question. How good
> is your model?
> 
>> 
>> 
>> When I tried to refine using the model refined without twin_law,
>> the target function was still ml, not twin_lsq_f although I specified twin_law.
>> Is this a bug?
> 
> Not sure, can you send (off-list) logfile of that run?
> 
>> 
>> 
>> When I used twin_law option, in the table "R-free likelihood based estimates",
>> "Scale factor" were None in all resolution bins.
>> Cannot scale factor be calculated during twin refinement?
> 
> The scale factor (one per dataset) is refined during twin refinement
> and subsequently fixed during positional and adp refinement. The
> lsq_twin target function doesn't have a resolution dependent scale
> factor.
> 
>> 
>> 
>> Thanks in advance and Wishing you the best holidays,
> 
> Same to you!
> 
> HTH
> 
> P
> 
> 
>> Keitaro
> 
> 
> 
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> 
> 
> 
> 
> -- 
> -----------------------------------------------------------------
> P.H. Zwart
> Research Scientist
> Berkeley Center for Structural Biology
> Lawrence Berkeley National Laboratories
> 1 Cyclotron Road, Berkeley, CA-94703, USA
> Cell: 510 289 9246
> BCSB:? ? ? http://bcsb.als.lbl.gov
> PHENIX:?? http://www.phenix-online.org
> SASTBX:? http://sastbx.als.lbl.gov
> -----------------------------------------------------------------
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Fri, 24 Dec 2010 23:32:58 -0800
> From: Pavel Afonine <pafonine at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Cc: Keitaro Yamashita <yamashita at castor.sci.hokudai.ac.jp>
> Subject: Re: [phenixbb] Questions about phenix.refine with twin_law
> Message-ID: <4D159E2A.70303 at lbl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
>  Hi Keitaro,
> 
> phenix.refine uses ml target all the time by default (or mlhl if 
> experimental phases are available). If you ask phenix.refine to use 
> information about twinning (by providing a twin law) then phenix.refine 
> will use a least-squares target function called "twin_lsq_f". So what 
> you observe is expected. Therefore I'm not sure I understand what 
> exactly you suspect as a bug...
> 
> The next CCN (Computational Crystallography Newsletter; 
> http://www.phenix-online.org/newsletter/) that comes out beginning of 
> January will contain an article about using ML target in twin 
> refinement, which will be implemented in some (hopefully near) future.
> 
> Also, when using "twin_lsq_f" some of refinement statistics is not 
> available and this is why you see "None" for some of those - this is 
> nothing to worry about but just a matter of fact.
> 
> May be you can explain some more what you believe is not right?
> 
>> When I tried to refine using the model refined without twin_law,
>> the target function was still ml, not twin_lsq_f although I specified twin_law.
>> Is this a bug?
> 
> This is weird... If you could send me the inputs that I can use to 
> reproduce this problem then I will be able to explain what is going on.
> 
> Thanks!
> Pavel.
> 
> 
> On 12/24/10 9:21 PM, Keitaro Yamashita wrote:
>> Dear Phenix developers,
>> 
>> I'm working with pseudo-merohedrally twinned data (fraction 45%),
>> using Phenix-dev-616.
>> 
>> I have three questions about phenix.refine with twin_law.
>> (running on the command line)
>> 
>> During refinement with twin_law, the log file says x-ray target
>> function is set to "twin_lsq_f".
>> Does it mean, we cannot use maximum likelihood target for twinned data?
>> If so, is it recommended to refine without twin_law at first several cycles?
>> 
>> 
>> When I tried to refine using the model refined without twin_law,
>> the target function was still ml, not twin_lsq_f although I specified twin_law.
>> Is this a bug?
>> 
>> 
>> When I used twin_law option, in the table "R-free likelihood based estimates",
>> "Scale factor" were None in all resolution bins.
>> Cannot scale factor be calculated during twin refinement?
>> 
>> 
>> Thanks in advance and Wishing you the best holidays,
>> 
>> Keitaro
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
> 
> 
> 
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> 
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