[phenixbb] Simple Phaser Question (Ed Pozharski

Ed Pozharski epozh001 at umaryland.edu
Sat Dec 25 15:18:48 PST 2010


If these differences are large enough to prevent PHASER from finding the
solution...   PHASER actually shifts the second solution to form a
"complex", but it is probably based on the shortest distance between
centers of mass, not maximum buried surface area.  So sometimes it may
misfire.

On Sat, 2010-12-25 at 13:15 -0800, Joseph Noel wrote:
> 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
> > ___________________________________________________________
> > 
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20101224/7891198a/attachment.html>
> > 
> > ------------------------------
> > 
> > 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
> > 
> > 
> > 
> > ------------------------------
> > 
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> > 
> > 
> > End of phenixbb Digest, Vol 61, Issue 27
> > ****************************************
> > 
> 
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