Re: [phenixbb] Simple Phaser Question (Ed Pozharski

Hi, That's right -- the test to choose which symmetry equivalent should be used is simply which one has its centre of mass closest. That works most of the time for things like dimers, but obviously is failing in this case. We would consider something more sophisticated, like buried surface, but that's not going to work when the models are distant relatives or lack surface loops, which is frequently the case in the difficult MR problems we're aiming at. Regards, Randy Read On 25 Dec 2010, at 23:18, Ed Pozharski wrote:

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:

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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: [email protected]

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, [email protected] 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)

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Message: 1 Date: Fri, 24 Dec 2010 17:11:37 -0800 From: Joseph Noel To: [email protected] Subject: [phenixbb] Simple Phaser Question Message-ID: <[email protected]> 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: [email protected]

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