[phenixbb] seeking advice on how to configure Phaser-MR (full-featured) to use a previous partial solution

Boaz Shaanan bshaanan at bgu.ac.il
Tue Aug 8 12:04:18 PDT 2017


I think that the Phaser tutorial is your friend here. There is a nice example of how to run two successive searches in one run to solve a n-domain structure (we actually used it recently to solve  a structure of a protein-DNA complex). I think that running your B+C search followed by an A search would solve your problem. If you haven't tried it yet it's worth trying.

Good luck,


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Emilia C. Arturo (Emily) [ecgarturo at gmail.com]
Sent: Tuesday, August 08, 2017 7:00 PM
To: PHENIX user mailing list
Subject: [phenixbb] seeking advice on how to configure Phaser-MR (full-featured) to use a previous partial solution


I have a 3-domain protein (let's say it's organized from N to C as
A-B-C) whose structure I am working to determine now. Although several
single- (A alone, B alone), double- (A+B and B+C) and 3-domain (A+B+C)
structures of this protein (from a different organism whose primary
sequence is, overall, ~85% identical to the one on which I'm working)
have already been determined and deposited in the PDB, I would ideally
like to use a minimal probe (i.e. as few domains as possible) in order
avoid model bias that could be imposed on the relative orientation of
domains A, B, and C.

So far, I have phase solutions (TFZ scores for all in the high-50s and
60s) using B-only, A+B, and B+C pdb files as probes. A-only structures
have not given a phase solution (TFZ is ~7 and autobuild gives a
solution that looks unbelievable in Coot), perhaps because A is
relatively small in size.

Here is my problem:
I suspect that A and B sit relative to one another in an interesting
way in this particular structure, so I'd like to use Phaser to search
for a solution given the fixed partial solution from a B-only search,
together with an A-only structure as a separate probe. So far no MR
solutions have been found when I configure the run with an A-only pdb
file and a B-only-derived Phaser result that is input as a fixed
partial solution. I'm writing to ask for advice on how to configure
the search. I think that the problem is my configuring the search, and
not that a solution cannot be found from these coordinates.

This is the reason I think that my problem is in configuring the
search; please correct me if I'm wrong:
Using a Phaser result derived from using an A+B structure as probe, I
cut up the resulting pdb file into 2 pdb files - one containing an A'
and another containing a B', where A' is the A domain of the Phaser
result, and B' is the B-only part. Then I configured a Phaser result
with B' as an ensemble that is a fixed partial solution, and A' as a
separate ensemble/probe. I searched for 4 of each since 4 chains is
the most likely composition in the ASU. I expected to get a result
similar to what Phaser calculated when I input the A+B structure as an
intact probe. Instead of getting a solution where 4 A+B chains were
placed as they were in the first Phaser result, which gave one
solution with a TFZ score of 65, I got 13 solutions, the top scoring a
TFZ of 7.5, and each solution having a total of 9 chains - 4 As and 5

Is anyone willing to help me troubleshoot the above before I throw up
my hands and settle on either manually building two domains onto the
single-domain solution, or one domain onto the 2-domain solution,
keeping in mind the potential for model bias? I am keen on using the
B-only solution as a fixed partial solution to place domain A because
all the B-only structures provide coordinate information for a portion
of domain B that is unresolved in any of the multi-domain structures
that contain domain B.

I am using the Phenix gui, version 1.12rc1-2807.


"Study as if you were going to live forever; live as if you were going
to die tomorrow." - Maria Mitchell

"I'm not afraid of storms for I'm learning to sail my ship."  - Louisa
May Alcott
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