[phenixbb] refinement problem

Sneha Rangarajan rsneha at umd.edu
Tue Sep 30 14:19:51 PDT 2014

Thanks for your response.

My protein has two chains linked by a linker.
So as per your suggestion, I used a homologous protein, split the two chains (as 2 different pdbs) and trimmed each one of them using sculptor.

I then tried doing Phaser MR (p212121) with 1) both chains together (as two ensembles): It gave a solution with LLG:145 and TFZ: 4.7. However the density of one of the chains was very good while that for the other chain was poor!
So I tried another approach-2) I did MR with just that chain (the one that looks good) and got a solution with good looking map (LLG:136, TFZ=13.7). Then I tried fixing that solution and asked Phaser to look for one copy of the other chain. However the results remained the same.

It probably sounds crazy but is there any way to use the molecule found in p21 to find the solution in p212121?

I am sending the log files to that email id. Could you please take a look?


From: Nathaniel Echols [mailto:nechols at lbl.gov]
Sent: Tuesday, September 30, 2014 11:34 AM
To: Sneha Rangarajan
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] refinement problem

On Tue, Sep 30, 2014 at 8:21 AM, Sneha Rangarajan <rsneha at umd.edu<mailto:rsneha at umd.edu>> wrote:
I have a 1.9A dataset for a single chain Fv-peptide complex that shows psedomerohedral twin operators in Xtriage (1 in p212121, 3 in p21 and 7 in p1).

Standard warning: don't worry about twin operators unless you have unusual intensity statistics - the mere fact that your lattice is compatible with twinning does not mean that anything is wrong.  What does the final verdict in Xtriage say?  (By the way, the new version in the nightly builds provides much clearer feedback.)

Although most programs (in CCP4) identify the best SG to be p212121, MR cannot find a solution with p212121 due to packing clashes.

Although it's possible that you have pseudosymmetry, I think this is ultimately the core problem - no matter what space group you try, the MR solution is incomplete, and probably for the same reason.  My guess is that the conformation of the search model is significantly different (either locally or globally) than that of the crystallized molecule.  If it's a homologous structure (not the same protein), try running Sculptor first to trim off the parts that don't agree.  If it's the same protein, either try cutting it into individual domains and searching for those, or trim off extended loops manually.  I would use P212121 symmetry if possible, but it doesn't hurt to try MR in all of the space groups for now.

If you want to send us the files separately to help at phenix-online.org<mailto:help at phenix-online.org>, we may be able to give a more specific answer.

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