[phenixbb] Problem with molecular replacement

Shramana Chatterjee schatter90 at gmail.com
Thu Apr 9 08:35:54 PDT 2020

Dear Randy,

Thank you for your suggestion. I should mention that I have tried with
single copy, best fitted dimer as well with the whole structure (on
different set of runs) but in al the cases PhaserMR is unable to produce
identical number of copies comparable with the solved structure although
the cell dimension and space group is same with the solved one. What can be
the possible reason and how to get rid of that?

Thanks again for your reply.

On Thu, Apr 9, 2020 at 4:30 AM Randy Read <rjr27 at cam.ac.uk> wrote:

> Dear Shramana,
> I may be reading this incorrectly, but it sounds like you’re providing the
> entire PDB file from the solved model to Phaser to solve the other
> structure by MR.  You need to edit the PDB file before using it as a model
> so that what you have is a sensible model for what is in the other crystal
> form, because Phaser will just take the whole thing as a single rigid
> body.  Given the 100% sequence identity, I would use a single copy as a
> model and search for the appropriate number of copies (perhaps 4, from what
> you say).  If the model was more distant, then it might be worth looking at
> it to see if it could plausibly be a dimer or tetramer in solution, and
> then you could use a higher-order structure.  But MR with identical models
> can usually place a reasonable number of copies independently, and then you
> don’t have to make any assumptions about quaternary structure.
> Best wishes,
> Randy Read
> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research     Tel: +44 1223 336500
> The Keith Peters Building                               Fax: +44 1223
> 336827
> Hills Road                                                       E-mail:
> rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
> > On 9 Apr 2020, at 04:43, Shramana Chatterjee <schatter90 at gmail.com>
> wrote:
> >
> > Hi,
> >
> > I am trying to solve a structure using a data solved by SAD as an
> reference (ensemble in phaser). The structure I am trying to solve has 100%
> sequence identity with the solved one. The problem that I am facing during
> Phaser MR is that, in the solved structure there are 6 molecules in the ASU
> although I am getting maximum 4 molecules in the ASU and also Rfree is
> around 0.49 just after the phaser. Phaser is showing a good values of LLG
> (>500) and TFZ (>8).
> >
> > It would be very helpful if I get any suggestion about the
> above-mentioned problem.
> >
> > Thank you in advance.
> >
> >
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