[phenixbb] Problem with molecular replacement

[Shramana Chatterjee]

Thanks a lot. The resolution is ~3ang. for both the cases and the space
group is tetragonal. I haven't tried yet just the rigid body refinement.I
will  start from only rigid body refinement, it may produce an identical
one.

Thanks and regards,
Shramana.

On 9 Apr 2020 2:29 pm, "Randy Read" <rjr27 at cam.ac.uk> wrote:

Dear Shramana,

I don’t know why MR is not working well with individual monomers, if you
have a refined model of the same thing.  Is the resolution particularly low?

However, the point you make here that perhaps wasn’t in the previous email
is that the space group and cell dimensions are the same.  Have you just
tried rigid-body refinement with the solved structure?  Perhaps this is a
space group (e.g. trigonal) where there are alternative ways to index the
data.  If it is, then you should see if there’s a way to make this data set
agree with the solved one using some alternative indexing, and then do
rigid-body refinement.

Of course, it is in principle possible that it’s just an accident that the
space group and cell dimensions are the same, but the crystal forms are
actually different, but this is less likely to be the case.

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 16:35, Shramana Chatterjee <schatter90 at gmail.com> wrote:
>
> 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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