[phenixbb] Problem with molecular replacement

[Shramana Chatterjee]

Using only rigid body refinement worked well with Rfree ~0.29. Can it
produce a bias map meaning is it possible to miss some important part (like
solvent or ligand) due to bias-ness of the map?

On Thu, Apr 9, 2020 at 3:07 PM Shramana Chatterjee <schatter90 at gmail.com>
wrote:

> 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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>
>
>
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