Dear Rajnesh,
I wonder about your chosen space group?
I commend that you expand your diffraction data into P1, then run molecular
replacement with Phaser in P1 and if a solution is determined by Phaser run the
coordinates through Zanuda to determine the space group.
Best wishes,
John
Emeritus Pr
could merge the
pdb files and see if you can refine the combined solutions.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von Eleanor Dodson
Gesendet: Mittwoch, 12. Februar 2020 14:04
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] problem in structure solution of multidomain
At 3A finding missing domains is tricky.. Can you increase that resolution
at all? Much easier at 2.5A!
But I would refine and rebuild the 4 domains to the best possible maps,
then see if there is any density unaccounted for.
(You will have to lower the COOT default contour level I guess..)
If
Hi,
One other option is to run MR in Phaser in one run with the tetramer made of the 4 monomers as model 1 and the single monomer as model 2. The gui offers this option and there is also an example in the documentaion.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion U
Hi,
you mentioned that there is no electron density for your 5th domain. If
there is nothing coming up even after refinement of the four domains, than
maybe your 5th domain is not there, or so disordered that it doesn't show
up.
Christian
On Wed, Feb 12, 2020 at 9:47 AM RAJNESH KUMARI YADAV
wrot
Thanks Clemens and Lumbini for your help.
I had tried both the things but none of them worked for this problem.
On Wed, Feb 12, 2020 at 1:56 PM Clemens Vonrhein
wrote:
> Hi,
>
> MOLREP [1] has a nice feature of searching for structures in electron
> density - with the known parts of your model f
Hi,
MOLREP [1] has a nice feature of searching for structures in electron
density - with the known parts of your model fixed. Basically follow
the recipe in [1] (search for "refmac.mtz" - but you can use any other
set of amplitudes/phases as well). In your case the 4-domain model
would be given to
Dear Rajnesh,
Why don't you try refining the 4 domain structure initially. Once the R
factor and R free value is sufficiently low then try to see if there is any
density build up for domain 5.
This has atleast worked for me.
On Wed, 12 Feb 2020, 12:53 Rajnesh Kumari Yadav, wrote:
> Hello everyon
Hello everyone,
I am working on a protein which have 5 domain in it, we have its 4 domain
structure and 3.0 Angstrom data of 5 domain protein crystal. While doing the
Molecular replacement we got solution with four domain with good electron
density and space for last domain without any density.
