Hi all,
thanks to several tremendously helpful replies I got the molecular
replacement, which I bugged the ccp4bb with during the last weeks, under
control. Thanks for all the input, I'll send out a summary soon.
One question remains, though:
With an improved search model, the molecular replaceme
I would stop trying to use a map! that is an act of desperation when you
have uninterpretable but possibly somewhat true experimentally phased
density..
If you have a model it is MUCH MUCH easier!
So as I said - I would find the best hexagonal dimer - you may know this
or you can dispatch the s
Yes- ALMN seems to have given one excellent match between the data sets
which is encouraging.
But since you are matching hexagonal to trigonal you get a large number
of symmetry equivalent peaks, relating a molecule from the P1 set to one
of the hexagonal set.
The angles are defined so that:
"T
The procedure of cutting out electron density, putting it into a large unit
cell, and backtransforming to get structure factors can be tricky (as
you've discovered), so we put some instructions on our webpage:
http://www-structmed.cimr.cam.ac.uk/phaser/density_as_model.html
The last time I tri
Hi all,
thanks a lot for the various responses. When I tried to use a map as the
serach model, I ran into various problems:
again, the starting point is a weak, yet convincing molecular replacement
solution in the hexagonal crystal form (1mol/asu) and no MR solution in P1
(2mol/asu, 2-fold in SRF).
If you take a PDB file from the solution for the hexagonal form as your
input model for a translation search in P1, then the cross-rotation peaks
that rotate the hexagonal data onto the P1 data should be the correct
orientations. (Phaser uses the same definition for Euler angles as ALMN.)
I'd g
One other idea idea:
1. Solvent flattening on the hexagonal crystal
2. use the flattening mask to cut out the density of one molecule,
put in a large P1 cell for calculating structure factors
3. Use the structure factors from the density of the hexagonal crystal
to solve the triclinic crysta
Hi all,
I have a tricky molecular replacement case. One protein in two different
crystal forms: hexagonal with 1 mol/asu, triclinic with 2 mol/asu (based on
packing and self rotation).
No experimental phases are available this far, however, there is a distant
homology model. For the hexagonal crys
