Re: [ccp4bb] mol rep help needed

[xaravich ivan]

HI Dave,
Have you tried PHASER. I think you might get all the four molecules in auto
mode. PHASER does a great job and it should be already installed along with
your ccp4i.

Ivan


On Fri, Oct 1, 2010 at 8:40 AM, David Roberts drobe...@depauw.edu wrote:

 Hi all,

 I'm relatively new to using CCP4 (I've done most of my crystallography
 using x-plor, phases, etc...).  But, I like ccp4, and so I'm using it in
 concert with amore (which I know is part of the ccp4i build now) for
 molecular replacement.

 I have a protein that I'm working on with data collected from Argonne.
  There are many forms, and I have several of these forms collected (metal
 bound, apo, mutants, etc...).  I have a solution for a wild-type form, and
 am presently working on solving a mutant form.  For molecular replacement, I
 used the wild type structure (obviously).  It's a homodimer, so I tried
 using both the monomer and the dimer form of the protein (it's possible that
 the mutant is conformationally different from the wild type, so it's not a
 clear-cut problem).

 Furthermore, they both crystallize in the same space group (P212121), but
 unit cells are different (I don't have the exact numbers now, but the
 general idea is the wild type is 30/60/120, while the mutant is 60/70/120).
  As a result, the wild type has 2 monomers per asu while the mutant has 4 (I
 think).

 When I look at results from mol rep (ccp4i, auto-molrep routine), I get 4
 molecules per asu with the monomer as a search.  2 of the molecules I think
 are right (map is good - they form a good dimer, etc...), while I think 2
 are incorrect (the dimer overlaps, and it just doesn't look good).

 My question - finally - how can I run automolrep with one dimer fixed,
 looking for the location of the other 2 monomers (so basically I want to fix
 a dimer as part of my solution, and then search for the other 2 molecules in
 the asu).  I know it's probably simple and possible, but it's not a world I
 am very familiar with (I seriously have just done MIR structures, they are
 easy for me, I have had very little work with mol rep).  Could I do this
 with Amore as well (so fix 2 molecules and then look for an additional 2
 using amore).

 Thanks for the help.  Have a great week-end

 Dave

Re: [ccp4bb] .cv to .mtz conversion

[Ezra's gmail]

 On 9/28/2010 10:41 AM, Jeremiah Farelli wrote:

We recently had this problem in our lab.

No matter what we tried, we could not get convert2mtz (or any other program) to 
work properly.  We were probably doing something wrong with the fortran?

Depending on how far along you are, you can try using phenix.refine.  Just 
input your model and the .cv file and phenix will export a new .cv file with 
Free-R flags intact.

If you aren't to the model building stage yet, this won't work however.
Use the program sftools - sorry no GUI... It can handle CNS format - and 
will convert the test set flag conversion

from CNS (TEST=1) to CCP4 (=0)

Ezra

[ccp4bb] R factor R free struck

[Jack Russel]

Hi all, 
I have collected  a data at 2.9 Å and the solved the structure using phaser . 
the space group comes to be P2 21 21. There are 4 molecules in Assymetric unit 
and an octamer is generated according to the symmetry. But after repeated 
rounds of rigid body refinement with REFMAC5 and model building with coot  the 
R factor had been struck at 40% and R free at 50%.  
So my first question is whether my solution after phaser is correct. And if it 
is how can i lower the  R factor and Rfree. 
The second question is it possible to have such a large difference between R 
factor and R free.
Thanks in advance