[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

OMIT problems

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Hello all,

	We have started using our CCP4 package (v 3.5) very recently.
Our protein has a solvent exposed loop section for which we need to 
trace the chain (a 4 residue stretch), as the map in those regions are
highly disordered. So, we intend to calculate an OMIT map. The structure
has been refined to a R-value of 19.30% with free_R 27.50% whose data was
collected at 90 degree K (cryo structure). The disorder can easily be
seen in the map still at low temperature. We have found that the B-values
in those four residues to be around 90 A square or above.

	We have incorporated all residues in our start pdb (including 
these biased portion) in our pdb and ran OMIT, by the following steps.

step1:-    take fob file and run f2mtz (for getting mtz)
step2:-    take pdb file and run pdbset (for getting the SCALE and CRYST card)
step3:-    now run sfall with inputs (obtained from 1&2). and get Fc and Phase.
step4:-    run cad (CCP4 convention) to bring the molecule in correct assy.unit.
step 5:-   take cad output mtz and run OMIT. (grid was chosen auto!).

	OMIT ran succesfully, giving an output ".map" file. 
     Anything wrong in this procedure?? Can anybody tell me?

	We are using FRODO Tom Marsillies Graphics program to do manual 
intervention in the refinement. 

Does the CCP4 package has any program to convert CCP4 map to FRODO map.?

	Moreover, we also ran "mapmask" in order to do a map extension of
5 A.
	Dr. Bart Hazes (after we enquired) gave a suggestion of using SFTOOLS
for converting maps (through MAPIN and MAPOUT options) for FRODO/O. But there
is still a problem that it was not yet in use.. and moreover, there was a
mismatch with the box size. (error is... box size is chosen outside the box
limit). So, how to rectify this problem also?

	So, may I ask the people to help me out in calculating the OMIT map.
Also, any suggestions regarding the detailed steps for doing the OMIT map will
be more appreciated and welcomed. 

My advance thanks to people who give valuable suggestions.



         			   S. RAVICHANDRAN

        __              Crystallography & Molecular Biology Division
       / /\             Saha Institute of Nuclear Physics           
      / /  \            Sector I, Block-AF, Bidhan Nagar
     / / /\ \           Calcutta- 700 064, INDIA.
    / / /\ \ \                                                             
   / /_/__\ \ \         E-MAIL:- ravi@cmb2.saha.ernet.in   
  /________\ \ \                 ravichu@hotmail.com      

	                FAX:-  (91)(033)-337-4637  
	                TEL:-  033-337 0659 (Ext. 306/308)
	                       033-337 4632 (Hostel)
_/                                                                          _/
_/                                                                          _/
_/                        BUT FEW GOOD HUMAN BEINGS.                        _/
_/                                                                          _/
_/                                                                          _/