There is also an option under MAP Utilities in the GUI which helps you.
It is essentially what happens under COOT
You need to know the transformation from Chain A to B, and chain A to C
- you can get the Alpha Beta Gamma and Tx Ty Tz values from a coordinate
utility - overlap structures
Then you need to make a mask from the chain A coordinates.
And then you can output the averaged map in CCP4 format..
As James Irving says - COOT is easier! It does all these steps internally..
And CCP4 people - shouldnt the GUI be extended to do the same?
Eleanor
James Irving wrote:
Dear Shankar,
There's a great function in coot that will generate averaged maps on
the fly; I would say this is the easiest way. Load your molecule and
maps into the program and select Calculate -> NCS Maps.
Also the 'NCS Phased Refinement' script (you will find the front-end
to this in the 'Refinement' sub-menu of ccp4i) will iteratively run
Refmac and DM, and will output an averaged 2fo-fc map. In the past I
have found the x-ray term weighting default used by this program
doesn't perform very well with low resolution structures, however
(having tried it with 2.7 - 3.0A datasets).
Good luck,
James
On 15/08/06, *Shankar Prasad Kanaujia* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
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Dear ccp4 users and xray-crystallographers,
I am a new user of ccp4 and just started working on a protein
which has
three monomers in the asymmetric unit. I want to calculate average
map.
It would be great help if somebody tell me how to go about it.
Space group: C222(1)
Cell values: a=77.013, b=130.658, c=131.686, alpha=beta=gamma=90.
Thanking you in advance.
With Best Regards,
Shankar Prasad Kanaujia
Ph.D Student
Bioinformatics Center, Department of SERC
IISc, Bangalore - 12
Mobile: 9845631581
--
Dr. James Irving
NH&MRC C.J. Martin Fellow
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Oxford University
Roosevelt Drive
Headington,
Oxford OX3 7BN
UK
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