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RE: [ccp4bb]: stucture factor calculation
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Dear Dr. Ibrahim
I had same experiece as you (PDB code 1IRU). Some residues converge in
disallowed region in CNS refinement.
Are these residues of your structure in hydrophobic environment ? I think
there is possibility that such residues are appereaed in disallowed regions.
Is it my misunderstanding ?
You can fix residues or atoms in CNS refinement (anneal.inp ), for example
atom_fix=(residue 240 and segid A), but I think it is not neccesary to do
so.
Best regards.
Masaki UNNO
Institute of Multidisciplinary Research for Advanced Materials (IMRAM)
2-1-1, Katahira, Aobaku, Sendai, 980-8577
JAPAN
tel +81-22-217-5117
fax +81-22-217-5118
> -----Original Message-----
> From: owner-ccp4bb@dl.ac.uk [mailto:owner-ccp4bb@dl.ac.uk]On
> Behalf Of syed ibrahim
> Sent: Thursday, April 24, 2003 10:32 AM
> To: ccp4
> Subject: [ccp4bb]: stucture factor calculation
>
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> Dear All,
> Hope u r fine. I am analysing the ramachandran plot
> for my structure. Some of the main cahin and side
> chains residues appearing in the disallowed region. I
> adjusted the phi, psi, chi1 and chi2 values using
> electron density. Then I refined the structure (in
> both Refmac5 and CNS - Rfactor does affected in CNS)
> and checked the ramchandran plot, the residues which i
> moved coming back to the same disallowed region. what
> can i do for?
> Is there anyway to calculate only structure factor by
> refinement for the (phi,psi, chi values adjusted)
> coordinates, to check whether it affects the R-factor?
> (so that i can use the adjusted coordinates without
> doing further refinement as such) i dont know how to
> do it?
> Pls help me. Thankz in advance.
>
> syed
>
>
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