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I am unable to check the geometry of my REFMAC refined model, to
confirm the geometric parameters using the option IDEAlise..
The program hangs out with an error
" IOT Trap ". and produces a large 'core' file..
Also, can anyone help me out that how to make sure of my restraints
such that the GEOMETRIC parameters viz. bond length/angle/torsion/
chiral volumes/planarity etc.. doesn't go bad, with the given MATRIX
In my case, a MATRIX WEIGHT card of 0.80 gave an R (18.8%) and freeR
of (25.8%), whereas the GEOMETRIC parameters shows slightly higher
RMS values in bond angles and PLanarity.. Also, in some stages of
the log file the program cannot be able to calculate RMS deviations of
Estimated bond angles.. I understand that the default weightage is
50% weightage for XRAY and GEOMETRY each...but normally, how one can
make sure of everything? and in what way??
Please help me out, as I am just switching over from XPLOR to CCP4
and facing such problems which is 'new' to me...
So, is it necessary to run 'idealise' after every sets of refinement.?
or, suitable weightage is needed in case of those parameters (by
giving 'tight' or 'loose' restraints?).
Please help me out..
Thanks in advance.
| [4m[5mS.Ravichandran[0m |
| Research Fellow -2 |
| Crystallography & Molecular Biology Division |
| Saha Institute of Nuclear Physics |
| Sector-I, Block-AF, Bidhan Nagar |
| Calcutta - 700 064, INDIA. |
| Email: email@example.com |
| Phone: 091-033-3375345-49 (5 lines) Ext.308 |
| Fax: 091-033-3374637 |