Fire up a recent version of coot and go through every step on the
validation menu - but most im protantly the Ramachandran plot, the
density fit analysis, unmodelled blobs, rotamer probabilities and
finally and most importantly difference maps peaks.
Then run molprobity (via the web site if you don't have it installed)
and read the things-to-do-list into coot.
Kevin
AA wrote:
Hello everyone,
Please forgive my ignorance about the field of crystallography. I have
recently started to process the diffraction data of a protein with a ligand
attached to it. we have the structure of this protein already known and also
known with different ligands. the way I did it is as flllows:
I process the images in mosflm and then integrate them using scala inccp4i.
After that I do molecular replacement by phaser. and finally refine it using
refmac. Am I doing it correctly?
Now since I am completely new to all this, I have not much clue about the
outputs I get and if they are correct or not. What are the key things you
should be looking at in the log files generated by phaser and refmac? Till
now I get overall R factor of 29.32 and Rfree of 34.94. Is this fine or can
I improve it more? If yes then what do I do to further improve the
statistics? What should be the RmsBond and Rms Angle values? Since the
structure is already solved a number of times with different ligands, what
final values should i aim for to get a decent density maps in which I can
fit my ligand structure.
Sorry for being so naive. Any sort of information or papers or links would
be very helpful.
Thanks a lot.
AA
