grade tutorial flavopiridol in 3blr

Clashscore, all atoms    	14.34
Clashscore percentile    	   96
Rotamer outliers         	 2.42%
Ramachandran outliers    	 0.18%
Ramachandran favored     	95.56%
CB deviations>0.25Angs   	    0
MolProbity score         	 2.26
MolProbity percentile    	   97
Residues with bad bonds  	 0.00%
Residues with bad angles 	 0.91%
REMARK  40  BAD ROTAMERS            :   2.4%   12/495    (TARGET  0-1%)
REMARK  40  RAMACHANDRAN OUTLIERS   :   0.2%    1/541    (TARGET  0.2%)
REMARK  40  RAMACHANDRAN FAVORED    :  95.6%  517/541    (TARGET 98.0%)

Calculate an initial autobuster map.

mkdir grade-tutorial
cd grade-tutorial
tar xf 3blr_tutorial.tgz
cd 3blr_tutorial

1. Calculate an initial autobuster map

refine -p 3blr/3blr.pdb -m 3blr/3blr.mtz -M MapOnly -d 1-MapOnly.dir > 1-MapOnly.log &
time grade_PDB_ligand CPB >& grade_PDB_ligand.CPB.log &

2. while the refinement is running, use mogul to look at the ligand geometry in 3blr.

grep CPB 3blr/3blr.pdb > 3blr-CPB.pdb

then load the ligand into mogul. Ask it about the rings.


You might also like to ask mogul's opinion on CPB.grade_PDB_ligand.cif

3. Produce (or download) an omit-map

refine -p 3blr-dry-omit.pdb -m 3blr/3blr.mtz -d dry-omit -L | tee dry-omit.lis

where the -L option runs BUSTER in ligand-chasing mode.

4a. Try to fit into the omit map using coot's default ligand generator

4b. Try to fit into the omit map using the GRADE dictionary

5a. Can autobuster tidy up the molecule entirely by itself?

refine -p 3blr/3blr.pdb -m 3blr/3blr.mtz -d no-dictionary

(or download no-dict.tgz and unpack it)

5b. Can autobuster tidy up the molecule if you give a GRADE dictionary?

refine -p 3blr/3blr.pdb -m 3blr/3blr.mtz -d grade-dict -l CPB.grade_PDB_ligand.cif | tee grade-dict.lis

(or download grade-dict.tgz and unpack it)