Dear All, I have a protein crystal co-crystallized with a rigid molecule (solved by small-molecule X-ray method). The color of that crystal is orange (native is colorless) after 2d cocrystallization experiment. Then I collected synchrotron data with a resolution at 1.25 Ang. I can solve it by MR. After I re-build slightly the protein and add some known ions/water, i found there are +ve connected blobs in the known active site of that protein. At first I suspect they are water/ion/EDO but many of them are partially connected within C-C/C-O distances (1.4-1.6 Ang) and in some part, i may imagine some broken six-membered ring, that are presumably found in that rigid molecule.
How can I "dock" or "confirm" that rigid molecule using CCP4 software or COOT smartly? I tried to look at all density regions bit by bit, but the density for the protein atoms always interfere with my vision. Is it possible to mask out the density of protein atoms, leaving the residue density of interest for the rest atoms (maybe the rigid molecule)? many thanks in advance. stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
