[ccp4bb] How to manually dock the rigid molecule into the active site
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)
Re: [ccp4bb] How to manually dock the rigid molecule into the active site
On Thu, 2011-12-08 at 17:49 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote: 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, Isn't that what difference density map is for? Usually one simply generates the ligand model by using prodrg and/or sketcher (which would give you a monomer description) and then tries to manually dock it into the density in coot. Some automation is available (e.g. coot can search for a ligand in the difference map throughout the cell), but I believe it does not substitute for the manual inspection (and, imho, neither is such complete replacement possible or even desirable). Things appear to be tricky in your case - at 1.25A a well ordered ligand should produce clearly interpretable density. What you are describing sounds like either disordered ligand or indeed solvent molecules, or the mix of the two (the worst-case scenario). Ultimately, it is up to you to interpret the density, but be careful to curb your imagination. You may be able to get a better advice if you post the density snapshots. Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs