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Re: [ccp4bb] Putting ligand in the protein structure |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Putting ligand in the protein structure From: Scott Pegan pegan {- at -} UIC {- dot -} EDU Date: 2008-10-01 The best why that I have put inhibitors in is by using the sketcher program in CCP4. Its a little unwieldy at first but if you get the hang of it, it provides pdb's and library files that can be directly inputed into refmac and Coot. The Coot ligand find function does a pretty good job of initially placing inhibitors in density. The only thing to be careful of is that sketcher tends to label hydrogens in a problematic way for large ligands. It labels the hydrogen based on the carbon number that it is attached too. Problems tend to occur if the hydrogens get three digit labels. Refmac won't necessarily recognize these causing problems with the cif file. If this problem occurs re-label the hydrogens to two digit numbers. Unless your using a ligand that requires more than 100 hydrogens. Then you will have to build it a different way. Scott On Wed, Oct 1, 2008 at 3:38 PM, Anastassis Perrakis > On Sep 30, 2008, at 9:56, Anshul Awasthi wrote: > > Hi all the crystallographers, >> >> I am trying to solve a structure of a protein with some inhibitor. I want >> to >> know how I can put in my inhibitor in the density map of the data i got. I >> can see some density in the active site where the inhibitor should be. I >> generated the topoly file of the inhibitor (in both pdba nd refmac5 top >> formats) from the Dundee PRODRG server. Now do i need to incorporate the >> structure of the inhibitor in ccp4 or can i do in coot?? I am not sure of >> how to do it. >> > > As one of many alternatives you can use "ARP/wARP Ligand Fit" from the > CCP4I > (provided you downloaded and installed the current version of ARP/wARP) > and then input your protein structure, the observed data, and the PDB of > your ligand. > > The script will calculate the mFo-DFc map, find the most likely site for > the ligand, > and then fir the ligand there, and refine it in real space. > > Tassos > > >> >> ANy sugegstion will be very valuable for me. >> > > -- Scott D. Pegan, Ph.D. Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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