Re: [ccp4bb] Putting ligand in the protein structure
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 <[EMAIL PROTECTED]>wrote: > 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
Re: [ccp4bb] Putting ligand in the protein structure
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.
Re: [ccp4bb] Putting ligand in the protein structure
Yes: There are details in the coot manual 1) Get a dictionary for your ligand from PRODRG or somewhere. - you have obviously done this.. 2) CHECK IT IS CORRECT!!! Right chirality, planar groups, etc.. 3) Import dictionary into coot, and a set of coordinates. 4) Import 2mFo-Dfc and mFo-Dfc maps ( auto mtz from REFMAC will do this) 5) Hit find ligand. 6) Real space refine it - you might need to do some brutal gradding and shoving of bits.. Eleanor George Kontopidis wrote: You need protein structure, a different e. density map (1Fo-1Fc) and your ligand structure. Then from COOT menu select Other Modelling Tools and click Find Ligand. You can also move manually the ligand into the density map. George -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Anshul Awasthi Sent: Tuesday, September 30, 2008 10:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Putting ligand in the protein structure 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. ANy sugegstion will be very valuable for me. No virus found in this incoming message. Checked by AVG - http://www.avg.com Version: 8.0.173 / Virus Database: 270.7.5/1697 - Release Date: 29/9/2008 7:25 ìì
Re: [ccp4bb] Putting ligand in the protein structure
You need protein structure, a different e. density map (1Fo-1Fc) and your ligand structure. Then from COOT menu select Other Modelling Tools and click Find Ligand. You can also move manually the ligand into the density map. George -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Anshul Awasthi Sent: Tuesday, September 30, 2008 10:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Putting ligand in the protein structure 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. ANy sugegstion will be very valuable for me. No virus found in this incoming message. Checked by AVG - http://www.avg.com Version: 8.0.173 / Virus Database: 270.7.5/1697 - Release Date: 29/9/2008 7:25 ìì
[ccp4bb] Putting ligand in the protein structure
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. ANy sugegstion will be very valuable for me.
