Hi Afshan, in Coot select calculate --> other modeling tools --> find ligands In 0.6.2, there is a message that ligands are limited to 400 atoms or less. Regards, Mitch
-----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Afshan Begum Sent: Wednesday, October 19, 2011 8:04 AM To: [email protected] Subject: Re: [ccp4bb] how can merge two PDB Dear Juergen Many thank for your response yes you have excatly understand my question we have a MR solution of the rest of our protein and just asking how to make my life easier to not built de novo 45-50 residues. so i could not find the option in coot find ligand so, from where i get it? Best Regards AFSHAN ________________________________ From: Afshan Begum <[email protected]> To: "Bosch, Juergen" <[email protected]> Sent: Wednesday, October 19, 2011 4:58 PM Subject: Re: [ccp4bb] how can merge two PDB H.EDU> To: [email protected] Sent: Wednesday, October 19, 2011 4:29 PM Subject: Re: [ccp4bb] how can merge two PDB why don't you read in that chain in Coot and run the find ligand option with flexible ligand turned on and select that 6kDa ligand ? You should also choose Fo-Fc map to fit the ligand to maybe at 2.7 sigma. You might have to split up the ligand into pieces, not sure what the limitations in Coot/Find Ligand are. You already have a MR solution of the rest of your protein right ? So you are just asking how to make your life easier to not built de novo 45-50 residues ? Jürgen On Oct 19, 2011, at 10:00 AM, Ed Pozharski wrote: Why not do the molecular replacement - 6kDa is rather small but it most likely will work On Wed, 2011-10-19 at 06:13 -0700, Afshan Begum wrote: Hello CCP4 user I have collected a data set 2.1 for my complex. Actually after first run of Rafmac i can see the density for my inhibitor but the problem is my inhibitor is 6 KDa and i know the sequence of my inhibitor as well this inhibitor already crystallize with other protein molecule present in PDB data bank so how can i put in to that electron density i mean are there any ways to combine two Pdb in one molecule? I would be thankful for your help Best Regards AFSHAN -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
