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 <afshan...@yahoo.com> To: "Bosch, Juergen" <jubo...@jhsph.edu> Sent: Wednesday, October 19, 2011 4:58 PM Subject: Re: [ccp4bb] how can merge two PDB H.EDU> To: CCP4BB@JISCMAIL.AC.UK 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/
