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Hi Jiri,

Open both pdb files in Coot.
Calculate -> SSM superpose (or LSQ, depending on what works in your case to position the peptide correctly)
Extensions -> Modelling -> Copy Fragment
Calculate -> Merge Molecules
File -> Save Coordinates
Done.

I don't know why your way didn't work ("does not work" is not enough information), maybe chain/residue ID conflict or you messed up the file format, but using Coot is a lot easier anyway.

HTH,

Julia

On 28/04/16 11:04, chemocev marker wrote:
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Hi
I am trying to take the peptide-ligand from 1 x-ray structure into the other x-ray structure. What I did is, I superimpose both structures and save the ligand as a PDB file and copy the text coordinates and paste it into the other X-ray structure, but it does not work. I know it can work but I don't know how to do that. CCP4MG program does not allow me to save the selected atom of 2 different PDB structure as one PDB file. If someone have any idea how it can be done.

best

Jiri



-- 
Dr. Julia Griese
Postdoctoral Researcher
Stockholm Center for Biomembrane Research
Department of Biochemistry and Biophysics
Stockholm University
106 91 Stockholm
Sweden

phone: +46-(0)8-163 246
email: [log in to unmask]