Hi Emmanuel,
I've never tried something quite as complex as a pseudopeptide but if you can build your lingand in the coot ligand builder coot will generate a cif file for you. Previously I have built my ligand, used real space refinement to get it into position, merged the protein and ligand and saved the model. Your coot may be different but my cif file always ended up in wincoot/new/examples/coot-ccp4/prodrg-out.cif. Make sure you rename this cif and move it to a new directory as I believe coot will just save over this when you make your next ligand.
Good luck,
Sam
Sam Horrell BSc (Hons)
Research Student
School of Life Sciences
Life Sciences Building
University of Liverpool
Crown Street
Liverpool L69 7ZB
United Kingdom
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From: CCP4 bulletin board [[log in to unmask]] on behalf of ΕΜΜΑΝΟΥΗΛ ΣΑΡΕΙΔΑΚΗΣ [[log in to unmask]]
Sent: 20 January 2015 15:32
To: [log in to unmask]
Subject: [ccp4bb] fitting peptide with non-standard and standard amino acids
Dear All,
I wonder if you could help me with this. I am trying to do some regularisation/real space refinement of a ligand with Coot. The ligand is a pseudopeptide with two non-standard aminoacids, followed by several standard ones. I assume that to do this correctly, I would need a cif file that specifies the two non-standard aa's plus the links between these two and between second and third (which is a standard one). When trying to generate a cif with a program such as eLBOW (using a pdb as the starting reference), each of the non-standard aa's gets a cif of its own, and the third, standard one, is ignored, meaning that there are no specified links between the first two (non-standard) and even less between second (non-standard) and third (standard). Coot of course keeps each aa as it should be, but breaks up the peptide chain completely.
Could you direct me how to built a cif that includes such bond specifications, starting from a reference pdb or otherwise? Is there an altogether different way of getting Coot to do what I want?
Many thanks,
Emmanuel
Dr. Emmanuel Saridakis
Researcher C
Institute of Nanoscience and Nanotechnology
National Centre for Scientific Research "DEMOKRITOS"
15310 Athens
GREECE
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