Hi all, I´m trying to refine a dataset which seems to have two different ligands with partial occupancy in the same active site. How do you refine this? When I put them over each other with say 50/50 occupancy Phenix either moves the ligands apart or mashes the two molecules into one strange composite ligand. In Refmac this works without any special settings, it accepts the occupancy distribution between the ligands. Any ideas? Regards, Damian Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: [email protected] phone: 0046 8 524 876 33 fax: 0046 8 736 04 39
Have you tried adding an altloc to the pdb (I believe it's column 18 in the
pdb file format)? If you make one conformer A and the other B then phenix
will know that they don't occupy the same space at the same time and keep
the atoms in their relative locations.
I hope this helps,
Katherine
On Mon, Jan 28, 2013 at 6:54 AM, Damian Niegowski
Hi all,
I´m trying to refine a dataset which seems to have two different ligands with partial occupancy in the same active site. How do you refine this? When I put them over each other with say 50/50 occupancy Phenix either moves the ligands apart or mashes the two molecules into one strange composite ligand. In Refmac this works without any special settings, it accepts the occupancy distribution between the ligands. Any ideas?
Regards,
Damian
Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: [email protected] phone: 0046 8 524 876 33 fax: 0046 8 736 04 39
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Hi Damian, this should work just fine without requiring you doing anything special (even setting input occupancies) as long as the input PDB file is correctly formatted. This is explained in details in phenix.refine manual: http://phenix-online.org/documentation/refinement.htm#anch111 Alternatively you can send me (to my email address, not the entire phenixbb) the PDB file and I will tell what's causing the problem. Pavel On 1/28/13 4:54 AM, Damian Niegowski wrote:
Hi all,
I´m trying to refine a dataset which seems to have two different ligands with partial occupancy in the same active site. How do you refine this? When I put them over each other with say 50/50 occupancy Phenix either moves the ligands apart or mashes the two molecules into one strange composite ligand. In Refmac this works without any special settings, it accepts the occupancy distribution between the ligands. Any ideas?
Regards,
Damian
Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: [email protected] phone: 0046 8 524 876 33 fax: 0046 8 736 04 39
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participants (3)
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Damian Niegowski -
Katherine Sippel -
Pavel Afonine