Hi: I have a 2.2Å structure containing a ligand in at least 2 alternate conformations. When the structure is refined via XYZ refinement + occupancy using phenix.refine, both ligand conformers are kicked out of the electron density. Is there a way to prevent this? Thank you, -Jerome Sent from my iPhone
On Thu, May 31, 2012 at 11:55 AM, Jerome Nwachukwu
I have a 2.2Å structure containing a ligand in at least 2 alternate conformations. When the structure is refined via XYZ refinement + occupancy using phenix.refine, both ligand conformers are kicked out of the electron density. Is there a way to prevent this?
You have to set the altloc identifier for the two conformations - it's the column next to the residue ID, i.e.: ATOM 5085 N AALA 270 19.772 -6.267 40.250 0.75 5.17 ATOM 5090 N BALA 270 19.733 -6.282 40.242 0.25 5.04 -Nat
Jerome, you may also want to check the ligand's cif file to make sure the library geometry is what you actually expect. Pavel On 5/31/12 11:55 AM, Jerome Nwachukwu wrote:
Hi: I have a 2.2Å structure containing a ligand in at least 2 alternate conformations. When the structure is refined via XYZ refinement + occupancy using phenix.refine, both ligand conformers are kicked out of the electron density. Is there a way to prevent this? Thank you, -Jerome
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Thank you so much, Adding the altloc identifier appears to fix the problem That seems to fix the problem. Best, -Jerome On Jun 1, 2012, at 5:09 AM, Pavel Afonine wrote:
Jerome,
you may also want to check the ligand's cif file to make sure the library geometry is what you actually expect.
Pavel
On 5/31/12 11:55 AM, Jerome Nwachukwu wrote:
Hi: I have a 2.2Å structure containing a ligand in at least 2 alternate conformations. When the structure is refined via XYZ refinement + occupancy using phenix.refine, both ligand conformers are kicked out of the electron density. Is there a way to prevent this? Thank you, -Jerome
Sent from my iPhone _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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participants (3)
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Jerome Nwachukwu -
Nathaniel Echols -
Pavel Afonine