Dealing with malformed ligand geometries in phenix.refine
Hi all I've got 3.0A data and I'm ending up with distorted ligand geometry in phenix.refine. The model is complete and fitting the ligand is the final step (refined with individual_sites and individual_sites_real_space as suggested by an earlier posting). I've tried with a wxc_scale of 0.001 and it still looks wonky (tetrahedral C's not being so, etc). My cif is coming from phenix's internal db. Any suggestions? F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Francis
Can you give me more details and perhaps send me, directly, the inputs
and outputs.
Nigel
NB. Any files sent to me will be held in strictest confidence.
On Fri, Aug 26, 2011 at 8:03 AM, Francis E Reyes
Hi all
I've got 3.0A data and I'm ending up with distorted ligand geometry in phenix.refine. The model is complete and fitting the ligand is the final step (refined with individual_sites and individual_sites_real_space as suggested by an earlier posting). I've tried with a wxc_scale of 0.001 and it still looks wonky (tetrahedral C's not being so, etc).
My cif is coming from phenix's internal db.
Any suggestions?
F
--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov
Hi Francis, You might have to open the cif file and change bond angles and restrains where you think the molecule is distorted. Shya On Fri, Aug 26, 2011 at 11:03 AM, Francis E Reyes < [email protected]> wrote:
Hi all
I've got 3.0A data and I'm ending up with distorted ligand geometry in phenix.refine. The model is complete and fitting the ligand is the final step (refined with individual_sites and individual_sites_real_space as suggested by an earlier posting). I've tried with a wxc_scale of 0.001 and it still looks wonky (tetrahedral C's not being so, etc).
My cif is coming from phenix's internal db.
Any suggestions?
F
--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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Francis E Reyes -
Nigel Moriarty -
Shya Biswas