Dear all, I am currently refining a structure using PHENIX 1.5-3 and have encountered some problems with "exploding residues". I have attached a image (small PNG file) highlighting the problem. Has anyone had a similar experience? Or know the solution to the problem? Change weighting in favour of geometry ? Many thanks, Tony Oliver . The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Tony, are things exploding right out of phenix when viewed in another program or when you do a real-space refinement in let's say coot? A likely culprit is probably a mismatch between the monomer definitions and your atom names. Try to narrow it down to the residues/ligands which are exploding, some of them looked OK in your picture, may be you have a non-standard aminoacid present? Then check the atom names and residue names against the monomer definitions. The monomer file location can be queried with phenix.where_mon_lib_list_cif. Cheers, Carsten
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Antony Oliver Sent: Tuesday, October 06, 2009 6:03 AM To: PHENIX user mailing list Subject: [phenixbb] PHENIX 1.5 and exploding residues
Dear all,
I am currently refining a structure using PHENIX 1.5-3 and have encountered some problems with "exploding residues". I have attached a image (small PNG file) highlighting the problem. Has anyone had a similar experience? Or know the solution to the problem? Change weighting in favour of geometry ?
Many thanks,
Tony Oliver
.
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Dear all, Making sure that the individual sites refinement was switched on (i.e. the tick box checked in the Refinement settings window) solved the problem. A slightly embarrassing error on my part I am afraid. The new GUI is taking a little while to get used to - but I am really appreciating the many new features! With regards, Tony. On 6 Oct 2009, at 12:50, Schubert, Carsten [PRDUS] wrote:
Tony,
are things exploding right out of phenix when viewed in another program or when you do a real-space refinement in let's say coot? A likely culprit is probably a mismatch between the monomer definitions and your atom names. Try to narrow it down to the residues/ligands which are exploding, some of them looked OK in your picture, may be you have a non-standard aminoacid present? Then check the atom names and residue names against the monomer definitions. The monomer file location can be queried with phenix.where_mon_lib_list_cif.
Cheers,
Carsten
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Hi I have downloaded new 1.5.2 version and running the refinement using gui and got the following error message, any help could be appreciated. File "/home/vk/pgm/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line 493, in refinement_machine monitor=monitors.monitor_xray) File "/home/vk/pgm/phenix-1.5-2/cctbx_project/mmtbx/refinement/tardy.py", line 168, in run =params.omit_bonds_with_slack_greater_than)) File "/home/vk/pgm/phenix-1.5-2/cctbx_project/cctbx/geometry_restraints/manager.py", line 108, in reduce_for_tardy edge_list=tardy_tree.cluster_manager.loop_edges) File "/home/vk/pgm/phenix-1.5-2/cctbx_project/scitbx/graph/utils.py", line 4, in construct_edge_sets assert i < j
participants (4)
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Antony Oliver -
r n -
Ralf W. Grosse-Kunstleve -
Schubert, Carsten [PRDUS]