[phenixbb] PHENIX 1.5 and exploding residues

Schubert, Carsten [PRDUS] CSCHUBER at its.jnj.com
Tue Oct 6 04:50:59 PDT 2009


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. 



> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] 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.

More information about the phenixbb mailing list