Hi Todias, it's hard to diagnose this without seeing the files. Could you please send me relevant files so that I can run refinement myself and reproduce the crash? Pavel On 4/20/16 22:40, Bock, Tobias wrote:
Dear colleagues,
I am trying to refine a protein-DNA complex. In this structure, 2 DNA double strands are present with 50% occupancy (or similar occupancy’s) and overlap at certain positions. Phenix.refine crashed due to a nonbonded interaction distance issue. To fix that, I tried to exclude the DNA strands using:
*pdb_interpretation { custom_nonbonded_symmetry_exclusions="chain E" custom_nonbonded_symmetry_exclusions="chain F" }*
Nevertheless, phenix.refine crashed with the same error message. Changing the “*nonbonded_distance_threshold*” works, but results in terrible statistics (since this applies for the complete structure, I guess).
Is there a way to exclude only the DNA strands (in regard to the clash guard) or a similar approach to refine the structure?
Thank you in advance for your help,
Tobias
------------------------------------------------------------------------
Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "*audit* beruf*und*familie" 50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50
Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]