Hello, you need to provide selections for TLS groups in order to do TLS refinement in PHENIX. Note that you do not need to provide any values to TLS matrices, but only selections for TLS groups. TLSMD server can also create TLS selections suitable for phenix.refine (thanks Ethan Merritt; http://skuld.bmsc.washington.edu/~tlsmd/) Example: phenix.refine model.pdb data.mtz strategy=individual_adp+individual_sites+tls tls_selections ordered_solvent=true Comments: - the above example will do three macro-cycles of refinement of individual coordinates, individual B-factors and TLS; - it will automatically update water (add/remove/refine); - the file "tls_selections" contains the selections for TLS groups. It looks like this: refinement.refine.adp { tls = chain A and (resid 2:135 or resid 410:525) tls = chain A and (resid 136:194 or resid 375:409) tls = chain A and (resid 195:374) tls = chain B and (resid 2:135 or resid 410:525) tls = chain B and (resid 136:194 or resid 375:409) tls = chain B and (resid 195:374) } For more examples, including atom selection syntax, look phenix.refine Manual: http://phenix-online.org/ http://phenix-online.org/documentation/refinement.htm or please do not hesitate to ask us any questions you may have. Pavel. On 7/2/2008 3:04 PM, nihmayerm wrote:
Hi,
I've just started to learn how to use PHENIX. I'd like to continue a refinement started with REFMAC for which I already have refined TLS parameters initially generated using the WUSTL TLSMD server.
Can I use the .tls file as input to PHENIX or do I have to redefine the TLS groups and tensors.
Thanks _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb