[phenixbb] using TLS files from Refmac

Pavel Afonine PAfonine at lbl.gov
Wed Jul 2 15:17:04 PDT 2008


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; 


phenix.refine model.pdb data.mtz 
strategy=individual_adp+individual_sites+tls tls_selections 


- 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 

or please do not hesitate to ask us any questions you may have.


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
> phenixbb at phenix-online.org
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