Hi Katya, - you can easily do it using phenix.refine GUI (please use the latest version of PHENIX for this). - if you are using the command line version, here is the example that illustrates how you can do it... Essentially, all you need is to specify the tls groups and add tls to the strategy (put "*" in front of "tls"). Here is how: The command: phenix.refine model.pdb data.hkl params.txt where the file "params.txt" contains the following lines: refinement { refine { strategy = *individual_sites rigid_body *individual_adp group_adp *tls \ *occupancies group_anomalous adp { tls = chain A and resseq 123:987 tls = chain B or chain C tls = chain D and resseq 0:100 } } } will refine three TLS groups defined with the above selections in addition to the default refinement of individual coordinates for all atoms, individual isotropic B-factors for all atoms (including water) and occupancies for atoms in alternative conformations of those having partial occupancies in input PDB file. You can create "params.txt" by running this command: phenix.refine --show-defaults=all > params.txt and then remove all the keywords that you are not going to modify and leave only those that you will be changing. You can obtain the selections for TLS groups by running your model through TLSMD server which creates ready-to-use TLS selections for phenix.refine: http://skuld.bmsc.washington.edu/~tlsmd/ Please let me know if you have any questions! Pavel. On 2/20/2009 2:09 PM, Katya Heldwein wrote:

Hi,

I would like to use TLS refinement for protein (I have selected TLS groups) and individual isotropic refinement for water. How can I specify this in phenix.refine?

Thanks,

Katya