Hi Nat, - the file with TLS selections produced by TLSMD server is just a piece of parameter file. I usually take that file and grow it by adding some other parameters, such as main.number_of_macro_cycles, etc... - I don't think it's a good idea to rely on file extensions... When you run phenix.refine from the command line you can give it a file with parameters and the name or extension of that file can be any. Why it's different in the GUI? - I think a prompt for a parameter file should be right next to the PDB, data and CIF file fields in "Input data" section of phenix.refine GUI, since it's pretty often that users have their own set of custom parameters. Pavel. On 1/11/2009 9:19 AM, Nathaniel Echols wrote:

...

Is there a way to load the TLS groups, generated so kindly by TLSMD in old phenix format, into the new gui? It would save a lot of typing.

The file extension must be .eff or .param, otherwise the GUI won't be able to figure out what kind of file it is. Once this is done, there are three ways to load it:

1. Make it a command-line argument when you launch phenix.refine_gui. (the goal is for the GUI to take all the same arguments as the command- line-only version - not sure if that made it into this installer, but it'll definitely load any named files that it recognizes.)

2. Place the file in phenix/defaults/ in whatever you picked as the project directory, and it'll be loaded on startup. The next installer will simplify this procedure.

3. Load it from the file menu. This is more problematic, but should be fine for tls groups. There isn't a space for this in the "input files" section of the window because these files are handled differently than pdb files etc., and they're difficult to undo. (this is just a quirk of the way configuration is handled in the background.)

I didn't realize that tlsmd would produce a file for phenix; I'll add a button to that dialog window for loading these files unmodified.

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What happens if you process in P64 - ie. the extra 2-folds come from some kind of pseudo symmetry. On Feb 2, 2009, at 12:47 PM, Maia Cherney wrote:

Hi all, I have a low resolution dataset in space group P6422 that has good chi squares, normal mosaicity (0.6), but abnormal Rsym. Even in the third bin Rsym is 0.5. The overall Rsym is 0.3. Can a merohedral twinning be the cause? Can I use xtriage for this space group to analyze the data? What else can I try?

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Hi Maia, yes, you can find it in .log file. Look for something like this: | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | Note that phenix.refine prints this table before and after refinement. The PDB file header also contains this information. Pavel. On 2/3/2009 2:40 PM, Maia Cherney wrote:

Hi all, is there somewhere in phenix.refine output files Figure of Merit number?

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