Hi Pavel, Thanks for your reply. I figured out that my colleague didn't specify 1 or 0 and so the reflection file editor used 1 for test. I then used Aimless to transfer the FreeR set from his mtz and I think the new test flags are now 0, as I didn't specify it in phenix.refine and it automatically guessed the test flags are 0 (as shown in the log file). As you said, if 1 and 0 are flipped, phenix will take 0 as test just going by the fraction if the test flags are actually 0. But in this case, when I specify (or force) the test flags as 1, it seems that phenix.refine cannot flip it back to 0 automatically....or it will not be able to flip as I tell (or force) 1 are the test flags? I guess what confused me before was that when I used Aimless to transfer the test flags, I didn't know whether Aimless knew that they were 1 or 0. If Aimless knew the test flags were 1, I was not sure whether Aimless would change them to 0 or the test flags would still be 1 (as I was going to use phenix.refine for refinement and I thought I had to specify it). My understanding is that Aimless (which uses CAD to transfer the test flags) doesn't actually care 1 or 0 but only the column labels (which is FreeR_flag), but since Aimless is part of ccp4, the "new test flags" I have now becomes 0 and so phenix.refine recognizes the test flags as 0. Please correct me if I am wrong. Thanks, Matt P.S. Since it's a mix of CCP4 and Phenix question, I have also forwarded this to the CCP4bb. On Sun, Sep 6, 2015 at 8:40 PM, Pavel Afonine wrote:

Hi Matt,

If asked to generate new flags, phenix.refine will use 1 for test and 0 for work. However, it uses a smart flags interpretation machinery that can guess the right choice, if possible (for example, if 1 and 0 are flipped, it will take 0 as test just going by the fraction). If you have flags from 0 to 19 it will figure it is ccp4 format and use 0 as test by default. On top of that the user always can tell what flags to use as test flag. Also, the log file will always tell what was chosen as test and work flags.

Bottom line is: for phenix.refine does not care what value is used for free/work flag as long as phenix.refine can guess it automatically or the user explicitly specifies it.

Reflection file editor from Phenix GUI can transfer the flags.

I suggest you just try to do what you want and let us know should you encounter any problem.

Pavel

On 9/4/15 13:24, Matthew Chu wrote:

Dear All,

I am trying to refine my model against a higher resolution dataset. My colleage's old-low resolution dataset was processed in HKL/scalepack and the FreeR was assigned by Phenix.reflection file editor, which I assume the test set was marked as "1". Now I got a new-higher resolution dataset, and plan to process it in XDS/Aimless. I want to transfer the FreeR set from his old mtz and also use his low res model for the new refinement. My question is, when I transfer the FreeR set from his old mtz with flag value as "1" in Aimless, is the flag value now "1" or "0" in the new mtz output by Aimless? Can Aimless recognize the FreeR flag from the old mtz which are marked as "1"?

I also read an old post from Nat Echols in 2011: "For Phenix, 1 is test, 0 is work, but you could reverse this and it will still figure out what to do automatically", so does it mean it doesn't matter if the FreeR is "1" or "0" in the mtz from Aimless, if I use phenix.refine for my new dataset, Phenix can figure out which is the correct FreeR value?

It's a mix of CCP4 and Phenix question, so I have crossed posted it in the CCP4bb as well.

Many thanks, Matt

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