[phenixbb] Transfer FreeR and FreeR test set flag value

Matthew Chu linghonmatthew at gmail.com
Sun Sep 6 22:19:38 PDT 2015

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.

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 <pafonine at lbl.gov> 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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