[phenixbb] Various problems with phenix.refine

[Francis E Reyes]

With regard to optimize_wxc and optimize_wxu I asked the same question  
a while ago. Here's Pavel's response.
On Aug 7, 2009, at 1:26 PM, Pavel Afonine wrote:

> HI Francis,
>
> currently these values are not preserved - they are re-determined at
> each macro-cycle.
>
> The reason for this is that they can be very different from run to  
> run,
> however I think I will make it possible to preserve them in the .def
> file - it's on my list now, so will be available in the future.
>
> The fact that the values that you picked up from "scale" did not work
> may well reflect what I said above: the values may change (sometimes)
> significantly between the macro-cycles.
>
> Pavel.
>
>
> On 8/7/09 8:56 AM, Francis E Reyes wrote:
>> Hi all
>>
>> I went through the time to optimize_wxc and optimize_wxu to help pull
>> out some density for ligands (i.e. all sequence assigned residues are
>> built). However, it would be nice if the resulting .def was updated
>> with the optimized wxc and wxu. Where are those values? I didn't  
>> think
>> for wxc it was scale=XX in the following lines..
>>
>>
>>       r_work= 0.2167 r_free= 0.2525 bonds= 0.003 angles=  0.70
>> scale=  7.00
>>       r_work= 0.2097 r_free= 0.2502 bonds= 0.004 angles=  0.96
>> scale=  8.00
>>       ... etc
>>
>> Refining with the scale= value that phenix ultimately chose didn't
>> work form me (resulted in awful geometry and high r/rfree).
>>
>>
>> Thanks
>>
>> FR
>>
>>
>> ---------------------------------------------
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>>
>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>
>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>>
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---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

On Sep 23, 2009, at 1:04 PM, Joe Krahn wrote:

> The optimize_wxc and optimize_wxu features are useful, but it is
> difficult to use the result to define an improved fixed scale on
> subsequent rounds, without having to optimize every time. It is not
> obvious whether the scale written in the log represents the new
> wxc_scale, or if it is a multiplier versus the current wxc_scale. The
> log also truncates to 2 decimal places. In my case, I only get one
> significant digit from scale=0.05. I propose that the optimizations
> write something like "Optimal wxc_scale = 0.533".

---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D