[phenixbb] red blobs (Andrea Smith)

[Kay Diederichs]

Hi Andrea,

Yes the mask optimisation worked. Just not with the desired outcome...

Thanks, Kay

15.03.2024 22:17:14 Andrea Smith <andrea.smith at uochb.cas.cz>:

> Hi Kay,
> 
> I checked the log files and yes, it seems that it did the optimization:
> 
> |-Mask optimization: start----------------------------------------------------|
> | Solvent (probe) radius= 1.10 Shrink truncation radius= 0.90                 |
> | all data:                         500 lowest resolution reflections:        |
> | r_work= 0.1640 r_free= 0.1843     r_work= 0.5012                            |
> |-----------------------------------------------------------------------------|
> 
> r_solv=  0.00 r_shrink=  0.00 r_work=0.1971 r_free=0.2188 r_work_low=0.5809
> r_solv=  0.10 r_shrink=  0.00 r_work=0.1912 r_free=0.2126 r_work_low=0.5665
> r_solv=  0.20 r_shrink=  0.00 r_work=0.1846 r_free=0.2054 r_work_low=0.5571
> r_solv=  0.30 r_shrink=  0.00 r_work=0.1780 r_free=0.1985 r_work_low=0.5402
> ...
> 
> Best,
> Andrea
> 
> 
> 
> On Friday, March 15, 2024 09:01 CET, Kay Diederichs <kay.diederichs at uni-konstanz.de> wrote:
>  
>> Hi Andrea,
>> 
>> hmm, did phenix.refine actually use optimize_mask=true ?
>> 
>> If you compare the logfiles of phenix.refine (for the default run with
>> opimize_mask=false, and the new run with optimize_mask=true)
>> side-by-side with xxdiff or vimdiff (yes this needs to be run from a
>> command-line) then there should be a difference.
>> 
>> Making peace with the red blobs is somewhat unsatisfactory from a
>> technical viewpoint, but probably not relevant from a biological one.
>> 
>> I'd guess that the authors of
>> https://journals.iucr.org/a/issues/2024/02/00/pl5035/index.html would be
>> interested to look at your case ...
>> 
>> Best wishes,
>> Kay
>> 
>> 
>> Am 15.03.24 um 08:27 schrieb Andrea Smith:
>>> Hi Kay,
>>>
>>> I tried the mask optimization and there is no change in how the final
>>> map looks like.
>>>
>>> Should I just make peace with it?
>>>
>>> Best,
>>> Andrea
>>>
>>> On Thursday, March 14, 2024 23:11 CET, Kay Diederichs
>>> <kay.diederichs at uni-konstanz.de> wrote:
>>>> Hi Andrea,
>>>>
>>>> in your case, phenix.refine seems to fill bulk solvent into volumes that
>>>> are not actually filled by solvent.
>>>> It might help to optimize the mask, see
>>>> https://phenix-online.org/documentation/reference/refinement.html#bulk-solvent-correction-and-anisotropic-scaling
>>>> "6. Mask parameters".
>>>>
>>>> Best,
>>>> Kay
>>>> --
>>>> Kay Diederichs http://strucbio.biologie.uni-konstanz.de
>>>> email: Kay.Diederichs at uni-konstanz.de Tel +49 7531 88 4049
>>>> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
>>>>
>>>> This e-mail is digitally signed. If your e-mail client does not have the
>>>> necessary capabilities, just ignore the attached signature "smime.p7s".
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>> Unsubscribe: phenixbb-leave at phenix-online.org
>> 
>> -- 
>> Kay Diederichs http://strucbio.biologie.uni-konstanz.de
>> email: Kay.Diederichs at uni-konstanz.de Tel +49 7531 88 4049
>> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
>> 
>> This e-mail is digitally signed. If your e-mail client does not have the
>> necessary capabilities, just ignore the attached signature "smime.p7s".
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20240315/67b5c77e/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 6410 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20240315/67b5c77e/attachment.p7s>