No subject
Sun Jun 4 19:40:30 PDT 2023
e end that the mosaic model is implemented in phenix. However, I don't =
know where. I went through the parameters in GUI and didn't find anythi=
ng that seemed to fit the description.
Could you please explain what setting I need to use in the refinement?
Thank you, best,
Andrea
On Friday, March 15, 2024 16:16 CET, Pavel Afonine <pafonine at lbl.gov> w=
rote:
=C2=A0Hi All,
The explanation of the reason for these blobs and the solution is both
detailed in depth in this paper:
https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909
Quick facts are:
- These blobs are artifacts of bulk-solvent modeling.
- You can efficiently deal with them in Phenix.
- In some cases (which I witnessed myself), it is important to deal wit=
h
them for map improvements elsewhere (for example, in regions of
interest, such as ligands).
Let me know if you have any questions!
All the best,
Pavel
On 3/15/24 07:39, Mitchell D. Miller wrote:
> Hi Andrea,
>
> =C2=A0 You can also put a few zero occupancy atoms in the negative
> density to force phenix.refine to exclude the region
> from the bulk solvent mask.
>
> (You may also need to set
> refinement.mask.ignore=5Fzero=5Foccupancy=5Fatoms =3D False
> so that the zero occupancy atoms are included in the mask)
>
> Regards,
> Mitch
>
>
>
> Quoting Kay Diederichs <kay.diederichs at uni-konstanz.de>:
>
>> Hi Andrea,
>>
>> hmm, did phenix.refine actually use optimize=5Fmask=3Dtrue ?
>>
>> If you compare the logfiles of phenix.refine (for the default run
>> with opimize=5Fmask=3Dfalse, and the new run with optimize=5Fmask=3D=
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 woul=
d
>> 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 volume=
s
>>>> 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, Universit=C3=A4t 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".
>>>> =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F
>>>> 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=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Tel +49 7531 88 4049
>> Fachbereich Biologie, Universit=C3=A4t Konstanz, Box M647, D-78457 K=
onstanz
>>
>> This e-mail is digitally signed. If your e-mail client does not have=
the
>> necessary capabilities, just ignore the attached signature "smime.p7=
s".
>
>
>
>
> =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
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Content-Type: text/html; charset=utf-8
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<html>Hi,<br /><br />I went through the paper quickly during the day th=
inking I will have a thorough look at home only to realize I don't have=
acces to it.<br /><br />From the quick look it seemed that my biologic=
al background will not be enough to understand all of it, but I re=
member that it said at the end that the mosaic model is implemented in =
phenix. However, I don't know where. I went through the parameters in G=
UI and didn't find anything that seemed to fit the description.<br /><b=
r />Could you please explain what setting I need to use in the refineme=
nt?<br /><br />Thank you, best,<br />Andrea<br /><br />On Friday, March=
15, 2024 16:16 CET, Pavel Afonine <pafonine at lbl.gov> wrote:<br /=
> <blockquote type=3D"cite" cite=3D"8053d5d7-dde8-464c-b0c1-29dff2=
06b194 at lbl.gov">Hi All,<br /><br />The explanation of the reason for th=
ese blobs and the solution is both<br />detailed in depth in this paper=
:<br /><br />https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909<b=
r /><br />Quick facts are:<br /><br />- These blobs are artifacts of bu=
lk-solvent modeling.<br />- You can efficiently deal with them in Pheni=
x.<br />- In some cases (which I witnessed myself), it is important to =
deal with<br />them for map improvements elsewhere (for example, in reg=
ions of<br />interest, such as ligands).<br /><br />Let me know if you =
have any questions!<br /><br />All the best,<br />Pavel<br /><br /><br =
/>On 3/15/24 07:39, Mitchell D. Miller wrote:<br />> Hi Andrea,<br /=
>><br />> You can also put a few zero occupancy atoms in t=
he negative<br />> density to force phenix.refine to exclude the reg=
ion<br />> from the bulk solvent mask.<br />><br />> (You may =
also need to set<br />> refinement.mask.ignore=5Fzero=5Foccupancy=5F=
atoms =3D False<br />> so that the zero occupancy atoms are included=
in the mask)<br />><br />> Regards,<br />> Mitch<br />><br=
/>><br />><br />> Quoting Kay Diederichs <kay.diederichs at u=
ni-konstanz.de>:<br />><br />>> Hi Andrea,<br />>><br=
/>>> hmm, did phenix.refine actually use optimize=5Fmask=3Dtrue =
?<br />>><br />>> If you compare the logfiles of phenix.ref=
ine (for the default run<br />>> with opimize=5Fmask=3Dfalse, and=
the new run with optimize=5Fmask=3Dtrue)<br />>> side-by-side wi=
th xxdiff or vimdiff (yes this needs to be run from a<br />>> com=
mand-line) then there should be a difference.<br />>><br />>&g=
t; Making peace with the red blobs is somewhat unsatisfactory from a<br=
/>>> technical viewpoint, but probably not relevant from a biolo=
gical one.<br />>><br />>> I'd guess that the authors of<br=
/>>> https://journals.iucr.org/a/issues/2024/02/00/pl5035/index.=
html would<br />>> be interested to look at your case ...<br />&g=
t;><br />>> Best wishes,<br />>> Kay<br />>><br />=
>><br />>> Am 15.03.24 um 08:27 schrieb Andrea Smith:<br />=
>>> Hi Kay,<br />>>><br />>>> I tried the ma=
sk optimization and there is no change in how the<br />>>> fin=
al map looks like.<br />>>><br />>>> Should I just ma=
ke peace with it?<br />>>><br />>>> Best,<br />>&g=
t;> Andrea<br />>>><br />>>> On Thursday, March 14=
, 2024 23:11 CET, Kay Diederichs<br />>>> <kay.diederichs at u=
ni-konstanz.de> wrote:<br />>>>> Hi Andrea,<br />>>=
;>><br />>>>> in your case, phenix.refine seems to fi=
ll bulk solvent into volumes<br />>>>> that<br />>>&g=
t;> are not actually filled by solvent.<br />>>>> It mig=
ht help to optimize the mask, see<br />>>>> https://phenix-=
online.org/documentation/reference/refinement.html#bulk-solvent-correct=
ion-and-anisotropic-scaling<br />>>>><br />>>>>=
"6. Mask parameters".<br />>>>><br />>>>> Best=
,<br />>>>> Kay<br />>>>> --<br />>>>&=
gt; Kay Diederichs http://strucbio.biologie.uni-konstanz.de<br />>&g=
t;>> email: Kay.Diederichs at uni-konstanz.de Tel +49 7531 88 4049<b=
r />>>>> Fachbereich Biologie, Universit=C3=A4t Konstanz, B=
ox M647, D-78457 Konstanz<br />>>>><br />>>>> T=
his e-mail is digitally signed. If your e-mail client does not<br />>=
;>>> have the<br />>>>> necessary capabilities, ju=
st ignore the attached signature<br />>>>> "smime.p7s".<br =
/>>>>> =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F<br />>>>> phenixbb mailing list<br />>&g=
t;>> phenixbb at phenix-online.org<br />>>>> http://phen=
ix-online.org/mailman/listinfo/phenixbb<br />>>>> Unsubscri=
be: phenixbb-leave at phenix-online.org<br />>><br />>> --<br =
/>>> Kay Diederichs http://strucbio.biologie.uni-konstanz.de<br /=
>>> email: Kay.Diederichs at uni-konstanz.de =
Tel +49 7531 88 4049<b=
r />>> Fachbereich Biologie, Universit=C3=A4t Konstanz, Box M647,=
D-78457 Konstanz<br />>><br />>> This e-mail is digitally =
signed. If your e-mail client does not have the<br />>> necessary=
capabilities, just ignore the attached signature "smime.p7s".<br />>=
;<br />><br />><br />><br />> =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F<br />> phenixbb mailing list=
<br />> phenixbb at phenix-online.org<br />> http://phenix-online.or=
g/mailman/listinfo/phenixbb<br />> Unsubscribe: phenixbb-leave at pheni=
x-online.org</blockquote></html>
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