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
------=_=-_OpenGroupware_org_NGMime-6276-1711632249.300445-14------
Content-Type: text/html; charset=utf-8
Content-Transfer-Encoding: quoted-printable
Content-Length: 6528
<html>Hi all,<br /><br />can anyone please tell me how to use the mosai=
c model? I went through the phenix documentation and didn't find anythi=
ng about how to use it.<br /><br />Thank you,<br />Andrea<br /><br /><b=
r /><br />On Friday, March 15, 2024 22:14 CET, "Andrea Smith" <andre=
a.smith at uochb.cas.cz> wrote:<br /> <blockquote type=3D"cite" ci=
te=3D"3841-65f4ba80-353-2259ac80 at 55057052">Hi,<br /><br />I went throug=
h the paper quickly during the day thinking 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 biological background will not be enough t=
o understand all of it, but I remember that it said at the end tha=
t the mosaic model is implemented in phenix. However, I don't know wher=
e. I went through the parameters in GUI and didn't find anything that s=
eemed to fit the description.<br /><br />Could you please explain what =
setting I need to use in the refinement?<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" c=
ite=3D"8053d5d7-dde8-464c-b0c1-29dff206b194 at lbl.gov">Hi All,<br /><br /=
>The explanation of the reason for these 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<br /><br />Quick facts are:<br /><b=
r />- These blobs are artifacts of bulk-solvent modeling.<br />- You ca=
n efficiently deal with them in Phenix.<br />- In some cases (which I w=
itnessed myself), it is important to deal with<br />them for map improv=
ements elsewhere (for example, in regions of<br />interest, such as lig=
ands).<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. Mi=
ller wrote:<br />> Hi Andrea,<br />><br />> You can als=
o put a few zero occupancy atoms in the negative<br />> density to f=
orce phenix.refine to exclude the region<br />> from the bulk solven=
t mask.<br />><br />> (You may also need to set<br />> refinem=
ent.mask.ignore=5Fzero=5Foccupancy=5Fatoms =3D False<br />> so that =
the zero occupancy atoms are included in the mask)<br />><br />> =
Regards,<br />> Mitch<br />><br />><br />><br />> Quotin=
g Kay Diederichs <kay.diederichs at uni-konstanz.de>:<br />><br /=
>>> Hi Andrea,<br />>><br />>> hmm, did phenix.refine=
actually use optimize=5Fmask=3Dtrue ?<br />>><br />>> If y=
ou compare the logfiles of phenix.refine (for the default run<br />>=
> with opimize=5Fmask=3Dfalse, and the new run with optimize=5Fmask=3D=
true)<br />>> side-by-side with xxdiff or vimdiff (yes this needs=
to be run from a<br />>> command-line) then there should be a di=
fference.<br />>><br />>> Making peace with the red blobs i=
s somewhat unsatisfactory from a<br />>> technical viewpoint, but=
probably not relevant from a biological one.<br />>><br />>&g=
t; I'd guess that the authors of<br />>> https://journals.iucr.or=
g/a/issues/2024/02/00/pl5035/index.html would<br />>> be interest=
ed to look at your case ...<br />>><br />>> Best wishes,<br=
/>>> Kay<br />>><br />>><br />>> Am 15.03.24 u=
m 08:27 schrieb Andrea Smith:<br />>>> Hi Kay,<br />>>&g=
t;<br />>>> I tried the mask optimization and there is no chan=
ge in how the<br />>>> final map looks like.<br />>>>=
<br />>>> Should I just make peace with it?<br />>>><=
br />>>> Best,<br />>>> Andrea<br />>>><br /=
>>>> On Thursday, March 14, 2024 23:11 CET, Kay Diederichs<br =
/>>>> <kay.diederichs at uni-konstanz.de> wrote:<br />>&=
gt;>> Hi Andrea,<br />>>>><br />>>>> in y=
our case, phenix.refine seems to fill bulk solvent into volumes<br />&g=
t;>>> that<br />>>>> are not actually filled by so=
lvent.<br />>>>> It might help to optimize the mask, see<br=
/>>>>> https://phenix-online.org/documentation/reference/r=
efinement.html#bulk-solvent-correction-and-anisotropic-scaling<br />>=
;>>><br />>>>> "6. Mask parameters".<br />>>=
>><br />>>>> Best,<br />>>>> Kay<br />>=
;>>> --<br />>>>> Kay Diederichs http://strucbio.b=
iologie.uni-konstanz.de<br />>>>> email: Kay.Diederichs at uni=
-konstanz.de Tel +49 7531 88 4049<br />>>>> Fachbereich Bio=
logie, Universit=C3=A4t Konstanz, Box M647, D-78457 Konstanz<br />>&=
gt;>><br />>>>> This e-mail is digitally signed. If y=
our e-mail client does not<br />>>>> have the<br />>>=
>> necessary capabilities, just 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 />>>>&g=
t; phenixbb mailing list<br />>>>> phenixbb at phenix-online.o=
rg<br />>>>> http://phenix-online.org/mailman/listinfo/phen=
ixbb<br />>>>> Unsubscribe: phenixbb-leave at phenix-online.or=
g<br />>><br />>> --<br />>> Kay Diederichs http://st=
rucbio.biologie.uni-konstanz.de<br />>> email: Kay.Diederichs at uni=
-konstanz.de  =
; Tel +49 7531 88 4049<br />>> 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 atta=
ched 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.or=
g<br />> http://phenix-online.org/mailman/listinfo/phenixbb<br />>=
; Unsubscribe: phenixbb-leave at phenix-online.org</blockquote></blockquot=
e></html>
------=_=-_OpenGroupware_org_NGMime-6276-1711632249.300445-14--------
More information about the phenixbb
mailing list