No subject
Fri Jul 31 09:19:06 PDT 2015
1.9-1692. I redid the command with 1.10-2155 and the restraints were
better. Clearly, the program has improved in the 13 months that 1.9 was
released and you should stop using it in preference for 1.10.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Mon, Oct 5, 2015 at 3:31 AM, Smith Liu <smith_liu123 at 163.com> wrote:
> Dear Pavel,
>
> My cif file was for ATP, which was rather easily got by eLBOW as for the
> Phenix contains it in its library. Attached is the ATP.cif file I used.
>
> In addition, I have run another 10 cycles of
> simulated_annealing+minimization_global, and the clash score was still 120
> (too high).
>
> Recently I fond for both the 1.9-1692 and 1.10.2155 version of
> phenix.real_spacea_refine, I got rather high clash score (higher than 20).
> In addition I found (recently?) the phenix.real_space_refine output PDB
> clash score was different from the Ramachandran clash score value. Is an
> possibility my Windows versions of phenix have something wrong?
>
> I am looking forward to getting your further comment.
>
> Smith
>
>
>
>
>
> At 2015-10-05 14:12:39, "Pavel Afonine" <pafonine at lbl.gov> wrote:
>
> Most likely wrong ligand CIF file.
> Pavel
>
> On 10/4/15 21:51, Smith Liu wrote:
>
> Dear All,
>
> I have tried a phenix.real_space_refine with a ligand cif and without
> ligand cif (both with ligand PDB in the whole protein-ligand PDB for
> refine), I find with ligand cif in the input can lead to significant
> increase of the clash score for the refined PDB.
>
> Will you please make comment on whether the clash score incensement by
> adding cif in the input was a general phenomenon, or only specific to my
> situation, and how to solve it?
>
> Best regards.
>
>
> Smith
>
>
>
>
>
> At 2015-10-05 02:14:28, "Pavel Afonine" <pafonine at lbl.gov> <pafonine at lbl.gov> wrote:
> >Yes.
> >Pavel
> >
> >On 10/4/15 02:19, Smith Lee wrote:
> >> Dear All,
> >>
> >> Does phenix.refine can process some ligands without the process by eLBOW, for example ATP, ADP,etc?
> >>
> >>
> >> Smith
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >> Unsubscribe: phenixbb-leave at phenix-online.org
> >
> >_______________________________________________
> >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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--001a11c14caa01985105215e3f2b
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable
<div dir=3D"ltr">Smith<div><br></div><div>From the comments in the file, yo=
u generated the ATP restraints with 1.9-1692. I redid the command with 1.10=
-2155 and the restraints were better. Clearly, the program has improved in =
the 13 months that 1.9 was released and you should stop using it in prefere=
nce for 1.10.</div></div><div class=3D"gmail_extra"><br clear=3D"all"><div>=
<div class=3D"gmail_signature"><div dir=3D"ltr"><div><div dir=3D"ltr">Cheer=
s<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriar=
ty<br>Building 33R0349, Physical Biosciences Division<br>Lawrence Berkeley =
National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709=C2=
=A0 =C2=A0=C2=A0 Email : NWMoriarty at LBL.gov<br>Fax=C2=A0=C2=A0 : 510-486-59=
09=C2=A0 =C2=A0 =C2=A0=C2=A0 Web=C2=A0 : <a href=3D"http://CCI.LBL.gov" tar=
get=3D"_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div>
<br><div class=3D"gmail_quote">On Mon, Oct 5, 2015 at 3:31 AM, Smith Liu <s=
pan dir=3D"ltr"><<a href=3D"mailto:smith_liu123 at 163.com" target=3D"_blan=
k">smith_liu123 at 163.com</a>></span> wrote:<br><blockquote class=3D"gmail=
_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:=
1ex"><div style=3D"line-height:1.7;color:#000000;font-size:14px;font-family=
:Arial"><div>Dear Pavel,</div><div><br></div><div>My cif file was for ATP, =
which was rather easily got by eLBOW as for the Phenix contains it in its l=
ibrary. Attached is the ATP.cif file I used.</div><div><br></div><div>In ad=
dition, I have run another 10 cycles of simulated_annealing+minimization_gl=
obal, and the clash score was still 120 (too high).</div><div><br></div><di=
v>Recently I fond for both the 1.9-1692 and 1.10.2155 version of phenix.rea=
l_spacea_refine, I got rather high clash score (higher than 20). In additio=
n I found (recently?) the phenix.real_space_refine output PDB clash score w=
as different from the Ramachandran clash score value. Is an possibility my =
Windows versions of =C2=A0phenix have something wrong?</div><div><br></div>=
<div>I am looking forward to getting your further comment.</div><span class=
=3D"HOEnZb"><font color=3D"#888888"><div><br></div><div>Smith<br><br><br><b=
r><br></div></font></span><div><div class=3D"h5"><div></div><div></div><div=
><br></div>At 2015-10-05 14:12:39, "Pavel Afonine" <<a href=3D=
"mailto:pafonine at lbl.gov" target=3D"_blank">pafonine at lbl.gov</a>> wrote:=
<br> <blockquote style=3D"margin:0px 0px 0px 0.8ex;padding-left:1ex;border-=
left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid">
=20
=20
=20
=20
Most likely wrong ligand CIF file.<br>
Pavel<br>
<br>
<div>On 10/4/15 21:51, Smith Liu wrote:<br>
</div>
<blockquote type=3D"cite">
<div style=3D"color:rgb(0,0,0);line-height:1.7;font-family:Arial;font=
-size:14px">
<div>Dear All,</div>
<div><br>
</div>
<div>I have tried a phenix.real_space_refine with a ligand cif
and without ligand cif (both with ligand PDB in the whole
protein-ligand PDB for refine), I find with ligand cif in the
input can lead to significant increase of the clash score for
the refined PDB.</div>
<div><br>
</div>
<div>Will you please make comment on whether the clash score
incensement by adding cif in the input was a general
phenomenon, or only specific to my situation, and how to solve
it?</div>
<div><br>
</div>
<div>Best regards.</div>
<div><br>
</div>
<div><br>
</div>
<div>Smith<br>
<br>
<br>
<br>
<br>
</div>
<div><br>
</div>
<pre>At 2015-10-05 02:14:28, "Pavel Afonine" <a href=3D"m=
ailto:pafonine at lbl.gov" target=3D"_blank"><pafonine at lbl.gov></a> wrot=
e:
>Yes.
>Pavel
>
>On 10/4/15 02:19, Smith Lee wrote:
>> Dear All,
>>
>> Does phenix.refine can process some ligands without the process by=
eLBOW, for example ATP, ADP,etc?
>>
>>
>> Smith
>> _______________________________________________
>> phenixbb mailing list
>> <a href=3D"mailto:phenixbb at phenix-online.org" target=3D"_blank">ph=
enixbb at phenix-online.org</a>
>> <a href=3D"http://phenix-online.org/mailman/listinfo/phenixbb" tar=
get=3D"_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a>
>> Unsubscribe: <a href=3D"mailto:phenixbb-leave at phenix-online.org" t=
arget=3D"_blank">phenixbb-leave at phenix-online.org</a>
>
>_______________________________________________
>phenixbb mailing list
><a href=3D"mailto:phenixbb at phenix-online.org" target=3D"_blank">phenixb=
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</pre>
</div>
<br>
<br>
<span title=3D"neteasefooter">
<p>=C2=A0</p>
</span>
</blockquote>
<br>
=20
</blockquote></div></div></div><br><br><span title=3D"neteasefooter"><p>=C2=
=A0</p></span><br>_______________________________________________<br>
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