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Fri Mar 24 12:28:07 PDT 2017


error because it's not finding the restraints in the restraints libraries
distributed with Phenix. Note all restraints files are shipped with Phenix.
Only the ones that we have checked carefully.

Can you tell me the ligand code?

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
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 Wed, Jun 21, 2017 at 5:47 PM, Joel Tyndall <joel.tyndall at otago.ac.nz>
wrote:

> Hi there,
>
>
>
> Having a few minor issues with my phenix setup on windows 10. I have the
> latest stable build Phenix1.11.1-2575.
>
>
>
> When introducing a new ligand that exists in the monomer library, Pheix
> complains it does not have the geometry restraints (cif file)  - somehow =
it
> is not seeing its own library. How can I set up the cif library as defaul=
t?
>
>
>
> Cheers
>
>
>
> Joel
>
>
>
>
>
> Joel Tyndall | BSc(Hons) PhD
>
> Associate Professor in Medicinal Chemistry
> School of Pharmacy | Te Kura M=C4=81tauraka Wai-whakaora
> University of Otago | Te Whare W=C4=81nanga o Ot=C4=81go
>
> PO Box 56 9054
>
> Dunedin | =C5=8Ctepoti
>
> New Zealand | Aotearoa
>
> Ph: 64 3 479 7293
> Skype: jtyndall
>
> Website | pharmacy.otago.ac.nz
>
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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<div dir=3D"ltr">Joel<div><br></div><div>From your description, you are say=
ing a ligand in your model is causing an error because it&#39;s not finding=
 the restraints in the restraints libraries distributed with Phenix. Note a=
ll restraints files are shipped with Phenix. Only the ones that we have che=
cked carefully.</div><div><br></div><div>Can you tell me the ligand code?</=
div></div><div class=3D"gmail_extra"><br clear=3D"all"><div><div class=3D"g=
mail_signature" data-smartmail=3D"gmail_signature"><div dir=3D"ltr"><div><d=
iv dir=3D"ltr"><div dir=3D"ltr">Cheers<div><br></div><div>Nigel<div><br></d=
iv><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349,=C2=A0Molecular=
 Biophysics and Integrated Bioimaging</div><div>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 : 510-486-5909=C2=A0 =
=C2=A0 =C2=A0=C2=A0 Web=C2=A0 : <a href=3D"http://CCI.LBL.gov" target=3D"_b=
lank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class=3D"gmail_quote">On Wed, Jun 21, 2017 at 5:47 PM, Joel Tyndal=
l <span dir=3D"ltr">&lt;<a href=3D"mailto:joel.tyndall at otago.ac.nz" target=
=3D"_blank">joel.tyndall at otago.ac.nz</a>&gt;</span> wrote:<br><blockquote c=
lass=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;=
padding-left:1ex">





<div lang=3D"EN-NZ" link=3D"#0563C1" vlink=3D"#954F72">
<div class=3D"m_3187711763315200921WordSection1">
<p class=3D"MsoNormal">Hi there,<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">Having a few minor issues with my phenix setup on wi=
ndows 10. I have the latest stable build Phenix1.11.1-2575.<u></u><u></u></=
p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">When introducing a new ligand that exists in the mon=
omer library, Pheix complains it does not have the geometry restraints (cif=
 file)=C2=A0 - somehow it is not seeing its own library. How can I set up t=
he cif library as default?<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">Cheers<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">Joel<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-f=
amily:&quot;Gill Sans MT&quot;,sans-serif;color:#365f91">Joel Tyndall |</sp=
an><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-family:&quot;Gill San=
s MT&quot;,sans-serif;color:#0070c0">
</span><span style=3D"font-size:9.0pt;font-family:&quot;Gill Sans MT&quot;,=
sans-serif;color:#555555">BSc(Hons) PhD</span><span lang=3D"EN-US" style=3D=
"font-size:9.0pt;font-family:&quot;Gill Sans MT&quot;,sans-serif"><br>
<span style=3D"color:#0070c0"><br>
</span><span style=3D"color:#365f91">Associate Professor in Medicinal Chemi=
stry<br>
School of Pharmacy |</span><span style=3D"color:#0070c0"> </span><span styl=
e=3D"color:#595959">Te Kura M</span></span><span style=3D"font-size:9.0pt;c=
olor:#555555">=C4=81</span><span lang=3D"EN-US" style=3D"font-size:9.0pt;fo=
nt-family:&quot;Gill Sans MT&quot;,sans-serif;color:#595959">tauraka
 Wai-whakaora</span><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-fami=
ly:&quot;Gill Sans MT&quot;,sans-serif;color:#0070c0"><br>
</span><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-family:&quot;Gill=
 Sans MT&quot;,sans-serif;color:#365f91">University of Otago |</span><span =
lang=3D"EN-US" style=3D"font-size:9.0pt;font-family:&quot;Gill Sans MT&quot=
;,sans-serif;color:#0070c0">
</span><span style=3D"font-size:9.0pt;font-family:&quot;Gill Sans MT&quot;,=
sans-serif;color:#555555">Te Whare W</span><span style=3D"font-size:9.0pt;c=
olor:#555555">=C4=81</span><span style=3D"font-size:9.0pt;font-family:&quot=
;Gill Sans MT&quot;,sans-serif;color:#555555">nanga
 o Ot</span><span style=3D"font-size:9.0pt;color:#555555">=C4=81</span><spa=
n style=3D"font-size:9.0pt;font-family:&quot;Gill Sans MT&quot;,sans-serif;=
color:#555555">go<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-f=
amily:&quot;Gill Sans MT&quot;,sans-serif;color:#365f91">PO Box=C2=A056 905=
4<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-f=
amily:&quot;Gill Sans MT&quot;,sans-serif;color:#365f91">Dunedin |</span><s=
pan lang=3D"EN-US" style=3D"font-size:9.0pt;font-family:&quot;Gill Sans MT&=
quot;,sans-serif;color:#0070c0">
</span><span style=3D"font-size:9.0pt;color:#555555">=C5=8C</span><span sty=
le=3D"font-size:9.0pt;font-family:&quot;Gill Sans MT&quot;,sans-serif;color=
:#555555">tepoti</span><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-f=
amily:&quot;Gill Sans MT&quot;,sans-serif;color:#0070c0"><u></u><u></u></sp=
an></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-f=
amily:&quot;Gill Sans MT&quot;,sans-serif;color:#365f91">New Zealand=C2=A0<=
/span><span style=3D"font-size:9.0pt;font-family:&quot;Gill Sans MT&quot;,s=
ans-serif;color:#365f91">|</span><span style=3D"font-size:9.0pt;font-family=
:&quot;Gill Sans MT&quot;,sans-serif;color:#555555">
 Aotearoa</span><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-family:&=
quot;Gill Sans MT&quot;,sans-serif;color:#0070c0">=C2=A0
</span><span style=3D"font-size:9.0pt;font-family:&quot;Gill Sans MT&quot;,=
sans-serif;color:#0070c0"><u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-f=
amily:&quot;Gill Sans MT&quot;,sans-serif;color:#365f91">Ph: 64 3 479 7293<=
br>
Skype: jtyndall<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-f=
amily:&quot;Gill Sans MT&quot;,sans-serif;color:#365f91">Website
</span><span style=3D"font-size:9.0pt;font-family:&quot;Gill Sans MT&quot;,=
sans-serif;color:#365f91">|</span><span style=3D"font-size:9.0pt;font-famil=
y:&quot;Gill Sans MT&quot;,sans-serif;color:#555555">
<a href=3D"http://pharmacy.otago.ac.nz" target=3D"_blank"><span style=3D"co=
lor:#0563c1">pharmacy.otago.ac.nz</span></a></span><span lang=3D"EN-US" sty=
le=3D"font-size:9.0pt;font-family:&quot;Gill Sans MT&quot;,sans-serif;color=
:#0070c0">=C2=A0</span><span lang=3D"EN-US" style=3D"font-size:9.0pt;font-f=
amily:&quot;Gill Sans MT&quot;,sans-serif;color:#365f91"><u></u><u></u></sp=
an></p>
<p class=3D"MsoNormal"><span lang=3D"EN-US" style=3D"font-size:10.0pt;font-=
family:&quot;Gill Sans MT&quot;,sans-serif;color:#0070c0"><u></u>=C2=A0<u><=
/u></span></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
</div>
</div>

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