No subject

Mon Jul 25 12:19:07 PDT 2016

From: Billy Poon
Sent: Wednesday, November 16, 2016 10:02 PM
To: R. D. Oeffner
Cc: Taimin Yang; PHENIX user mailing list
Subject: Re: [phenixbb] Why can't I use in cctbx to compilephe=

Hi Taimin,

Also, you need to accept the licensing terms for Phenix before you can down=
load it ( You have t=
o use the email address from your academic institution.

You will then get a password which will allow you to download Phenix. We ha=
ve precompiled packages or you can download the source and compile Phenix y=

Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909

On Wed, Nov 16, 2016 at 12:39 PM, R. D. Oeffner <rdo20 at> wrote:
I don't think building Phenix with bootstrap is yet possible using only ano=
nymous access to all the necessary repositories. Many repositories require =
authentication. However, it is possible to rebuild the Phenix C++ libraries=
 in an existing Phenix installation.



Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
Wellcome Trust/MRC Building
Hills Road
Cambridge CB2 0XY
tel: +44(0)1223 763234
mobile: +44(0)7712 887162
-----Original Message----- From: Taimin Yang
Sent: Wednesday, November 16, 2016 8:20 PM
To: phenixbb at
Subject: [phenixbb] Why can't I use in cctbx to compile phenix=

Dear Professor,

My name is Taimin Yang and I am a PhD student in Stockholm University. I tr=
y to compile my own phenix using but here is the error informa=

root at Linux-main:/usr/local/crystallography_software/phenix# python bootstra= --builder=3Dphenix --with-python=3D/usr/local/anaconda2/bin/python hot=
 update build
Performing actions: hot update build
Traceback (most recent call last):
=C2=A0File "", line 2034, in <module>
=C2=A0 =C2=A0run()
=C2=A0File "", line 2029, in run
=C2=A0 =C2=A0enable_shared=3Doptions.enable_shared,
=C2=A0File "", line 926, in __init__
=C2=A0 =C2=A0map(self.add_module, self.get_codebases())
=C2=A0File "", line 1051, in add_module
=C2=A0 =C2=A0action =3D MODULES.get_module(module)().get_url(
=C2=A0File "", line 553, in get_url
=C2=A0 =C2=A0raise Exception('No anonymous access method defined for module=
: %s. Try with --%s'%(self.module, e.args[0]))
Exception: No anonymous access method defined for module: chem_data. Try wi=
th --cciuser

What should I do to compile my own phenix?
Thank you very much.

Best regards,

phenixbb mailing list
phenixbb at
Unsubscribe: phenixbb-leave at
phenixbb mailing list
phenixbb at
Unsubscribe: phenixbb-leave at

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<html xmlns:o=3D"urn:schemas-microsoft-com:office:office" xmlns:w=3D"urn:sc=
hemas-microsoft-com:office:word" xmlns:m=3D"
fice/2004/12/omml" xmlns=3D""><head><meta ht=
tp-equiv=3DContent-Type content=3D"text/html; charset=3Dutf-8"><meta name=
=3DGenerator content=3D"Microsoft Word 15 (filtered medium)"><style><!--
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--></style></head><body lang=3DEN-US link=3Dblue vlink=3D"#954F72"><div cla=
ss=3DWordSection1><p class=3DMsoNormal>Hello all,</p><p class=3DMsoNormal>T=
hanks for your reply. I checked the content in the It seems t=
hat there is no anonymous method for phenix and xfel and cciuser option is =
only for developers. It seems that the only way is enter the password and d=
ownload the source and compile from the downloaded source. </p><p class=3DM=
soNormal><o:p>&nbsp;</o:p></p><p class=3DMsoNormal>Cheers,</p><p class=3DMs=
oNormal>Taimin<o:p></o:p></p><p class=3DMsoNormal><o:p>&nbsp;</o:p></p><p c=
lass=3DMsoNormal>From Windows 10 Email Application</p><p class=3DMsoNormal>=
<span style=3D'font-size:12.0pt;font-family:"Times New Roman",serif'><o:p>&=
nbsp;</o:p></span></p><div style=3D'mso-element:para-border-div;border:none=
;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=3DMsoNo=
rmal style=3D'border:none;padding:0in'><b>From: </b><a href=3D"mailto:bkpoo=
n at">Billy Poon</a><br><b>Sent: </b>Wednesday, November 16, 2016 10:0=
2 PM<br><b>To: </b><a href=3D"mailto:rdo20 at">R. D. Oeffner</a><br>=
<b>Cc: </b><a href=3D"mailto:taiminyang at">Taimin Yang</a>; <a href=
=3D"mailto:phenixbb at">PHENIX user mailing list</a><br><b>S=
ubject: </b>Re: [phenixbb] Why can't I use in cctbx to compile=
phenix?</p></div><p class=3DMsoNormal><span style=3D'font-size:12.0pt;font-=
family:"Times New Roman",serif'><o:p>&nbsp;</o:p></span></p><div><p class=
=3DMsoNormal><span style=3D'font-size:12.0pt;font-family:"Times New Roman",=
serif'>Hi Taimin,</span><span style=3D'font-size:12.0pt;font-family:"Times =
New Roman",serif'><o:p></o:p></span></p><div><p class=3DMsoNormal><span sty=
le=3D'font-size:12.0pt;font-family:"Times New Roman",serif'><o:p>&nbsp;</o:=
p></span></p></div><div><p class=3DMsoNormal><span style=3D'font-size:12.0p=
t;font-family:"Times New Roman",serif'>Also, you need to accept the licensi=
ng terms for Phenix before you can download it (<a href=3D"http://www.pheni=">
request/index.cgi</a>). You have to use the email address from your academi=
c institution.<o:p></o:p></span></p></div><div><p class=3DMsoNormal><span s=
tyle=3D'font-size:12.0pt;font-family:"Times New Roman",serif'><o:p>&nbsp;</=
o:p></span></p></div><div><p class=3DMsoNormal><span style=3D'font-size:12.=
0pt;font-family:"Times New Roman",serif'>You will then get a password which=
 will allow you to download Phenix. We have precompiled packages or you can=
 download the source and compile Phenix yourself.<o:p></o:p></span></p></di=
v></div><div><p class=3DMsoNormal><span style=3D'font-size:12.0pt;font-fami=
ly:"Times New Roman",serif'><br clear=3Dall><o:p></o:p></span></p><div><div=
><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=
=3DMsoNormal><span style=3D'font-size:12.0pt;font-family:"Times New Roman",=
serif'>--<o:p></o:p></span></p></div><div><p class=3DMsoNormal><span style=
=3D'font-size:9.5pt;font-family:"Times New Roman",serif'>Billy K. Poon</spa=
n><span style=3D'font-size:12.0pt;font-family:"Times New Roman",serif'><o:p=
></o:p></span></p></div></div><div><p class=3DMsoNormal><span style=3D'font=
-size:12.0pt;font-family:"Times New Roman",serif'>Research Scientist, Molec=
ular Biophysics and Integrated Bioimaging<o:p></o:p></span></p></div><div><=
p class=3DMsoNormal><span style=3D'font-size:12.0pt;font-family:"Times New =
Roman",serif'>Lawrence Berkeley National Laboratory<o:p></o:p></span></p></=
div><div><p class=3DMsoNormal><span style=3D'font-size:12.0pt;font-family:"=
Times New Roman",serif'>1 Cyclotron Road, M/S 33R0345<o:p></o:p></span></p>=
</div><div><p class=3DMsoNormal><span style=3D'font-size:12.0pt;font-family=
:"Times New Roman",serif'>Berkeley, CA 94720<o:p></o:p></span></p></div><di=
v><p class=3DMsoNormal><span style=3D'font-size:12.0pt;font-family:"Times N=
ew Roman",serif'>Tel: (510) 486-5709<o:p></o:p></span></p></div><div><p cla=
ss=3DMsoNormal><span style=3D'font-size:12.0pt;font-family:"Times New Roman=
",serif'>Fax: (510) 486-5909<o:p></o:p></span></p></div><div><p class=3DMso=
Normal><span style=3D'font-size:12.0pt;font-family:"Times New Roman",serif'=
>Web:&nbsp;<a href=3D"" target=3D"_blank">https://=</a><o:p></o:p></span></p></div></div></div></div></div></=
div></div></div></div></div></div></div></div></div><p class=3DMsoNormal><s=
pan style=3D'font-size:12.0pt;font-family:"Times New Roman",serif'><o:p>&nb=
sp;</o:p></span></p><div><p class=3DMsoNormal><span style=3D'font-size:12.0=
pt;font-family:"Times New Roman",serif'>On Wed, Nov 16, 2016 at 12:39 PM, R=
. D. Oeffner &lt;<a href=3D"mailto:rdo20 at" target=3D"_blank">rdo20=</a>&gt; wrote:<o:p></o:p></span></p><blockquote style=3D'border:=
none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:=
4.8pt;margin-right:0in'><p class=3DMsoNormal><span style=3D'font-size:12.0p=
t;font-family:"Times New Roman",serif'>I don't think building Phenix with b=
ootstrap is yet possible using only anonymous access to all the necessary r=
epositories. Many repositories require authentication. However, it is possi=
ble to rebuild the Phenix C++ libraries in an existing Phenix installation.=
<br><br>Regards,<br><br>Rob<br><br>-- <br>Robert Oeffner, Ph.D.<br>Research=
 Associate, The Read Group<br>Department of Haematology,<br>Cambridge Insti=
tute for Medical Research<br>University of Cambridge<br>Cambridge Biomedica=
l Campus<br>Wellcome Trust/MRC Building<br>Hills Road<br>Cambridge CB2 0XY<=
br><br><a href=3D"" =
el: <a href=3D"tel:%2B44%280%291223%20763234" target=3D"_blank">+44(0)1223 =
763234</a><br>mobile: <a href=3D"tel:%2B44%280%297712%20887162" target=3D"_=
blank">+44(0)7712 887162</a><br>-----Original Message----- From: Taimin Yan=
g<br>Sent: Wednesday, November 16, 2016 8:20 PM<br>To: <a href=3D"mailto:ph=
enixbb at" target=3D"_blank">phenixbb at</a><=
br>Subject: [phenixbb] Why can't I use in cctbx to compile phe=
nix?<o:p></o:p></span></p><div><div><p class=3DMsoNormal style=3D'margin-bo=
ttom:12.0pt'><span style=3D'font-size:12.0pt;font-family:"Times New Roman",=
serif'><br><br><br><br>Dear Professor,<br><br><br>My name is Taimin Yang an=
d I am a PhD student in Stockholm University. I try to compile my own pheni=
x using but here is the error information:<br><br><br>root at Lin=
ux-main:/usr/local/crystallography_software/phenix# python --b=
uilder=3Dphenix --with-python=3D/usr/local/anaconda2/bin/python hot update =
build<br>Performing actions: hot update build<br>Traceback (most recent cal=
l last):<br>&nbsp;File &quot;;, line 2034, in &lt;module&g=
t;<br>&nbsp; &nbsp;run()<br>&nbsp;File &quot;;, line 2029,=
 in run<br>&nbsp; &nbsp;enable_shared=3Doptions.enable_shared,<br>&nbsp;Fil=
e &quot;;, line 926, in __init__<br>&nbsp; &nbsp;map(self.=
add_module, self.get_codebases())<br>&nbsp;File &quot;;, l=
ine 1051, in add_module<br>&nbsp; &nbsp;action =3D MODULES.get_module(modul=
e)().get_url(auth=3Dself.get_auth())<br>&nbsp;File &quot;;=
, line 553, in get_url<br>&nbsp; &nbsp;raise Exception('No anonymous access=
 method defined for module: %s. Try with --%s'%(self.module, e.args[0]))<br=
>Exception: No anonymous access method defined for module: chem_data. Try w=
ith --cciuser<br><br>What should I do to compile my own phenix?<br>Thank yo=
u very much.<br><br>Best regards,<br>Taimin<br><br><br><br><br><br><o:p></o=
:p></span></p></div></div><p class=3DMsoNormal><span style=3D'font-size:12.=
0pt;font-family:"Times New Roman",serif'>__________________________________=
_____________<br>phenixbb mailing list<br><a href=3D"mailto:phenixbb at phenix=" target=3D"_blank">phenixbb at</a><br><a href=3D=
"" target=3D"_blank">http=
://</a><br>Unsubscribe: <a href=
=3D"mailto:phenixbb-leave at" target=3D"_blank">phenixbb-lea=
ve at</a> <br>______________________________________________=
_<br>phenixbb mailing list<br><a href=3D"mailto:phenixbb at"=
 target=3D"_blank">phenixbb at</a><br><a href=3D"http://phen=" target=3D"_blank">http://phenix-on=</a><br>Unsubscribe: <a href=3D"mailto:ph=
enixbb-leave at" target=3D"_blank">phenixbb-leave at phenix-onl=</a><o:p></o:p></span></p></blockquote></div></div><p class=3DMsoNor=
mal><span style=3D'font-size:12.0pt;font-family:"Times New Roman",serif'><o=
:p>&nbsp;</o:p></span></p><p class=3DMsoNormal><o:p>&nbsp;</o:p></p></div><=


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