No subject
Mon Dec 16 02:28:28 PST 2019
phenix.version
This should tell you your version of phenix, and it will also show that
phenix is present in this terminal window.
Now type:
phenix_regression.list auto_sharpen
This will then list a command that you can run on your computer to test
auto_sharpen. On mine it looks like:
libtbx.python
"/net/anaconda/raid1/terwill/misc/PHENIX/modules/phenix_regression/segment_and_split_map/tst_auto_sharpen.py"
Copy and paste whatever is printed there and make sure that it runs and
ends with "OK". In particular, one of the tests will be:
"Testing auto_sharpen with model and remove_aniso"
This will be testing your problem case.
Let me know (off-list) if this test fails and I will try to help you debug
the problem.
All the best,
Tom T
On Wed, Aug 19, 2020 at 1:28 AM sangeeta niranjan <sangeeta.19apr at gmail.com>
wrote:
> Hello,
> I am trying to use Auto Sharpen feature of a CyoEM refined map into Phenix
> but the job is getting failed every time with the following error:
> Missing the model file:
> followed with model file name and location.
>
> Although it was working before but now it's showing the same error for all
> the auto sharpen runs including Models/PDBs.
>
>
> Thank you
> --
> Sangeeta Niranjan
> Ph.D. Student, Lab of structural Biology
> Lab-6 NB
> National Centre for cell Science
> Ganeshkhind, Pune, India
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
--
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
--00000000000022352005ad39c042
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable
<div dir=3D"ltr">Hi Sangeeta,<div><br><div>I'm sorry for the problem wi=
th phenix.auto_sharpen!=C2=A0 Can you possibly try these things that may he=
lp figure out the problem:</div><div><br></div><div>From the command line, =
type this:</div><div><br></div><div>=C2=A0 =C2=A0 phenix.version</div><div>=
<br></div><div>This should tell you your version of phenix, and it will als=
o show that phenix is present in this terminal window.</div><div>Now type:<=
/div><div><br></div><div>=C2=A0 =C2=A0 phenix_regression.list auto_sharpen<=
br></div><div><br></div><div>This will then list a command that you can run=
on your computer to test auto_sharpen.=C2=A0 On mine it looks like:</div><=
div><br></div><div>libtbx.python "/net/anaconda/raid1/terwill/misc/PHE=
NIX/modules/phenix_regression/segment_and_split_map/tst_auto_sharpen.py&quo=
t;<br></div><div><br></div><div>Copy and paste whatever is printed there an=
d make sure that it runs and ends with "OK".=C2=A0 In particular,=
one of the tests will be:</div><div><br></div><div>=C2=A0 =C2=A0"Test=
ing auto_sharpen with model and remove_aniso"<br></div><div><br></div>=
<div>This will be testing your problem case.</div><div><br></div><div>Let m=
e know (off-list) if this test fails and I will try to help you debug the p=
roblem.</div><div><br></div><div>All the best,</div><div>Tom T</div></div><=
/div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">O=
n Wed, Aug 19, 2020 at 1:28 AM sangeeta niranjan <<a href=3D"mailto:sang=
eeta.19apr at gmail.com">sangeeta.19apr at gmail.com</a>> wrote:<br></div><blo=
ckquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left=
:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><div>Hello,<=
/div><div>I am trying to use Auto Sharpen feature of a CyoEM refined map in=
to Phenix but the job is getting failed every time with the following error=
:<br></div><div>Missing the model file:</div><div>followed with model file =
name and location.</div><div><br></div><div>Although it was working before =
but now it's showing the same error for all the auto sharpen runs inclu=
ding Models/PDBs.</div><div><br></div><div><br></div><div>Thank you<br></di=
v><div>-- <br><div dir=3D"ltr"><div dir=3D"ltr"><div><div dir=3D"ltr"><div>=
<div dir=3D"ltr">Sangeeta Niranjan<div>Ph.D. Student, Lab of structural Bio=
logy<br><div>Lab-6 NB</div><div>National Centre for cell Science</div><div>=
Ganeshkhind, Pune, India</div><div><br></div></div></div></div></div></div>=
</div></div></div></div>
_______________________________________________<br>
phenixbb mailing list<br>
<a href=3D"mailto:phenixbb at phenix-online.org" target=3D"_blank">phenixbb at ph=
enix-online.org</a><br>
<a href=3D"http://phenix-online.org/mailman/listinfo/phenixbb" rel=3D"noref=
errer" target=3D"_blank">http://phenix-online.org/mailman/listinfo/phenixbb=
</a><br>
Unsubscribe: <a href=3D"mailto:phenixbb-leave at phenix-online.org" target=3D"=
_blank">phenixbb-leave at phenix-online.org</a></blockquote></div><br clear=3D=
"all"><div><br></div>-- <br><div dir=3D"ltr" class=3D"gmail_signature"><div=
dir=3D"ltr"><div><div dir=3D"ltr"><div><div dir=3D"ltr"><div><div dir=3D"l=
tr"><div dir=3D"ltr">Thomas C Terwilliger<div>Laboratory Fellow, Los Alamos=
National Laboratory</div><div>Senior Scientist, New Mexico Consortium</div=
><div>100 Entrada Dr, Los Alamos, NM 87544</div><div>Email: <a href=3D"mail=
to:tterwilliger at newmexicoconsortium.org" target=3D"_blank">tterwilliger at new=
mexicoconsortium.org</a></div><div>Tel: 505-431-0010</div><div><br></div></=
div></div></div></div></div></div></div></div></div>
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