-biology-and-drug-discovery/
Registration fee: £50 (includes catering)
Venue: EPN campus, Grenoble, France.
Dates: 13-14 May 2024
Best regards,
Jon Agirre on behalf of the organising committee: Jose A. Marquez
(Instruct-ERIC), Magalie Matthieu (Sanofi-Aventis), Rebecca Thompson
(ThermoFisher), Max Nanao
s. Another
> piece of info is that my computer has 8 CPU but when running CCP4i2 it only
> uses one.
>
>
>
> Does anybody have an idea of which could be the problem?
>
>
>
> Best regards,
>
> Marian
>
>
>
> --
>
> To
-discovery/
Registration fee: £50 (includes catering)
Venue: EPN campus, Grenoble, France.
Dates: 13-14 May 2024
Best regards,
Jon Agirre, on behalf of the organising committee: Jose A. Marquez
(Instruct-ERIC), Magalie Matthieu (Sanofi-Aventis), Rebecca Thompson
(ThermoFisher), Max Nanao (ESRF), Ca
te the email and
> attachment.
>
> Any views or opinions expressed by the author of this email do not
> necessarily reflect the views of the University of Nottingham. Email
> communications with the University of Nottingham may be monitored
> where permitted by law.
>
>
>
>
nburg, Jon Agirre and Paul Bond
--
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, Yor
Dear all,
Applications are invited for a Postdoctoral Research Associate position,
funded by the Royal Society, for up to 30 months to work with Dr Jon Agirre in
the Department of Chemistry. The successful applicant will join a vibrant
team of researchers at the heart of the world-leading York
preliminary programme on our website:
https://www.ccp4.ac.uk/schools/ccp4-summer-school/index.php
The organisers,
Johan Turkenburg, Jon Agirre and Paul Bond
--
Dr Jon Agirre
Royal Society University Research Fellow (assistant professor)
CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo (Elixir
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Dear all,
Applications are invited for a Postdoctoral Research Associate position,
funded by the Royal Society, for up to 30 months to work with Dr Jon Agirre
in the Department of Chemistry. The successful applicant will join a
vibrant team of researchers at the heart of the world-leading York
t; Dr Clare E.M. Stevenson
>
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>
> Norwich Research Park
>
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>
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>
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guidelines.
Best wishes,
Jon, Alan, Robbie and Karen
On Mon, 4 Nov 2019 at 11:37, Jon Agirre wrote:
> Dear colleagues,
>
> We are pleased to announce the opening of the first CCP4 Study Weekend
> illustration competition, made possible by CCP4’s long standing
> collaboration wit
king forward to receiving your images!
Jon Agirre, Alan Roseman, Robbie Joosten and Karen McIntyre
--
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemi
anuary 2020.
> We are very much looking forward to welcoming you in Nottingham. And yes,
> there will be a Cèilidh (https://en.wikipedia.org/wiki/Cèilidh).
>
> Registration and programme details: https://tinyurl.com/ccp4sw2020
>
> Best wishes,
>
> Robbie Joosten (@Robbie_Joo
Cèilidh (https://en.wikipedia.org/wiki/Cèilidh).
Registration and programme details: https://tinyurl.com/ccp4sw2020
Best wishes,
Robbie Joosten (@Robbie_Joosten),
Alan Roseman (@AlanRoseman3),
Jon Agirre (@glycojones),
and the rest of CCP4 (@ccp4_mx)
--
Dr Jon Agirre
Royal Society University Research
nsubscribe from the CCP4BB list, click the following link:
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Dr Jon Agirre
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York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
ht
list, click the following link:
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Thank you all for your help with this - it looks like John's link was being
wiped out from the e-mail by an ad-blocking extension (?). So if you can't
find the link, make sure you try deactivating whatever ad-blocker your
browser is using :)
On Thu, 4 Apr 2019 at 15:56, Jon Agirre wr
Trust Genome Campus
>
> Hinxton
>
> Cambridge CB10 1SD UK
>
> Tel: +44 1223 492529
>
>
>
> http://www.pdbe.org
>
> http://www.facebook.com/proteindatabank
>
> http://twitter.com/PDBeurope
>
>
>
> ------
>
> To unsubscribe from the C
crystallography
> entrance
> and ring me or the department office from the internal phone by the door
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>
> Post-doctoral Fellow,
> Crystal and Structural Chemistry,
> Utrecht University
>
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>
> To unsubscribe from the CCP4BB list, click the following link:
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> Twitter <https://twitter.com/DrAntonioAriza?lang=en>
>
> *Check out my latest paper!!!*
> Structural insights into the function of ZRANB3 in replication stress
> response <http://www.nature.com/articles/ncomms15847>
>
> ---
ed.
Yours sincerely,
Jon & Mark
--
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +
or reviews.
The URL for submitting papers is: http://submission.iucr.org/submit/f?Qconf=
glycoproteins
Tentative deadline: 1st of January.
Yours sincerely,
Jon & Mark
--
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
Univ
YSBL Professor Tony Wilkinson (tony.wilkin...@york.ac.uk; +44
(0)1904 328261)
Link:
https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885&p_web_page_id=325077
*Closing date:* 9 October 2017
*Interviews will be held in York on:* 29 November 2017
--
Dr Jon Agirre
Royal Society Un
ing, say, sftools.
>
> Cheers,
>
> Ed.
>
> ---
> Hurry up, before we all come to our senses!
> Julien, King of Lemurs
>
>
--
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.yo
ve received this message in error, please contact
> the sender by reply e-mail message and destroy all copies of the
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Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, En
> CVMO
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429 <(925)%20209-7429>
>
> +43 676 571 0536 <+43%20676%205710536>
>
> --
>
> Many plausible ideas vanish
As far as I know, OpenMP only works with C, C++ and Fortran.
In addition to Phaser, there are a few other crystallographic programs
I know are using OpenMP: XDS (Fortran), CCP4mg (surface calculations
in C++), Privateer (C++), Sharp...
Other programs may take advantage of multithreading themselve
://jobs.york.ac.uk/wd/plsql/wd_portal.show
_job?p_web_site_id=3885&p_web_page_id=297414
Deadline for applications: 05/02/2017
--
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemi
plsql/wd_portal.show
_job?p_web_site_id=3885&p_web_page_id=297412
Deadline for applications: 12/02/2017
--
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staf
Hi,
you want to use these keywords:
REFInement BONLY
Good luck,
Jon
On 23 December 2016 at 06:52, Peng wrote:
>
> Dear all,
> How can I refine B-factors only in CCP4 REFMAC?
> I do not want to refine the XYZ coordinations.
> Thanks
> Peng
>
>
>
>
>
>
t; Would this mailing list be better or worse if mails with pdfs were blocked?
>
--
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
+44 (0) 1904 32 8270
eich
> Tel. +43 662 8044-7283
>
> FAX +43 662 8044-7209
> http://www.uni-salzburg.at/xray
> --
>
>
>
--
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
+44 (0) 1904 32 8270
>
> The current version of CCP4 does not contain mtzdump.
>
It surely does on my machine:
$ which mtzdump
/Applications/ccp4-6.5/bin/mtzdump
--
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, Eng
about interfaces, and is also accessible within CCP4.
Hope this helps,
Jon
--
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253
t;
--
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253
gt; I am experiencing some troubles with running Privateer. It seems to fail
> to read a PDB file. The Error message:
>
> Reading xxx.pdb... MMDBfile: read_file error: xxx.pdb :3
> terminate called after throwing an instance of 'clipper::Message_fatal'
> Aborted
>
&
figure out this problem?
>
> regards
>
> Atul
>
--
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253
?
>
> Thank you,
> Patrick
> --
> [image: 3D Earth Screensaver Preview] <http://www.inbox.com/earth>
> *Free 3D Earth Screensaver*
> Watch the Earth right on your desktop! Check it out at www.inbox.com/earth
>
--
Dr Jon Agirre
York Structural Bi
facilities known for their successful crystallization of
>> proteins.
>>
>> Has anyone else run into this problem and seen light at the other side??
>> Any suggestions are appreciated.
>>
>>
>
--
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/research/jagirre/
+44 (0) 1904 32 8253
try and wish to help us remedy this
> situation, please contact us
> .
> Back to EDS home page <http://eds.bmc.uu.se/eds>
>
> The reported R-value for the () PDB entry is 0.16 than how 0.309?
> could anyone please explain about this!
> Sincerely,
> S.M. Jaimohan, Ph.
load Coot, because the slight difference in
performance doesn't justify the massive increase in both temperature and
power consumption.
Presentation software like CCP4mg or pymol are much more resource-hungry
than Coot, and still the HD series hold themselves up quite decently.
Jon
--
Dr
---
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Icedove - http://www.enigmail.net/
>
unctions U(a,x)
> (http://en.wikipedia.org/wiki/Parabolic_cylinder_functions). The nice thing
> about this method is one can generalise it to calculate the
> Bayesian-corrected F and I as well as arbitrary moments and get rid of F &
> W's cubic spline interpolation code
Espript will do. http://espript.ibcp.fr/
Good luck,
Jon
On 9 Mar 2013 11:52, "LISA" wrote:
> Hi all,
> I want to make a topological figure of my protein with a b-sheet and
> helix based on its crystal structure. Please recommend some online sever of
> software?
> Thank you.
>
> lisa
>
I)= .
> XMAX(I)=-.
> 5 CONTINUE
> C
> C OPEN INPUT FILE
> C
> WRITE (*,10)
>10 FORMAT(///,25X,'*',
> . /,25X,'* *',
>
>
> --
> Fred. Vellieux (B.Sc., Ph.D., hdr)
>
ot;REMARK 290"
> section and use the matrix in the pdbset.
>
> so I have to convert the matrix from
> r11r12r13tx
> r21r22r23ty
> r31r32r33tz
>
> to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz.
>
> How can I do it?
>
>
27;s the matrix format accepted by the "transform file" keywords of the
> pdbset program?
> is it "r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz"?
> And how to covert from the "pdb file format" to the "pdbset format"?
>
> What's th
ll need to install XQuartz (Apple are no longer
> supplying their own X11 builds) but that's just a couple of clicks in
> the box that pops up the first time you run an program that needs X.
>
> The (on by default) versioning auto save is a PITA if you ever use
> textedit to edit
Work.Pages ApplePersistence -bool no
defaults write com.apple.iWork.Numbers ApplePersistence -bool no
defaults write com.apple.iWork.Keynote ApplePersistence -bool no
Cheers,
Jon
--
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://sourceforge.net/projects/projectrecon/
+34656756888
uot;. I got error on compiling. Thanks in advance
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Usin
s quite convinced that it was an XQuartz.app (aka X11
for OS X) related bug and therefore never reported it.
Jon
--
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
http://sourceforge.net/projects/projectrecon/
+34656756888
http://rexpalmer2010.homestead.com
>
>
>
> --
> Fred. Vellieux (B.Sc., Ph.D., hdr)
> IBS / ELMA
> 41 rue Jules Horowitz
> F-38027 Grenoble Cedex 01
> Tel: +33 438789605
> Fax: +33 438785494
>
>
--
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
http://sourceforge.net/projects/projectrecon/
+34656756888
crystals. I have already tried varying a number of parameters like
> salt, precipitant concentration and buffer pH but that didn't help.
>
> Thanks.
>
--
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
http://sourceforge.net/projects/projectrecon/
+34656756888
uld share with me about these
> instruments? Feel free to email off list if you want.
> Thanks!
> -Sam
>
--
Jon Agirre, PhD
Biophysics Unit (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
+34656756888
conditions. Some conditions gave crystals but mass
> spec of crystals show only either one protein present. I am thinking of
> antibody but don't know where to start. Can I use the anti-His tag antibody?
>
> Thank you.
>
--
Dr. Jon Agirre
Biophysics Unit (CSIC-UPV/EHU)
http://www.ehu.es/jon.agirre
+0034946013357
they should be reported to the wwPDB authorities.
>
> Paul.
>
--
Dr. Jon Agirre
Postdoctoral Scientist - Protein and
Virus X-ray Crystallography Group
Biophysics Unit (CSIC-UPV/EHU)
+0034946013357
> include links to all the projects, input, output and log files.
>
> Thanks in advance.
> Regards
>
> --
> Sonali Dhindwal
>
> “Live as if you were to die tomorrow. Learn as if you were to live
> forever.”
>
--
Dr. Jon Agirre
Postdoctoral Scientist - Protein an
oritise some for reproductions at my lab?
> Can detergents crystallise and produce colours under polarising light?
>
> Thank you.
>
> Theresa
>
--
Dr. Jon Agirre
Postdoctoral Scientist - Protein and
Virus X-ray Crystallography Group
Biophysics Unit (CSIC-UPV/EHU)
+0034946013357
napshots
> >
> > On Fri, Feb 10, 2012 at 12:29 PM, James Stroud
> wrote:
> >> How could they not be snapshots of conformations adopted in solution?
> >
> > Packing billions of copies of an irregularly-shaped protein into a
> > compact lattice and freezing it t
ar Research Laboratory
> OFLG/102
> Paul Scherrer Institut
> CH-5232 Villigen PSI
> Switzerland
>
> Tel.: +41-(0)56-310-2332
> Email: florian.brueck...@psi.ch
>
>
>
>
>
--
Dr. Jon Agirre
Postdoctoral Scientist - Protein and
Virus X-ray Crystallography Group
Biophysics Unit (CSIC-UPV/EHU)
+0034946013357
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