of a team.
The posts are located at the Research Complex at Harwell
(http://www.rc-harwell.ac.uk/), within the group of Martyn Winn in the
Scientific Computing Department of STFC (http://www.stfc.ac.uk/scd/), and
alongside the core team of CCP4. The Research Complex is located on the Harwell
IIRC the CCP4 library (i.e. mmdb) can handle 2-character chain names. There may
be something specific in pdbset which interferes. You can try pdbcur as an
alternative. Something like:
pdbcur xyzin toxd_AA.pdb xyzout toxd_out.pdb eof
translate * frac 0 0.2 0
end
eof
I just tried it on a little
, pdbcur will
work equally well with mmCIF files.
Cheers
Martyn
*
* Dr. Martyn Winn
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
* Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH)
* E-mail: martyn.w...@stfc.ac.ukmailto:martyn.w...@stfc.ac.uk Skype
. Martyn Winn
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
* Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH)
* E-mail: martyn.w...@stfc.ac.uk Skype: martyn.winn
*
--
Scanned by iCritical.
Many, many years ago, the man pages used to be nroff-formatted .1 files. We
converted these to html files, and used lynx to automatically generate ASCII
.doc files which could be used as man pages. AFAIK this is still the case.
I mention this in case anyone wants to get nostalgic about
PM, Martyn Winn wrote:
Many, many years ago, the man pages used to be nroff-formatted .1
files. We converted these to html files, and used lynx to
automatically generate ASCII .doc files which could be used as man
pages. AFAIK this is still the case.
I mention this in case anyone wants
As advertised at the Study Weekend, CCPBioSim is the sister CCP in biomolecular
simulation. The annual conference will take place in Edinburgh in May, see
details below.
Cheers
Martyn
Dear Colleagues,
The third annual CCP-BioSim conference will be held at the John McIntyre
conference
Quick reminder that the deadline for abstracts for the CCPBioSim annual
conference is next Monday.
Cheers
Martyn
Dear Colleagues,
The third annual CCP-BioSim conference will be held at the John McIntyre
conference centre, Edinburgh First, from Wednesday 21st to Friday 23rd May
2014. The
and IRC50666. Further
information is available there. Informal enquiries may be made to Martyn Winn
(martyn.winn at stfc.ac.uk).
Best wishes,
Martyn Winn, Richard Henderson, Alan Roseman, Peter Rosenthal, Helen Saibil and
Ardan Patwardhan
Certainly different programs and different scoring matrices will give different
answers. There is not necessarily a correct answer either, just different
educated guesses. With high sequence identity, the answers should be fairly
consistent. As you reduce the sequence identity (i.e. as it gets
Reflection cif files from the PDB do not always have cell and symmetry
information in them, particularly the older ones, and it sounds like this is
your case.
In that case, you need to manually copy the cell information from the PDB web
page into the ccp4i interface before running.
HTH
Martyn
But that's not what Paul said. I am sure we all agree the information _should_
be there, but I took Paul to mean that it _is_ there.
If I look at PDBe for 2gs7, go to Downloads and Structure Factors, then the
cell and symmetry is _not_ there.
If I go to RCSB, and click on Structure Factors on
--
***
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* Dr. Martyn Winn *
* *
* STFC Daresbury
. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
* Fax: +44 1925 603634
of a team.
The core group of CCP-EM is based at the Research Complex at Harwell, alongside
the core group of CCP4, but the postholders will be expected to travel
throughout the UK and interact with international groups to support the
collaboration. Informal enquiries may be made to Martyn Winn
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***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk
I'd just like to comment that In Our Time is usually pretty good. I caught the
end of this morning's program on the Borgias. After hearing about murder,
nepotism and incest, it was a bit disorientating to hear Melvyn announce
crystallography as the next subject :)
m
-Original
. Martyn Winn
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
* Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH)
* E-mail: martyn.w...@stfc.ac.uk Skype: martyn.winn
*
--
Scanned by iCritical.
Complex at Harwell, within the
Computational Biology group of Martyn Winn in the Scientific Computing
Department of STFC. Further information is available online (see
http://www.ccpem.ac.uk/positions.php and links to TopCareer site), and informal
enquiries may be made to Martyn Winn martyn.w
, and to register, visit
http://www.structuralbiology.eu/content/instruct-biennial-structural-biology-meeting
Best wishes,
The Instruct Operations Team
*
* Dr. Martyn Winn
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
* Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH
from the Molecular Graphics
and Modelling Society for selected junior researchers.
For full details and to register, see: http://www.ccpbiosim.ac.uk
*
* Dr. Martyn Winn
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
* Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH
. Further details at:
http://www.ccpbiosim.ac.uk/?q=annualconfs/conf2013
Cheers
Martyn
*
* Dr. Martyn Winn
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
* Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH)
* E-mail: martyn.w...@stfc.ac.uk Skype: martyn.winn
to Survey Monkey. We plan to publish an anonymized summary of the survey on
the BioMedBridges web site.
Kind Regards,
Ingvar Lagerstedt Ardan Patwardhan, PDBe and Martyn Winn, STFC
*
* Dr. Martyn Winn
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
* Tel: +44 1925
I think Phil saw something nasty in the woodshed ...
HTH
Martyn
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Roberto Battistutta
Sent: 02 May 2013 11:07
To: ccp4bb
Subject: [ccp4bb] Why the name aimless
Hi everyone,
just a curiosity,
Yes, this script should work. You can also use OUTPUT CNS.
But the GUI is not up-to-date with the program. This is fixed now. You
can pick up fixes via the Problems Page
http://www.ccp4.ac.uk/problems.php#6.0.2-export-hl
or it will be in the next release.
Tip for newbies: you can always get
I wouldn't call it numerical error, as such. Refmac doesn't
restrain/constrain the T, L or S values at all. In particular, the L
value can refine stably and accurately to a negative value.
Refmac is refining a set of ADPs constrained to fit a certain functional
form with parameters T, L and S.
-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf
Of Martyn Winn
Sent: 05 March 2007 12:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] MTZ to Shel-X?
A glance through the CVS history of mtz2various and f2mtz shows that
there has been a lot of work keeping
PS Meant to say, I am aware the GUI doesn't give you the option to
specify I for SHELX. Will fix in due course (meanwhile RunView Com)
m
On Tue, 2007-03-06 at 13:43 +, Martyn Winn wrote:
Hi Ian,
Thanks for your helpful analysis. There are now updated versions of the
source code
CCP4 is a collaboration between many and varied authors, so the exact
answer depends on which bit of the ccp4 interface you are talking about!
Generally, most CCP4 programs will work with standard PDB files. The
spacegroup on the CRYST1 line is only needed if a program can't get the
symmetry
[Posted on behalf of Lydia Tabernero. Full text of this posting
available here: http://www.ccp4.ac.uk/martyn/MSc-Leaflet.doc ]
1 year MSc in Structural Biology and Biophysics at Manchester, UK,
starting in September 2007
Aims Objectives: Structural and biophysical analyses are essential in
These are under TLSANL i.e. for analysing TLS parameters (1st is the
program reference, second is the original TLS formulation).
For TLS _refinement_ look under refmac.
If you used TLSMD, then there are separate references for that.
Regards
Martyn
On Wed, 2007-05-09 at 09:25 -0400, Nalam,
The level of detail in the GUI is a matter of constant debate. The
underlying programs are far far richer, so the question is how much to
expose in the GUI. We try to get a balance between ease-of-use and
coverage, but it won't always work. BTW I don't think we ever claimed
that ccp4i (or anything
The CCP4 program rwcontents includes the data from
Carugo Bordo, Acta Cryst D, 55, 479 (1999)
Headline figures are 1.0 waters per protein residue at 2.0A, and 1.6-1.7
waters per protein residue at 1.0A. They use mainly room temperature,
but also some cryo structures.
And, as Clemens said, you
.
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD
this? Is it related to the OS or to
CCP4?
Thanks for helping another time justin
--
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* *
* Dr. Martyn Winn
first?
-bryan
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* *
* Dr. Martyn Winn
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury
.
--
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* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury
(as a part of the main
CCP4 in the choice).
Enjoy!
Martyn
--
***
* *
* Dr. Martyn Winn
.
*'
--
***
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* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K
--
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
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/)
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* STFC Daresbury Laboratory
--
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* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4
--
***
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* Dr. Martyn Winn *
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* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] *
* Fax: +44
--
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* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington
Chemistry
Hannover Medical School
Germany
--
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* Dr. Martyn Winn
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: [EMAIL PROTECTED
, Na+, Mg2+ are generally OK, Ca2+, Fe, Mn,
etc. are much more tricky, especially in a quick and dirty simulation.
On Thu, 2008-07-03 at 12:20 +0100, Martyn Winn wrote:
Gromacs www.gromacs.org
It is GPL. It can certainly handle metals, although as is always the
case, you have
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany
--
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* *
* Dr. Martyn Winn
anybody know how to fix it?
Petr
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* Dr. Martyn Winn
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury
/
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* STFC Daresbury Laboratory, Daresbury
__
The Famous, the Infamous, the Lame - in your browser. Get the TMZ
Toolbar Now!
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of)
Feedback to the usual locale ([EMAIL PROTECTED])
Thanks
Charles and the rest of us here at DL.
--
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* Dr. Martyn Winn
)2 5267273
--
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* *
* Dr. Martyn Winn
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury
.
ftp://ftp.ccp4.ac.uk/ccp4/6.1/
Thanks,
justin
--
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* *
* Dr. Martyn Winn
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail
,
PhD Student,
School of Medicine - Sungkyukwan University, Korea
Lab: http://smsb1.skku.ac.kr/
--
***
* *
* Dr. Martyn Winn
angles, in two columns far to the right.
Ed
--
***
* *
* Dr. Martyn Winn
. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
* Fax: +44 1925 603825Skype
. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
* Fax: +44 1925 603825Skype
this before...
phx
--
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* Dr. Martyn Winn
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
* Fax
. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
* Fax: +44 1925 603634
Actually, zero spacegroup should be tolerated by the CCP4 library now.
We were recently alerted to another problem, caused by non-zero origin in the
EM map header. But I think this is different to the problem of the original
poster.
It's probably fair to say we haven't tested enough against
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K
!
Thanks,
Huw
--
Dr Huw Jenkins
Astbury Centre for Structural Molecular Biology
University of Leeds
--
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* *
* Dr. Martyn Winn
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory
will clean up
CCP4 Fortran programs at least.
m
--
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* *
* Dr. Martyn Winn
p.a.
Informal enquiries
Dr Alan Roseman
Tel: + 44 (0) 161 275 7226
Email alan.rose...@manchester.ac.uk
--
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* *
* Dr. Martyn Winn
Fax: (+44) - 1865 - 287547
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* Dr. Martyn Winn
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory
78FD 6669 67BA 8D5D
--
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* *
* Dr. Martyn Winn
Forwarded on behalf of Alan Roseman [mailto:alan.rose...@manchester.ac.uk] so
please contact him not me.
Happy New Year to all,
Martyn
Software Developer/ Scientific Computer
.
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K
tlsextract in the CCP4 suite (from Jay Painter and Ethan Merritt).
Martyn
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jochen
Kuper
Sent: 03 February 2011 08:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] TLS from PDB records
Dear All,
sorry for the probably silly
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk
oops, I did that ... and I'd forgotten all about it ... simpler option than
pointless
m
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
James Holton
Sent: 18 March 2011 15:49
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Data file
I agree there are probably much better and simpler ways of doing this.
But to answer the question, you could probably use MrBUMP to do this, using the
local PDB file option. It will require a bit of scripting to deal with all the
file names, and will take forever.
Other points:
1) you don't
that dataset that we are handling is large.
I thank you all in advance for your help.
Best,
Krishan
--
***
* *
* Dr. Martyn Winn
Can you post details of versions. Version of CCP4. Version of Phaser (look at
top of log file).
At one point, the interface was lagging behind the program, but should be ok
now.
Martyn
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ylva
Lindqvist
Sent: 28 May 2011 13:31
As well as pdbset, you can use pdbcur. A combination of keywords genunit, symop
and symcommit.
I’d probably use genunit (applicable to whatever spacegroup you have), followed
by a second call using symop/symcommit to apply unit cell translations.
Cheers
Martyn
From: CCP4 bulletin board
.
Could you help me?
Thank you very much!
--
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* *
* Dr. Martyn Winn
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk
--
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury
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* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury
supervisor or other person who may be
consulted if necessary. All this information will be treated confidentially.
Participants are encouraged to bring their own data.
Martyn Winn
Isabel Uson
Garib Murshudov
. This is the get-out method if cif2mtz fails. Edit the item
name to something that is recognised.
Cheers
Martyn
--
***
* *
* Dr. Martyn Winn
supervisor or other person who may be consulted if necessary. All this
information will be treated confidentially. Participants are encouraged
to bring their own data.
Martyn Winn
Isabel Uson
Garib Murshudov
.
Registered in England No. 2155347 Registered Charity No. 800579
Registered office 12 Union Road, Cambridge CB2 1EZ.
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--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
* Fax
--
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* Dr. Martyn Winn
the problem.
Cheers,
Dialing
--
***
* *
* Dr. Martyn Winn
Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk
--
***
* *
* Dr. Martyn
://erecruit.cclrc.ac.uk/), telephone 01235 446677 or e-mail
recruitment-...@rl.ac.uk quoting the relevant reference number. Informal
enquiries may be made to Martyn Winn (martyn.w...@stfc.ac.uk).
Closing date for applications is 26 Jun 2009
Interviews will be held between 16th and 24th July
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