[ccp4bb] 2 positions available for software developers in cryoEM

2013-05-09 Thread Martyn Winn
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

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-08-30 Thread Martyn Winn
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

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-09-02 Thread Martyn Winn
, 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

[ccp4bb] Position available in biomolecular simulation

2013-09-24 Thread Martyn Winn
. 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.

Re: [ccp4bb] ccp4 man-pages

2013-11-15 Thread Martyn Winn
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

Re: [ccp4bb] ccp4 man-pages

2013-11-15 Thread Martyn Winn
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

[ccp4bb] *conference reminder* 3rd annual CCP-BioSim conference - Frontiers of Biomolecular Simulation - University of Edinburgh - 21st-23rd May 2014

2014-02-12 Thread Martyn Winn
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

[ccp4bb] *abstract deadline 10th March* 3rd annual CCP-BioSim conference - Frontiers of Biomolecular Simulation - University of Edinburgh - 21st-23rd May 2014

2014-03-04 Thread Martyn Winn
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

[ccp4bb] reminder: CCP-EM positions now available

2012-05-08 Thread martyn . winn
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

Re: [ccp4bb] Off topic about program for multiple protein sequence alignment

2012-05-15 Thread martyn . winn
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

Re: [ccp4bb] Covert Structure Factor to mtz

2012-05-17 Thread martyn . winn
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

Re: [ccp4bb] Covert Structure Factor to mtz

2012-05-18 Thread martyn . winn
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

[ccp4bb] CCP-BioSim workshop on QM/MM methods for modelling enzyme-catalysed reactions

2012-06-21 Thread martyn . winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury

Re: [ccp4bb] brix/mrc to ccp4 (was Re: [ccp4bb] AW: [ccp4bb] Postdoctoral position - University of Edinburgh)

2012-06-25 Thread 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 603634

[ccp4bb] Senior computational scientist required for CCP-EM, Harwell, UK (IRC50666)

2012-08-30 Thread martyn . winn
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

[ccp4bb] CCP-BioSim workshop on Free energy methods for modelling of protein-ligand interactions

2012-10-17 Thread martyn . winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk

Re: [ccp4bb] Crystallography on BBC Radio 4 next week

2012-11-22 Thread Martyn Winn
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

[ccp4bb] 2013 CCP-BIOSIM ANNUAL CONFERENCE: Frontiers of Biomolecular Simulation

2012-12-07 Thread Martyn Winn
. 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.

[ccp4bb] two positions available in computational electron cryo-microscopy

2012-12-17 Thread Martyn Winn
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

[ccp4bb] Instruct Biennial Meeting 22-24th May - Registration Open

2013-01-18 Thread Martyn Winn
, 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

[ccp4bb] Register now for the CCP-BioSim Conference: Frontiers of Biomolecular Simulation

2013-01-18 Thread Martyn Winn
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

[ccp4bb] CCPBioSim workshop on MD and Annual Conference

2013-02-25 Thread Martyn Winn
. 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

[ccp4bb] Questionnaire on shape/volume fitting in structural biology

2013-03-05 Thread 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

Re: [ccp4bb] Why the name aimless

2013-05-02 Thread Martyn Winn
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,

Re: [ccp4bb] mtz to hkl conversion

2007-02-15 Thread Martyn Winn
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

Re: [ccp4bb] TLSANL: negative mean-sq displacements?

2007-02-27 Thread Martyn Winn
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.

Re: [ccp4bb] MTZ to Shel-X?

2007-03-05 Thread Martyn Winn
- 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

Re: [ccp4bb] MTZ to Shel-X?

2007-03-06 Thread Martyn Winn
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

Re: [ccp4bb] ccp4 pdb format

2007-03-20 Thread Martyn Winn
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

[ccp4bb] MSc in Structural Biology and Biophysics at Manchester, UK

2007-04-19 Thread Martyn Winn
[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

Re: [ccp4bb] references for TLS refinement

2007-05-09 Thread Martyn Winn
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,

Re: [ccp4bb] CCP4 GUI

2007-05-10 Thread Martyn Winn
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

Re: [ccp4bb] Slightly off topic, ~H2O/residue vs resolution

2007-05-17 Thread Martyn Winn
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

Re: [ccp4bb] More than 70 TLS groups

2007-08-09 Thread Martyn Winn
. -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD

Re: [ccp4bb] Logfile Problem on Dual-Core Intal Mac with Os X Server 10.4 and CCP4 6.0.1

2007-10-30 Thread Martyn Winn
this? Is it related to the OS or to CCP4? Thanks for helping another time justin -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's

2007-11-09 Thread Martyn Winn
first? -bryan -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] PISA standalone

2007-11-27 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

Re: [ccp4bb] Protein interface prediction tool?

2007-11-29 Thread Martyn Winn
. -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

[ccp4bb] Updated package: Phaser 2.1.1 available from CCP4 download pages

2007-12-03 Thread Martyn Winn
(as a part of the main CCP4 in the choice). Enjoy! Martyn -- *** * * * Dr. Martyn Winn

[ccp4bb] BIOXHIT/BCO protein crystallography course in Oulu, Finland

2007-12-06 Thread Martyn Winn
. *' -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K

Re: [ccp4bb] convert .cif to .mtz

2008-01-29 Thread Martyn Winn
-- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

2008-03-13 Thread Martyn Winn
/) -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory

Re: [ccp4bb] Rant: B vs TLS, anisou, and PDB headers

2008-03-31 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4

[ccp4bb] [Fwd: Re: [ccp4bb] CCP4 Coot on Ubuntu]

2008-06-10 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44

Re: [ccp4bb] CCP4 Coot on Ubuntu

2008-06-10 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington

Re: [ccp4bb] need test data set

2008-06-13 Thread Martyn Winn
Chemistry Hannover Medical School Germany -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Molecular Dynamics for dummies.

2008-07-03 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED

Re: [ccp4bb] Molecular Dynamics for dummies.

2008-07-03 Thread Martyn Winn
, 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

Re: [ccp4bb] Parameter MAXSAVE exceeded

2008-07-04 Thread Martyn Winn
Research Student Institute for Biophysical Chemistry Hannover Medical School Germany -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Missing space group in ?.mtz file

2008-07-08 Thread Martyn Winn
anybody know how to fix it? Petr -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] pdbset bug - seqres record

2008-07-11 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K

[ccp4bb] Using the BB for file sharing

2008-07-15 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury

Re: [ccp4bb] What is the meaning of Fbar in solve ?

2008-07-17 Thread Martyn Winn
/ -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

Re: [ccp4bb] Acorn question

2008-07-24 Thread Martyn Winn
__ The Famous, the Infamous, the Lame - in your browser. Get the TMZ Toolbar Now! -- *** * * * Dr. Martyn Winn

[ccp4bb] ccp4 6.0.99e test release

2008-07-25 Thread Martyn Winn
of) Feedback to the usual locale ([EMAIL PROTECTED]) Thanks Charles and the rest of us here at DL. -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] TLS parameter representation

2008-09-26 Thread Martyn Winn
)2 5267273 -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] PDB atom names in Coot Refmac

2008-10-08 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

Re: [ccp4bb] CCP4 6.1 release date? (again)

2008-11-28 Thread Martyn Winn
. ftp://ftp.ccp4.ac.uk/ccp4/6.1/ Thanks, justin -- *** * * * Dr. Martyn Winn

[ccp4bb] sftools interface problem

2008-12-19 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455

Re: [ccp4bb] Max number of TLS groups in Refmac5 -

2009-01-09 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail

[ccp4bb] polls on ccp4bb

2009-01-14 Thread Martyn Winn
, PhD Student, School of Medicine - Sungkyukwan University, Korea Lab: http://smsb1.skku.ac.kr/ -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Ramachandran plot, in a text list

2009-01-15 Thread Martyn Winn
angles, in two columns far to the right. Ed -- *** * * * Dr. Martyn Winn

[ccp4bb] Postdoctoral position in Protein Crystallography, Manchester UK

2009-01-27 Thread 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

Re: [ccp4bb] Checking for gremlins in deposited diffraction data] (fwd)

2009-03-09 Thread 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

Re: [ccp4bb] Low-level disable ccp4i database...?

2009-04-21 Thread Martyn Winn
this before... phx -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] TLSANL total B factor question

2010-05-21 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

Re: [ccp4bb] How to calculate real-space CC by section?

2010-05-26 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax

Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot

2010-06-02 Thread 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 603634

Re: [ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4 format

2010-07-13 Thread martyn . winn
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

Re: [ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4 format

2010-07-14 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K

Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC

2010-07-15 Thread Martyn Winn
! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Fd-3m with pdbset

2010-09-06 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory

Re: [ccp4bb] Fd-3m with pdbset

2010-09-06 Thread Martyn Winn
will clean up CCP4 Fortran programs at least. m -- *** * * * Dr. Martyn Winn

[ccp4bb] Job for scientific programmer, for Electron microscopy applications

2010-09-07 Thread Martyn Winn
p.a. Informal enquiries Dr Alan Roseman Tel: + 44 (0) 161 275 7226 Email alan.rose...@manchester.ac.uk -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] protein ligand energy

2010-10-13 Thread Martyn Winn
Fax: (+44) - 1865 - 287547 -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Bug in c_truncate?

2010-10-28 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory

Re: [ccp4bb] limit for number of files for CAD...

2010-11-03 Thread Martyn Winn
78FD 6669 67BA 8D5D -- *** * * * Dr. Martyn Winn

[ccp4bb] Job posting: EM Software Developer

2011-01-02 Thread 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

Re: [ccp4bb] Saxs reviews or books

2011-01-11 Thread Martyn Winn
. -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K

Re: [ccp4bb] TLS from PDB records

2011-02-03 Thread martyn . winn
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

Re: [ccp4bb] Data file wrangling question

2011-03-18 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk

Re: [ccp4bb] Data file wrangling question

2011-03-18 Thread martyn . winn
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

Re: [ccp4bb] MR with MD trajectories

2011-03-30 Thread martyn . winn
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

Re: [ccp4bb] Script / program to change chain ID 's in symmetry mates

2011-04-08 Thread Martyn Winn
that dataset that we are handling is large. I thank you all in advance for your help. Best, Krishan -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Phaser_EP

2011-05-29 Thread 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

Re: [ccp4bb] generate large symmetry model

2011-06-30 Thread martyn . winn
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

Re: [ccp4bb] low resolution refinement

2011-07-12 Thread Martyn Winn
. Could you help me? Thank you very much! -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] protein segments from pdb

2011-08-10 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk

Re: [ccp4bb] Pyroglutamate in structure calculation

2011-08-16 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory

Re: [ccp4bb] identifying hinges in flexible proteins

2011-08-26 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

Re: [ccp4bb] converting mmcif to mtz failure

2011-09-07 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

[ccp4bb] Course announcement: Computational methods for macromolecular phasing and refinement, 11-16th March 2012

2011-12-20 Thread 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

Re: [ccp4bb] How to patch CCP4 cif2mtz so it can handle PDB entries with Map Coefficients

2011-12-21 Thread martyn . winn
. This is the get-out method if cif2mtz fails. Edit the item name to something that is recognised. Cheers Martyn -- *** * * * Dr. Martyn Winn

[ccp4bb] Course reminder: Computational methods for macromolecular phasing and refinement, 11-16th March 2012

2012-01-09 Thread 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

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

2012-01-10 Thread Martyn Winn
. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ. -- *** * * * Dr. Martyn Winn

[ccp4bb] CCPBioSim workshop: How to set up a Protein Simulation

2012-02-22 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax

Re: [ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work

2012-02-29 Thread Martyn Winn
-- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Fw: [ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work

2012-02-29 Thread Martyn Winn
the problem. Cheers, Dialing -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] REFMAC Riding Hydrogens

2012-03-08 Thread 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

[ccp4bb] 3 positions available in the CCP4 core group

2009-06-03 Thread Martyn Winn
://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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