Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

You can also try the CCPEM list for more cryoEM-orientated advice https://www.jiscmail.ac.uk/CCPEM and look in CCP-EM for more fitting, refinement, validation tools. Certainly, the map doesn’t look 3A, unless you have filtered it for these pictures. The CC for the middle and C-terminal domains

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

You can also try the CCPEM list for more cryoEM-orientated advice https://www.jiscmail.ac.uk/CCPEM and look in CCP-EM for more fitting, refinement, validation tools. Certainly, the map doesn’t look 3A, unless you have filtered it for these pictures. The CC for the middle and C-terminal domains

[ccp4bb] CoSeC Conference 2023 | Call for Presentations

Dear All, Please see below an announcement from our umbrella organisation CoSeC. This is an annual meeting with a wider scope of computational science. Cheers Martyn Computational Science Centre for Research Communities (CoSeC) 2023 Conference 6th of December 2023 Call for Presentations -

[ccp4bb] FW: MRC Molecular and Cellular Medicine Board; Board Member Vacancy

Hi all. I'm forwarding this announcement on behalf of Robert Deller at the MRC: As you may be aware, MRC conducts an annual recruitment exercise to fill vacancies across its boards and panels.

Re: [ccp4bb] help for motion correction

Might be better posted to cc...@jiscmail.ac.uk m -Original Message- From: CCP4 bulletin board On Behalf Of Jing Sent: 16 July 2022 20:56 To: ccp4bb Subject: [ccp4bb] help for motion correction Hello All, I have a question about gain reference file. When I try to work on Motion

Re: [ccp4bb] Help with One dimensional electron density calculation

Hi, It’s not clear why you don’t use MAPMAN if that does what you want. If availability is the problem, it is still here https://github.com/martynwinn/Uppsala-Software-Factory If you are prepared to do some Python, then 2 other options: https://mrcfile.readthedocs.io/en/latest/readme.html

[ccp4bb] abstract deadline for ECM33 now 31st May

Hi all, A heads-up that the deadline for abstract submissions has been extended until the end of the month (31st May), see https://www.ecm33.fr/ and https://hopscotch.key4events.com/abstract.aspx?e=281 I'm chairing MS1 on "MX/Cryo-EM software development" and would very much like to have a

[ccp4bb] MRC Biophysics and Biosimulation Community Engagement Event

[Posted on behalf of Robert Deller UKRI-MRC] The MRC Data Science Strategic Advisory Group and BBSRC Transformative Technologies Strategy Advisory Panel have founded a task force to better understand the computing needs, including the associated training/skills, software and services, of the

Re: [ccp4bb] Calculating RMSD of a loop

This is probably a good opportunity to say that the USF has moved to https://github.com/martynwinn/Uppsala-Software-Factory Gerard asked for this so that they wouldn't be lost. I haven't put any effort into checking the binaries or compilation, but I will do what I can on a best effort basis

Re: [ccp4bb] AW: [ccp4bb] how many crystallographers are there?

When I last looked a couple of years ago, the number of subscribers to the BB was 6396. Given the many crystallographers who don’t subscribe to the BB, and the EMers who are not ex-crystallographers, I could well believe 20 or 30 thousand. HTH m From: CCP4 bulletin board

[ccp4bb] CCPBioSim annual conference 2019, 4-6 Sept, Bristol

>From CCPBioSim. Note that the theme for the invited speakers is synthetic >biology and biomolecular design, but contributed talks and posters can be on >any aspect of biomolecular modelling and simulation. m Dear All, We are pleased to announce that registration is now open for the 7th

Re: [ccp4bb] Current "best" software for computing volumes of active sites

Hi, At the request of Gerard, I have rescued the USF packages into github https://github.com/martynwinn/Uppsala-Software-Factory So far, I have done nothing with this, so no guarantees that the code still compiles or that the old binaries still work. Nevertheless, it does contain a cavity.lib

Re: [ccp4bb] CTF correction of tomograms

There is an IMOD mailing list, and David Mastronarde is very good at answering queries. See https://bio3d.colorado.edu/imod/joinlist.html There seems to be a tutorial for ctfplotter at https://bio3d.colorado.edu/imod/doc/CTFexamples.html and the manual

Re: [ccp4bb] fit pdb on cryo-EM map

Use CCP-EM! Which has your favourite CCP4 programs adapted for cryoEM, plus some others. See www.ccpem.ac.uk There is a hierarchy from rigid body fitting (of your xtal monomer), to flexible fitting (to account for adjustments in the new form), to de novo building and

Re: [ccp4bb] building into EM map

You could look at the CCP-EM software http://www.ccpem.ac.uk/download.php which includes CCP4 programs adapted to cryoEM (e.g. allowing input of cryoEM map). There is a range of possibilities from rigid body fitting of components, flexible fitting or de novo building. At 4 A, you may struggle

[ccp4bb] FW: CCPBioSim conference

on behalf of Jon Essex: === The 5th annual CCPBioSim conference "Frontiers of Biomolecular Simulation" will be held at the University of Southampton, from Wednesday 13th to Friday 15th September 2017. The aim of the event is to bring together computational and

Re: [ccp4bb] Cryo-em model building with Balbes

Hi, MRC is a map format, and doesn't hold the reciprocal space structure factors that Balbes expects, and that are referred to in the error message. Yes, you will need to calculate structure factors, which are held in the MTZ format. Simplest way is to use Refmac, which deals with issues like

[ccp4bb] EMBO practical course on image processing for cryo-electron microscopy

Elena Orlova, Helen Saibil, Peter Rosenthal, and Carolyn Moores * * 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 *

Re: [ccp4bb] Docking crystal structure into EM model

Yes, it can certainly be error-prone and subjective. A nice survey of issues and scoring functions (including use of Laplacian filter) is in http://www.ncbi.nlm.nih.gov/pubmed/21296161 You might find some useful tips in our recent workshops:

[ccp4bb] CCPBioSim one day training workshop on free energy calculations

) * * 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 * -- Scanned by iCritical.

Re: [ccp4bb] CCPBioSim 1-day training course: How to set up a protein simulation, 29th Sept, Oxford

://eventbooking.stfc.ac.uk/news-events/ccpbiosim-how-to-set-up-a-protein-simulation-228 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] Time on the UK national supercomputing service (Archer) from the HECBioSim consortium

for HECBioSim, please drop me a line. * * 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 * -- Scanned by iCritical.

[ccp4bb] CCPBioSim 1-day training course: How to set up a protein simulation, 29th Sept, Oxford

-a-protein-simulation-228 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 * -- Scanned by iCritical.

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

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

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

Re: [ccp4bb] ccp4 man-pages

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

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] Position available in biomolecular simulation

. 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] Fractional coordinate shift with two-character chain names?

, 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

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

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

[ccp4bb] 2 positions available for software developers in cryoEM

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] Why the name aimless

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,

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

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

[ccp4bb] CCPBioSim workshop on MD and Annual Conference

. 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] Instruct Biennial Meeting 22-24th May - Registration Open

, 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

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] two positions available in computational electron cryo-microscopy

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

. 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] Crystallography on BBC Radio 4 next week

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

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

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

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

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

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

-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury

Re: [ccp4bb] Covert Structure Factor to mtz

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

Re: [ccp4bb] Covert Structure Factor to mtz

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] Off topic about program for multiple protein sequence alignment

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

[ccp4bb] reminder: CCP-EM positions now available

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] REFMAC Riding Hydrogens

Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk -- *** * * * Dr. Martyn

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

-- *** * * * Dr. Martyn Winn

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

the problem. Cheers, Dialing -- *** * * * Dr. Martyn Winn

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

-- *** * * * 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] unusual bond lengths in PRODRG cif file

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

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

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

. 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 announcement: Computational methods for macromolecular phasing and refinement, 11-16th March 2012

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] converting mmcif to mtz failure

-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

Re: [ccp4bb] identifying hinges in flexible proteins

-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

Re: [ccp4bb] Pyroglutamate in structure calculation

-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory

Re: [ccp4bb] protein segments from pdb

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

Re: [ccp4bb] low resolution refinement

. Could you help me? Thank you very much! -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] generate large symmetry model

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] Phaser_EP

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] Script / program to change chain ID 's in symmetry mates

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

Re: [ccp4bb] MR with MD trajectories

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] Data file wrangling question

-- *** * * * 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

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] TLS from PDB records

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] Saxs reviews or books

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

[ccp4bb] Job posting: EM Software Developer

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] limit for number of files for CAD...

78FD 6669 67BA 8D5D -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Bug in c_truncate?

-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory

Re: [ccp4bb] protein ligand energy

Fax: (+44) - 1865 - 287547 -- *** * * * Dr. Martyn Winn

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

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

Re: [ccp4bb] Fd-3m with pdbset

-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory

Re: [ccp4bb] Fd-3m with pdbset

will clean up CCP4 Fortran programs at least. m -- *** * * * Dr. Martyn Winn

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

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

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

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

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

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] Converting cif-files into pdb-files / reading cif -files into coot

. 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] How to calculate real-space CC by section?

-- *** * * * 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] TLSANL total B factor question

-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

Re: [ccp4bb] automise ncont

-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4

Re: [ccp4bb] _diffrn.detail in PDB sf.cif releases

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

Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)

the csymmatch example program of the clipper library, it does part of what I intend to do. Thanks a lot, Francois. -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] methews coefficient and validation of 60mer

, Chandigarh, INDIA -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] refmac

Described at: http://www.ccp4.ac.uk/dist/html/refmac5/keywords/xray-principal.html#scal Simple scaling doesn't take into account the bulk solvent at all, whereas Babinet is a simple fix. A more sophisticated treatment of bulk solvent is given by the SOLVENT keyword:

Re: [ccp4bb] refmac5/ccp4i GUI error

| -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E

Re: [ccp4bb] converting .cv to mtz

Your format string works for me. It's hard to say what has gone wrong without seeing how you ran it. Perhaps you could send me the complete log file? If you choose column type X X-plor Rfree, then it should convert automatically between the conventions. HTH Martyn -Original Message-

Re: [ccp4bb] edit mtz cell in header?

Well, yes, that's how I would do it (but with Emacs). But I guess the official way would be with Reflection Data Utilities - Edit MTZ Datasets which will edit the dataset cells. It wraps keywords of CAD. Martyn -Original Message- From: CCP4 bulletin board on behalf of Ed Pozharski

Re: [ccp4bb] pdbcur failed with the error message 'child process exited abnormally'

The big problem here is that it doesn't recognise the NOANISOU keyword. So I presume that you are picking up an old version of CCP4, or more likely a Coot version of pdbcur. Mmmm the fact that the banner doesn't report user or date or time suggests a dodgy version. I would have to defer to a Mac

Re: [ccp4bb] Problem in MAKE_U_POSITIVE

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

Re: [ccp4bb] anisotropic temp for H2O

of the Negev Ph: 972-8-6461325‎ -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] How to work around strange naming XYZIN convention?

the programs _not_ append a useless extension .brk in a scripted environment? -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Reporting crashes to CCP4BB...

data, which you may or may not be able to provide of course. Hope that helps! Kevin -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] ccp4i, OS X 10.5.7, security enforcement

/local/ccp4-6.1.1/bin/ccp4i line 5) -- *** * * * Dr. Martyn Winn

[ccp4bb] Research technician at oxford University

-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury

Re: [ccp4bb] combine more than 9 datasets

Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319 -- *** * * * Dr. Martyn Winn

[ccp4bb] Reminder: 3 positions available in the CCP4 core group

Reminder that the closing date for our jobs is this Friday. Although good candidates can always contact me directly after this date. Cheers Martyn On Wed, 2009-06-03 at 16:52 +0100, Martyn Winn wrote: 3 COMPUTATIONAL SCIENTIST POSITIONS IN THE CCP4 PROJECT FOR MACROMOLECULAR CRYSTALLOGRAPHY

Re: [ccp4bb] Problem about Molecular Replacement with identity 30% model

I make sure my rotated and translated MR model is right and can be used for next model building and refinement? -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] mtz2various is broken [ was: Another pointless question ]

-- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4

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