Re: [ccp4bb] cryoEM molecular replacement

Hi Gloria, I agree that ChimeraX is the easiest starting point for this. After that, the CCP-EM suite has a variety of rigid and flexible fitting methods that you can try (including em_placement in the latest). Also many validation functions, which are kind of important 😊 Our annual Icknield

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 - De

[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. https://www.ukri.org/about-us/work-for-us/join-an-advisory-committee-panel-or-network/mrc-board-and-pa

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 Cor

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 all

[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 goo

[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 r

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 [mailto:CCP4BB@JISCMAI

[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 An

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 https://bio3d.colorado.edu/imod/doc/man/ct

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

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 w

[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 expe

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

rely yours 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: http://www.ccpem.ac.uk/training/icknield_2016/ickniel

[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

at https://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: m

[ccp4bb] Time on the UK national supercomputing service (Archer) from the HECBioSim consortium

e 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

-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 aim

[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 centre,

Re: [ccp4bb] ccp4 man-pages

oc; done #> bash makeman.sh > > That's good enough for me. > > Regards, > Tim > > On 11/15/2013 03:46 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

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 nroff/gro

[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.uk<mailto:martyn.w...@stfc.ac.uk>

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 < -Original Message- > From: CCP4 bulletin board [mailto:CC

[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 c

[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

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

bursaries 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 1

[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] 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

osim.ac.uk * * 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] 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 Message

[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)

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)

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

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

n-CCP4 post" -- *** * * * Dr. Martyn Winn * *

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 th

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 m

[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

y (i.e. stereochemically correct) > > model. > > >> > > > > > > and here are the results of more or less systematic test that > > prove this: > > > > > > see "On contribution of hydrogen atoms to X-ray scattering" > >

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

n status 0 "child process excited anormally". > > I am looking forward to getting a reply from you on how to > solve the problem. > > Cheers, > > Dialing > > > &g

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

to getting a reply from you on how to > solve the problem. > > Cheers, > > Dialing > > > > > -- ******

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

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

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

t; > Regards > > John > > > > Dr John W. Liebeschuetz > > Research & Applications Manager > > Cambridge Crystallographic Data Centre > > 12 Union Rd., Cambrid

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

r research 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

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

es. This is the get-out method if cif2mtz fails. Edit the item >name to something that is recognised. Cheers Martyn -- *** * * * D

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

ur reseach 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

ror message > child process exited abnormally > *** > > > #CCP4I TERMINATION STATUS 0 "child process exited ab

Re: [ccp4bb] identifying hinges in flexible proteins

x27;unbiased' way? > > thanks for your suggestions, > > Stephen Cusack > > > -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] Pyroglutamate in structure calculation

a definitions? > > > Thanks justin > > -- *** * * * Dr. Martyn Winn * *

Re: [ccp4bb] protein segments from pdb

ommand would be much quicker. > > Thanks. > > > Andreas > > -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laborato

Re: [ccp4bb] low resolution refinement

tion? > > > > BTW, is that simulator annealing not suitable for low resolution > > structure? I used the simulator annealing method of CNS and > > phenix.refine, but the geometry of the structure is always destroyed > > seriously. > > > > Could you help me? > > > > Thank you very much! -- *

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 [mailto:

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] MrBUMP, P43212 and P41212

I thought so too It seems to me that there is a typo in the spacegroup name in the code. I'll send you some fixed files offline. Ronan is the expert on queueing systems, but I though the keyword "CLUSTER" should be enough. It is supposed to work with SGE. There also seems to be an undocume

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

e are interested in > script because that dataset that we are handling is large. > I thank you all in advance for your help. > Best, > > Krishan -- *** *

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 nee

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 wra

Re: [ccp4bb] Data file wrangling question

like a simple thing someone would want to do. > > > Thanks, > > > Graeme -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Lab

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 que

Re: [ccp4bb] Saxs reviews or books

Regards, > > > > Rojan > > > > -- > > This message has been scanned for viruses and > > dangerous content by MailScanner, and is > > bel

[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 Progra

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

Sc. > > 215 UCB > > University of Colorado at Boulder > > > > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > > > > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D > -- ***

Re: [ccp4bb] Bug in c_truncate?

X flagging > > > > convention is "1" for working and "-1" for test. So I manually tagged > > > > the working set with "1" using vi: > > > > > > >

Re: [ccp4bb] protein ligand energy

rer > and Head of Research Computing, > Wellcome Trust Centre for Human Genetics, > Roosevelt Drive, Oxford OX3 7BN, UK > > Emails: rob...@strubi.ox.ac.uk Tel: (+44) - 1865 - 287783 > and rob...@esnouf.comFax: (+44) - 1865 - 287547

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

s > > Dr Alan Roseman > Tel: + 44 (0) 161 275 7226 > Email alan.rose...@manchester.ac.uk -- ******* * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4A

Re: [ccp4bb] Fd-3m with pdbset

n't help with Coot problems, but I will clean up CCP4 Fortran programs at least. m -- *** *

Re: [ccp4bb] Fd-3m with pdbset

ot for such a > small molecule). > > Kind regards, Tim > > P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3 > -- ******* * * *

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

B 3.' 'B 3.' C2 > RANGE 'B 3.' 'B 3.' O2 > RANGE 'B 3.' 'B 3.' N3 > RANGE 'B 3.' 'B 3.' C4 > RANGE 'B 3.' 'B 3.' O4 > RANGE 'B 3.' 'B 3.' C5 > RANGE 'B 3.' 'B 3.' C6 > > I guess I've got the syntax of

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

bytes" that spell "MAP ", or a value of nsymbt that indicates > the > presence of additional symmetry information following the > header, which > is then missing. > > Chimera ignores most of these issues. > > -Christoph

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 rea

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

ewert (Vorsitzender), Ulf > Bialojahn, Dr. Matthias Braun, > Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, > Dr. Heinz Riederer > > * > >

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

HOLE region define by > the section range? > > Thanks! > > Best Regards, Hailiang -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury

Re: [ccp4bb] TLSANL total B factor question

and how > can I print my total B factors. > > > Thanks > Regards > Shiva Kumar -- *** * * * Dr. Martyn Winn

Re: [ccp4bb] automise ncont

Thank you for your time! > > Best wishes, > Thomas -- *** * * * Dr. Martyn Winn * *

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

a-gathering protocol where exposure increased over time. > > Tom -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, War

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

> does part of what I intend to do. > > Thanks a lot, > Francois. -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +

Re: [ccp4bb] H32 or R 3 2 :H

o accept both? > Eleanor -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-m

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

D Scholar > Crystallography Laboratory > Division of Protein Science & Engg. > IMTECH , Chandigarh, INDIA -- *** *

Re: [ccp4bb] refmac5/ccp4i GUI error

one have any ideas on what is going > wrong? I see one similar message in the archives, but there were no > responses at that time. > > Thanks. > > -ben > > -- > | Ben E

Re: [ccp4bb] Data harvesting file corrupted in refmac

Comparing to one of my refmac jobs, it is slightly different because of different system and options. However, I would guess that the missing labels are: r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other But don't take my word for it - c

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: http://www.ccp4.ac.uk/dist/ht

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- Fr

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 Sent

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 p

Re: [ccp4bb] Problem in MAKE_U_POSITIVE

-- > > Anything is possible if you don't know > > what you are talking about. > > - > > > > > > -- *** * * * Dr. Martyn Winn * *

Re: [ccp4bb] anisotropic temp for H2O

version) > > > > thanks Elad > > > > > > > > Elad Binshtein > > Ph.D student > > Department of Life Science > > Ben Gurion University of the Negev > > Ph: 972-8-6461325‎ > > -- ****

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

t file named >$tempfile.brk > > Is there any way to make the programs _not_ append a useless extension > ".brk" in a scripted environment? > -- *** *

[ccp4bb] CCP4 at the ECM

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

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

to the bulletin board and send more information to any developer who > asks. In the hardest cases, the developer may need access to your data, > which you may or may not be able to provide of course. > > Hope that helps! > Kevin > -- *****

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

; chernev 12% ccp4i > CCP4I_TCLTK is /usr/local/X11/bin > Error in startup script: can't read "CCP4I_TCLTK": no such variable > while executing > "exec ${CCP4I_TCLTK}/bltwish "$0" -- ${1+"$@"}" > (file "

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