Re: [ccp4bb] New BUILT of XDS for academic users

Dear Wei, I have seen a similar problem with the latest ifort compiler (that I use) but thought it didn't occur with the (old) ifort version that is used for the production binaries that are on the XDS download server. Please show me an exact copy of the full error message (more is better). I w

Re: [ccp4bb] New BUILT of XDS for academic users

Dear Kay, I updated this version and noticed some error message that I haven't experience before. When I cp latest geometry description over previous one and rerun integrate & correct, there's a very large chance to get "!!! ERROR !!! CANNOT OPEN OR WRITE SCRATCH FILE IN "STRONGHKL1"". xds_par the

[ccp4bb] REMINDER, job opportunities in Melbourne, Australia

Dear All: The Elmlund laboratory (http://simplecryoem.com), Monash University, Melbourne, develops methods for single particle electron microscopy and conducts an integrative structural biology research program, focussing on Eukaryotic transcription regulation. We study the large but transient pro

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Dear all, thank you for your comments! Also, Dr Gildea, it is not your fault but mine. I used bookmarked page and saved this link some time ago. Google gives correct link to DIALS github page. 2016-12-10 21:01 GMT+03:00 Richard Gildea : > The documentation you linked to is out of date (our fault)

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

The documentation you linked to is out of date (our fault), the new DIALS homepage is: http://dials.github.io The precise behaviour of the dials.index parameter filter_ice is described more explicitly in the current documentation: http://dials.github.io/documentation/programs/dials_index.html

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Dear Eugene, This is only in dials.index, and even then it is only in the initial maximum cell estimation that reflections from ice rings are excluded by default. They are included in the basis vector determination and further refinement. If you wish to exclude ice ring reflections from all ste

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Dear Eugene Yes this is just indexing and refinement Clearly the documentation needed to be more explicit Best wishes Graeme On 10 Dec 2016, at 17:21, Eugene Osipov mailto:e.m.osi...@gmail.com>> wrote: Dear RIchard, It is probably my problems with understanding. >From this page: http://dials.

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Dear RIchard, It is probably my problems with understanding. >From this page: http://dials.sourceforge.net/documentation/programs/dials_index.html I understood that : filter_ice = True is default parameter and by default DIALS will not consider spots at typical ice resolutions. Or it is only tru

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

"E.g. DIALS by default do not process reflections near ice rings," I'm not sure where you got this information from, but this is not correct - by default DIALS will process all reflections. Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd

Re: [ccp4bb] Modeling protein tertiary structure

Phyre2 absolutely deserves a mention. My 'threader' of choice. --- Antony W Oliver --- --- sent from my mobile account --- On 10 December 2016 at 00:05, Myeongseon Lee (이명선) <0e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk> wrote: Hi, all. C

Re: [ccp4bb] Modeling protein tertiary structure

Dear Myeongseon, my favourites are SwissModel (especially good for modelling close homologues, since it keeps conserved side chains & backbone as in the template; very fast (5-50 min), nice interactive user interface) RaptorX (good for more remote homologues too, also gives you secondary structure

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

E.g. DIALS by default do not process reflections near ice rings, 2016-12-09 21:05 GMT+03:00 Phil Evans : > For some reason there is no data in that resolution bin > > Phil > > > On 9 Dec 2016, at 17:30, Xiao Lei wrote: > > > > Hi All, > > > > I have an x ray diffraction dataset of protein and dn

Re: [ccp4bb] Modeling protein tertiary structure

I would recommend Haddock Prof. em. Ylva Lindqvist Dept. of Medical Biochemistry & Biophysics Div. of Molecular Structural Biology KAROLINSKA INSTITUTET Tomtebodavägen 6 S-171 77 Stockholm, Sweden Phone +46 8 52487695 Mobile +46 708 264356 Fax +46 8 327626 Email: ylva.lindqv...@ki.se URL: htt