Re: [ccp4bb] shadow at the edge

it to work. We have done this work for the DLS I04 format class - if you let me know (off list) the location of your data on disk at Diamond I can try to help you process the data taking into account the goniometer shadowing. Thanks, Richard Dr Richard Gildea Data Analysis Scientist Tel: +4412

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

max_cell_estimation .expert_level = 1 { filter_ice = True .help = "Filter out reflections at typical ice ring resolutions before" "max_cell estimation." .type = bool } Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441

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 Li

Re: [ccp4bb] Spot Integration Vs Fitting

Dear Jacob, DIALS and MOSFLM each output both of the intensities you describe (although DIALS does 3D profile fitting whereas MOSFLM does 2D profile fitting). The first, Isum, are the summation integrated intensities, the second, Iprf, are the profile-fitted intensities. The scaling program

Re: [ccp4bb] Writing .xplor or CCP4 maps from raw data

Hi Anthony, You can achieve this easily using the cctbx. I assume that your 3D grid of floating points is a numpy array - if so you will have to convert this to a cctbx flex array as shown in the simple example below. The cctbx can also has the functionality to write out xplor maps - if needed

Re: [ccp4bb] mmCIF as working format?

The cctbx provides comprehensive tools for handling mmcif files (and indeed all types of cif files - it is not fussy), freely available under the BSD-style cctbx licence. Cheers, Richard On 7 Aug 2013, at 19:16, Jeffrey, Philip D. pjeff...@princeton.edu wrote: Are all the APIs open source ?

Re: [ccp4bb] CCP4 Update victim of own success

Perhaps there needs to be a separate update manager to manage updates to the update manager: [image: Inline images 1] (from http://xkcd.com/1197/) Cheers, Richard -- Richard Gildea Software Developer Physical Biosciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd Mail

Re: [ccp4bb] Off-topic: Best Scripting Language

-- Richard Gildea Software Developer Physical Biosciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd Mail Stop 64R0121 Berkeley CA 94720-8118 On 13 September 2012 10:02, Patrick Shaw Stewart patr...@douglas.co.ukwrote: Like most computer users and many scientists I don't write

Re: [ccp4bb] IUCr checkCIF server.

PDB files (the mmcif dictionary differs significantly from the core CIF dictionary which is used for small molecules), or indeed whether any checkcif output would be meaningful for a macromolecule. Cheers, Richard -- Richard Gildea Software Developer Physical Biosciences Division Lawrence

Re: [ccp4bb] Anybody knows why SSRL is unaccessible ?

They were hit by a lightning strike on Thursday evening which took out their power: https://slacportal.slac.stanford.edu/sites/esh/emergency/Pages/default.aspx Cheers, Richard On Apr 14, 2012 9:28 AM, Bosch, Juergen jubo...@jhsph.edu wrote: neither the websites nor ssh works to any of the