Re: [ccp4bb] real real-space-refinement

2020-07-31 Thread Fischmann, Thierry
Jim wrote: "technically, not in Phenix either. The real-space refinement in Phenix simply picks peaks in the density and then pulls nearby atoms toward them. . Like a black hole gobbling up nearby planets (snip)" Do you have a reference to support this assertion? "It took me a while to realize

Re: [ccp4bb] real real-space-refinement

2020-07-31 Thread James Holton
Not in CCP4, no. And, technically, not in Phenix either.  The real-space refinement in Phenix simply picks peaks in the density and then pulls nearby atoms toward them.  Like a black hole gobbling up nearby planets. It took me a while to realize that! If you manage to turn off geometry

[ccp4bb] Sanofi Postdoctoral Fellowship: Computational Scientist for Antibody Engineering (Framingham, MA)

2020-07-31 Thread Qiu, Yu PH/US
Dear CCP4 community, The Protein Engineering group within Sanofi Large Molecule Research Department is seeking a highly talented Computational Scientist for a postdoctoral position. We use leading-edge structural biology and computational tools to support biologics project needs from Sanofi's

Re: [ccp4bb] Help With Setting up a Stereo view system

2020-07-31 Thread Marian Oliva
Dear all. Issue solved. It was a matter of installing the MATE desktop environment. Now everything is up and kicking Thanks a lot for all the help Marian Oliva CSIC-Centro de Investigaciones Biológicas Margarita Salas 9, Ramiro de Maeztu 28040-Madrid (Spain) phone: 0034 91 8373112 (x4380)

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2020

2020-07-31 Thread Manfred S. Weiss
Dear all, the next MX-proposal application deadline: September 01, 2020 is approaching As usual, all proposals will be handled by our electronic user portal GATE, https://www.helmholtz-berlin.de/pubbin/hzbgate Hereby we would like to invite the submission of new proposals for MX-beamtime at

Re: [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-31 Thread Eleanor Dodson
Is the R factor for the best solution really > 40% - if so there must be some major errors to correct. Eleanor On Fri, 31 Jul 2020 at 11:08, John R Helliwell wrote: > Dear Rafal, > The difference map you show in your attachment has an echo of the main > structure sort of look. So, I suggest you

Re: [ccp4bb] Problems with refinement of nucleic acid structure

2020-07-31 Thread John R Helliwell
Dear Rafal, The difference map you show in your attachment has an echo of the main structure sort of look. So, I suggest you examine your diffraction images specifically looking out for a supercell of weak intensity spots, not picked up by the autoindexing, between the main lattice of

Re: [ccp4bb] Help With Setting up a Stereo view system

2020-07-31 Thread Dirk Kostrewa
Dear Marian Oliva, in my experience, MATE, XFCE and Plasma 5/KDE work well with 3D stereo if the compositor is disabled. You don't even have to disable COMPOSITE in the xorg.conf - for those desktops, it is sufficient to disable composite in the respective desktop/compositor/window manager

Re: [ccp4bb] Help With Setting up a Stereo view system

2020-07-31 Thread Kay Diederichs
we use the Mate desktop; this interacts well with the composite extension. HTH Kay On Thu, 30 Jul 2020 16:01:20 +0200, Marian Oliva wrote: >Thanks Matthias & Pedro, > >Yes, this was the initial point. I needed to connect the monitor through a DVI >port and not through the display port. > >Now