Re: [ccp4bb] can anyone please give the link for downloading the software O

2011-01-24 Thread Tim Gruene
For 'O' just google for alwyn O it takes you quickly to http://xray.bmc.uu.se/alwyn/O_to_Go/O_to_Go_frameset.html which tells you how to get O. I am sure Ghostview is available for nearly all linux distributions and unless you install something like linux-from-scratch (but then you would not

[ccp4bb] Merging statistics and systematic absences

2011-01-24 Thread Graeme Winter
Dear ccp4bb, I had an interesting question from a xia2 user last week for which I did not have a good answer. Here's the situation: - spacegroup is P212121, which was specified on the command-line - xia2 processes this as oP, assigns the spacegroup as P212121 before running scala - generates

Re: [ccp4bb] Merging statistics and systematic absences

2011-01-24 Thread Phil Evans
My immediate response to this is that anyone worrying about the number of reflections should get out more. More seriously, is assessing the quality of measurements then multiple observed measurements of systematically absent reflections should agree within their error estimates and (ideally)

Re: [ccp4bb] Merging statistics and systematic absences

2011-01-24 Thread Eleanor Dodson
I absolutely agree with Phil. However I think it is very important NOT to remove systematic absences before scala. There are many cases of mis-assigned space groups where systematic absences are misleading - due to NC translation or bad measurement or whatever Eleanor On 01/24/2011

[ccp4bb] sodium vs water near methionine sulfur

2011-01-24 Thread chandan kishore
Dear All, Electron density picture is attached here. or https://docs.google.com/leaf?id=0B89uj7DSbtUWNDRmMzZhNTAtMzlkMC00MDllLTgxYmItNDI0NzUwMjdlNTlihl=en I am working on a structure at 1.45 Ang resolution. I have noticed a density that looks like water. However, it is surrounded by by six

Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?

2011-01-24 Thread Guenter Fritz
Hi Amir, I have VMware WindowsXP (guest) running on Centos5 (host) running. Open GL - 3D does not work. VMware emulates the graphics board. VMware 6.5 supports only Direct X. I don't know whether a newer version will do; I doubt. Guenter Hi, Does newer 3-D hardware work using VMWare/Windows

Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?

2011-01-24 Thread Pedro M. Matias
No, it requires a native system (Windows/Linux) installed. The graphics drivers installed by VMWare do not emulate the full HW capabilities of the Quadro card. Pedro Matias At 12:36 24-01-2011, Amir Khan wrote: Hi, Does newer 3-D hardware work using VMWare/Windows on a Mac? Thanks! Amir

[ccp4bb] Post-Doctoral Position/Scientific Programmer on PROXIMA 2

2011-01-24 Thread SHEPARD William
Dear Colleagues, We are seeking a motivated young scientist or engineer with excellent skills in programming and computing to join the PROXIMA 2 team at Synchrotron SOLEIL. Please forward the announcement below to any interested parties. Kind regards, Bill Post-doctoral Position -

Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?

2011-01-24 Thread Bosch, Juergen
I might be missing something here... The Zalman(s) work fine in Coot Pymol on a Mac (any Mac to be precise, from iBook to MacPro). Just add this to your coot.scm file: (add-key-binding switch to Zalman stereo z (lambda () (set-font-size 3) (set-graphics-window-size 1680 1050)

Re: [ccp4bb] low expression and aggregation of protein

2011-01-24 Thread m zhang
Thanks, Lin. I am sorry for being short of information. I was actually not sure what kind of information is needed. Well, the cells were grown at 27 degree in Insect-Xpress. I tried to grow cells both in shaker and stationery flask. Anything else I can try? Best, Min Date: Sat, 22 Jan 2011

Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?

2011-01-24 Thread Padmaja Mehta-D'souza
Zalman uses passive LCD stereo, however. From the thread of this discussion, it appears that active LCD stereo (using a 120Hz monitor, NVidia graphics card etc.) will not work on a Mac? Has anyone had a successful experience using active LCD stereo on a Mac? Padmaja On Jan 24, 2011, at

Re: [ccp4bb] Stereo Microscope advice

2011-01-24 Thread Sampson, Jared
Hi Kevin - 1) I can only imagine that LEDs would produce vastly less heat than halogen lamps. In general, they are small, efficient, long-lasting and don't produce a lot of heat. Here's a start for more information http://en.wikipedia.org/wiki/Light-emitting_diode . Also, a quick search got

Re: [ccp4bb] Stereo Microscope advice

2011-01-24 Thread Andrew T. Torelli
Hi Kevin, We have 3 Olympus microscopes with three different lighting options. The three variations we have on our microscopes are: 1. a microscope with a reflective light base (internal mirror) that reflects light directed into the microscope base from an external halogen light-box.

Re: [ccp4bb] Stereo Microscope advice

2011-01-24 Thread Adrian Goldman
Just one comment on LEDs as we have them as part of an imaging system. While it is true that the LEDs themselves emit cool light, the associated electronics is hotter than I would have expected. FYI. Adrian Sent from my iPhone On 24 Jan 2011, at 19:24, Sampson, Jared jared.samp...@nyumc.org

Re: [ccp4bb] Merging statistics and systematic absences

2011-01-24 Thread Ronald E Stenkamp
Maybe counting reflections is dull and boring, but doesn't it make you wonder sometimes when two programs read the same file and end up with different reflection counts? What sophisticated mathematics or logical conditions make it such that progams can't mimic adding machines? What else are

Re: [ccp4bb] Stereo Microscope advice

2011-01-24 Thread Artem Evdokimov
'White' LED light produced by most integrated white LED packages is in fact a mixture of blue (~460nm), produced by the LED itself and a broad-band yellow (560nm), produced by a secondary phosphor, typically directly coating the semiconductor that emits the primary light. The net effect is a

Re: [ccp4bb] sodium vs water near methionine sulfur

2011-01-24 Thread Sean Seaver
Hi Chandan, The closest sodium-sulfur interaction that I know of within a protein is in entry 2BDG, Na (Atom 402, Chain A) to a CYS with a distance of 3.3 Angstroms. A couple of examples exist of sodium-sulfur interactions that involve coenzyme A (1FY7 and 1MJ9). I hope that helps. Take