[ccp4bb] Offtopic - In vitro protein interaction analysis using Diazirine crosslinkers.

2009-11-04 Thread Rohan Agashe
Apologies for an off topic question. I was hoping for some advice regarding the use of sulfo-NHS diazirine crosslinker (Pierce linkhttp://www.piercenet.com/products/Browse.cfm?fldID=DB013E61-5056-8A76-4EC4-473A6F2468A1) for in vitro protein interaction analysis. Have tried labeling the protein

[ccp4bb] FW: Refmac5: Open failed: Unit: 7, File: /tmp/refmac-nm_temp1.21850_new.crd

2009-11-04 Thread Czerminski, Ryszard
Hello, I am working with refmac-nm code derived from refmac5 and I am encountering an error below [...] Open failed: Unit: 7, File: /tmp/refmac-nm_temp1.21850_new.crd (logical: /tmp/refmac-nm_temp1.21850_new.crd) BFONT COLOR=#FF!--SUMMARY_BEGIN-- Refmac_5.2.0019: Open failed:

[ccp4bb] Special position refinement

2009-11-04 Thread Jan Dohnalek
Dear all, we have seen again with the 5.5.0102 version that water O or Fe ion are not held on the crystallographic axis automatically. What should we do except using possibly the restrain keyword? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of

[ccp4bb] Offtopic - In vitro protein interaction analysis using Diazirine crosslinkers.

2009-11-04 Thread Rohan Agashe
Apologies for an off topic question. I was hoping for some advice regarding the use of sulfo-NHS diazirine crosslinker (Pierce linkhttp://www.piercenet.com/products/Browse.cfm?fldID=DB013E61-5056-8A76-4EC4-473A6F2468A1) for in vitro protein interaction analysis. Have tried labeling the protein

[ccp4bb] Offtopic - In vitro protein interaction analysis using Diazirine crosslinkers.

2009-11-04 Thread Rohan Agashe
Apologies for an off topic question. I was hoping for some advice regarding the use of sulfo-NHS diazirine crosslinker (Pierce - http://www.piercenet.com/products/Browse.cfm?fldID=DB013E61-5056-8A76-4EC4-473A6F2468A1) for in vitro protein interaction analysis. Have tried labeling the protein

[ccp4bb] Off topic - nickel magnetic beads

2009-11-04 Thread P Hubbard
Hi all, I'm looking at getting some nickel magnetic beads. I've never used them before, and they seem pretty expensive. Does anyone know of a good inexpensive supplier? Thanks in advance for any replies!

[ccp4bb] Zalman monitor on Linux and Coot

2009-11-04 Thread Ajit Datta
Hello everyone, Sorry for a non-CCP4 related question again. Can anyone let me know how to make stereo work on linux with Zalman monitor with Coot? Is it as simple as what we do with CRT monitors? Or do we need something else? We presently use CRT monitors on a Quadro FX 4600 graphics

Re: [ccp4bb] Zalman monitor on Linux and Coot

2009-11-04 Thread Justin Hall
Hi Ajit; One of our CRT monitors broke recently, and in the context of bemoaning the loss to a friend I was told that LCD monitors will not work for stereo viewing. I understood the reason to be related to the difference in refresh rates (?), with LCD's not being fast enough so that the

Re: [ccp4bb] Zalman monitor on Linux and Coot

2009-11-04 Thread J├╝rgen Bosch
Rubbish, excuse my English :-) I have four Zalman's running in stereo although I have to confess they're all running on various Macs (MacBook Pro, Mac Mini, MacPro) under 10.5 or 10.6. I have no clue if the Zalman runs under linux. Regarding the stereo effect it is superior than conventional

Re: [ccp4bb] Zalman monitor on Linux and Coot

2009-11-04 Thread Anastassis Perrakis
The Zalman defeats these with a very smart trick. We got out first one, and it's really very good, albeit not perfect in some details. Pymol and Coot worked just like that with it. Sent from my iPhone On 4 Nov 2009, at 19:26, Justin Hall hallj...@onid.orst.edu wrote: Hi Ajit; One of our

Re: [ccp4bb] Zalman monitor on Linux and Coot

2009-11-04 Thread Jim Fairman
I can personally verify that the new Nvidia 3D Vision system on 120 Hz LCD monitors and a Nvidia Quadro FX Video Card display stereo flawlessly in Pymol, Wincoot, UCSD Chimerica, and any other application that uses OpenGL or Direct3D as its display media within both Windows Vista and Windows 7

Re: [ccp4bb] Zalman monitor on Linux and Coot

2009-11-04 Thread Justin Hall
Thanks to everyone for the info on Zalman monitors, sorry to have muddied the waters for you Ajit. Best wishes~ ~Justin Quoting Justin Hall hallj...@onid.orst.edu: Hi Ajit; One of our CRT monitors broke recently, and in the context of bemoaning the loss to a friend I was told that LCD

Re: [ccp4bb] Zalman monitor on Linux and Coot

2009-11-04 Thread Paul Emsley
I should add that I have only seen Joel Bard's Zalman monitor briefly. We tweaked the settings a bit to improve the representation in the following way: 1) use nvidia-settings to override application anti-aliasing - crank it up to 16x if you have a good graphics card 2) add to ~/.coot file

[ccp4bb] Index, glossary and errata for BMC

2009-11-04 Thread Bernhard Rupp
Dear All, as a first step towards building the web resources for my book Biomolecular Crystallography: Principles, Practice and application to Structural Biology I have made publicly available the Index and the Glossary in searchable PDF format. I hope this might help locating contents more

[ccp4bb] map display in pymol

2009-11-04 Thread Raja Dey
Dear Friends, I can create a mesh in pymol as follows: isomesh 2ffmesh, nov42_001_2mFo-DFc.map, 2.5, sele, carve=1.6, where the 'sele' is a particular residue and the map is created ommiting that residue from the pdb. But, I can't create the mesh in pymol when I am using Fo-Fc