Re: [ccp4bb] X-ray photon correlation length

2009-01-30 Thread Nave, C (Colin)
Hi Both transverse and longitudinal coherence length need to be considered in this. These parameters are detemined by monochromators, focusing optics and the position of the specimen along the path not just the undulator (or x-ray generator). Matching to the specimen is not necessarily as

Re: [ccp4bb] X-ray photon correlation length

2009-01-30 Thread Ian Tickle
Bernhard Yes I stand corrected, 'coherence length' it is. I think I did mean 'coherence' and not 'correlation', it's just that I had 'correlation' on my mind from something else I was doing. What I need is a 'concept checker' in addition to a spelling grammar checker! -- Ian -Original

Re: [ccp4bb] difficult MAD dataset

2009-01-30 Thread Bram Schierbeek
Hi Alison, You wrote: We recently collected a complete 2.5A MAD dataset. However, finding a solution has not been as straightfoward for reasons unclear to us. Is there radiation damage in one or more of the later sets? Did you try 1 or 1.5 wavelength? (See Dauter, /Acta Cryst./ (2002).

Re: [ccp4bb] OT: VectorNTI alternatives

2009-01-30 Thread Jeffrey Wilson
On Jan 28, 2009, at 3:47 AM, Darren Hart wrote: ps anyone using VNTI might consider a backup of their work by exporting files to .gb format. I don't know if a locked up (expired) version permits this and you will have no notice that it is about to expire. My license recently expired. I

Re: [ccp4bb] OT: VectorNTI alternatives

2009-01-30 Thread Darren Hart
Hello, I spoke to Invitrogen (France) today and they said that, if asked, they would provide a 2 month free license so that people could do exactly this and recover their files. The also said they would send me details on a simple procedure to extract the data from a locked version which I will

Re: [ccp4bb] Nvidia 3D

2009-01-30 Thread Scott Pegan
Warren, If we are buying a system from scratch, can I get the GeForce 2 card and 3D bundle and have it work for winCoot? Scott On Tue, Jan 27, 2009 at 2:58 PM, Warren DeLano war...@delsci.com wrote: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S

Re: [ccp4bb] Nvidia 3D

2009-01-30 Thread Bernhard C. Lohkamp
If we are buying a system from scratch, can I get the GeForce 2 card and 3D bundle and have it work for winCoot? I very much doubt it. If I understand it correctly this systems only works with DirectX applications. Since (Win)Coot uses OpenGL rather than DirectX it is unlikely to work

Re: [ccp4bb] temperature after 30 minutes using microscopes ?

2009-01-30 Thread Jeffrey Wilson
On Jan 21, 2009, at 6:35 PM, matthew.frank...@imclone.com wrote: My light source is halogen, but it's coupled to the microscope through a fiber optic light pipe. I know from experience that the older model scopes with the bulb right in the base get quite warm after they've been on for a

Re: [ccp4bb] difficult MAD dataset

2009-01-30 Thread Borhani, David
Alison, Given: There is a pseudo-translation with 55 % peak at a fractional coordinate of 0.5, 0.5, 0.48. I don't think you can be certain about: Systematic absences along a and b axis were observed thus the dataset was scaled in P21212 space group. Try testing all eight possible Ortho.

Re: [ccp4bb] OT: VectorNTI alternatives

2009-01-30 Thread Thomas Schalch
I'm not sure if it was already mentioned, but for those who use Vector NTI's ContigExpress to assemble and analyze sequencing data, the Staden package (http://staden.sourceforge.net/) is a great alternative. Cheers, Thomas

Re: [ccp4bb] difficult MAD dataset

2009-01-30 Thread Stefan Arold
Dear Alison, Christian Dumas of our institute has recently developed and published a program for HA detection. Being extremely powerful, and easy to use (http://www.cbs.cnrs.fr/SP/crystal/SUPERFLIP/), it has produced very precise HA positions for datasets that no other program could treat

[ccp4bb] Job opportunity: Systems Specialist II - Automation, Protein Crystallography

2009-01-30 Thread Mitch Kocen
For more than 30 years, Genentech has been at the forefront of the biotechnology industry, using human genetic information to develop novel medicines for serious and life-threatening diseases. Today, Genentech is among the world's leading biotech companies, with multiple therapies on the market

Re: [ccp4bb] Transfer Rfree flag

2009-01-30 Thread Gerard DVD Kleywegt
Can someone tell me if there is a relatively straightforward way of transferring Free R flags between two CNS format reflection files ? DATAMAN - http://xray.bmc.uu.se/usf/dataman_man.html#S63 --dvd **

Re: [ccp4bb] sparse matrix screen design

2009-01-30 Thread Gerard DVD Kleywegt
Are there any good free programs for the design of one's own sparse matrix screens? I am looking for something in the lines of a set of mixtures of what gives you the best coverage of, say, seven variables with five states each in 96 experiments. If memory serves, both Stefan Knight

Re: [ccp4bb] X-ray photon correlation length

2009-01-30 Thread James Holton
Ethan Merritt wrote: My impression is that the coherence length from synchrotron sources is generally larger than the x-ray path through a protein crystal. But I have not gone through the exercise of plugging in specific storage ring energies and undulator parameters to confirm this impression.

[ccp4bb] Refmac5.scripts error -

2009-01-30 Thread Jonathan Marvin Caruthers
All: I'm trying to get the latest version of Refmac up and running - the one bundled into ccp4 6.1.0 - and have come across an error I've never seen before: #CCP4I TERMINATION STATUS 0 Error from script /usr/local/ccp4-6.1.0/ccp4-6.1.0/ccp4i/scripts/refmac5.script: can't read space_group: no

Re: [ccp4bb] mapping sequence conservation metrics on the B factor column ...

2009-01-30 Thread Miguel Ortiz Lombardia
Hi Tassos, I very much like Homolmapper: http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm You can map several conserved properties onto your structures, not just plain sequence. Best, Miguel Le 29 janv. 09 à 22:25, Anastassis Perrakis a