[ccp4bb] Seeking collaborators.

2007-08-14 Thread cry
Dear all, Our laboratory can undertake Academic or Commercial Project in protein expression, crystallization of protein/nucleic acid/complex and some functional study with considerable low cost (or you have to apply in conjunction with us for the funding of Chinese government). We have

Re: [ccp4bb] CCP4 rotation convention

2007-08-14 Thread Ian Tickle
Hi Eleanor We seem to agree completely, i.e. the relevant statement from my second (corrected) e-mail in this thread (the one you replied to) was: R = Rz(a).Ry(b).Rz(g) i.e. first by gamma about z, then by beta about the *fixed* y axis, then by alpha about the *fixed* z axis, which

Re: [ccp4bb] extra density on Cysteine

2007-08-14 Thread mesters
Rather difficult to decide. It depends on whether BME was present during all protein purification steps. Also, BME is somewhat short lived. You have to add new BME every few days or so. At least one looks like it could be oxidized, a process that cannot be reversed by BME J. Artem

[ccp4bb] coot in stereo

2007-08-14 Thread Paul D. Cook
Hello, I'm running stereocoot on linux (centos) machines with nvidia video cards and stereographics emitters and glasses. The setup seems to work fine most of the time, but the stereo will invert every now and then (the right eye is shown the left image and vice versa). This seems to happen

Re: [ccp4bb] coot in stereo

2007-08-14 Thread Schubert, Carsten [PRDUS]
Paul: that is a problem with the NVIDIA hardware. In some old release notes 2 years ago they spoke of some instabilities of the GPU with regards to stereo. This happens more under linux than under windows, which points to a driver issue. To my knowledge there is not much you can do. May be

Re: [ccp4bb] extra density on Cysteine

2007-08-14 Thread Stephen Graham
2cystein.jpeg looks just like oxidation of cysteine to S-hydroxy-cysteine (a.k.a. cysteine sulfenic acid). I have seen this repeatedly in one of my structures (E. coli aminopeptidase P, see 1WL9 for an example). We discuss this a bit in Graham et al (2005) Biochemistry 44: 13820-36 - see Figure

Re: [ccp4bb] CCP4 rotation convention

2007-08-14 Thread Ian Tickle
Bernhard - In case you're still trying to follow the convoluted arguments in my previous long answer, here's the short answer (for your summary!): Replace the word 'new' (twice) in this sentence in Phil's AC 2001 article with the word 'fixed': ... rotate by gamma around z, then by beta around

[ccp4bb] question

2007-08-14 Thread Mirek Cygler
Hi, Here is a question from a Windows illiterate. I would like to run pdbcur with parameters that are not accessible through the CCP4i interface. Need to create symmetry-related molecule. I can modify the script file but I do not know how to execute the program. I guess that I only know

[ccp4bb] Computer/X-ray Crystallography Laboratory Manager at Scripps-Florida

2007-08-14 Thread Izard, Tina
A staff scientist position is advertised in Science online on http://aaas.sciencecareers.org job code 22507-J211364P. For details please refer to http://aaas.sciencecareers.org/texis/jobsearch/details.html?id=46c082924a0280q=scripps-floridaqField=AllqSort=dateqMatch=allpp=20view=1page=1

Re: [ccp4bb] coot in stereo

2007-08-14 Thread mjvdwoerd
Paul: We are running Coot under Centos with Nvidia video cards, emitters and glasses. Although our system is relatively new and therefore has not been used as extensively as I would like to see, we have never encountered your problem and hopefully will not. There are programs (VMD) in which

[ccp4bb] Postdoctoral fellow / Research Associate position with the Structural Genomics Consortium, Toronto

2007-08-14 Thread alexey bochkarev
The Structural Genomics Consortium (SGC) is adopting a biology-centered approach to structural genomics: dedicated biology groups with target-specific expertise work on getting the proteins soluble, and biophysical and functional characterizations feature prominently. Interesting biological

Re: [ccp4bb] coot in stereo

2007-08-14 Thread Kay Diederichs
Paul D. Cook schrieb: Hello, I'm running stereocoot on linux (centos) machines with nvidia video cards and stereographics emitters and glasses. The setup seems to work fine most of the time, but the stereo will invert every now and then (the right eye is shown the left image and vice versa).