Re: [ccp4bb] Crystal rescue

2010-01-27 Thread Frederic VELLIEUX
Hi Zhiyi, There are two ways you can go about this (RT data collection). Either mount the crystals in capillaries (not all beam lines at synchrotrons have sufficient space on the goniometer setup to allow data collection on capillary-mounted crystals) or use a Humidifier (the latter is briefly

Re: [ccp4bb] reforigin on 2FKA

2010-01-27 Thread Ian Tickle
Francois, the possible non-equivalent alternate origins for F432 are: 1 0. 0. 0. 2 0.2500 0.2500 0.2500 3 0.5000 0.5000 0.5000 4 0.7500 0.7500 0.7500 plus of course the symmetry-equivalent origins generated from these 4 by the space-group centring (F) t

Re: [ccp4bb] Crystal rescue

2010-01-27 Thread Flip Hoedemaeker
Zhiyi, You can use a thin cap over your cryo loop, just put a drop of mother liquor in the top, place over the loop and make it airtight at the base. Not sure who sells these things though, I guess you can make it from a capillary too. Then remove the cryo stream or put it at a temp above fr

Re: [ccp4bb] Refining against images instead of only reflections

2010-01-27 Thread James Holton
John R Helliwell wrote: Dear James, I enjoyed your simulations. Thank you! Re your conclusion:- "However, if the disorder is correlated across the entire mosaic domain, then the "diffuse scatter" intensity pattern migrates from in between the spots to influencing the spots themselves!

Re: [ccp4bb] Crystal rescue

2010-01-27 Thread Matthew BOWLER
Hi Fred and Zhiyi, the EMBL and ESRF have also developed a dehydration device that can also be used for room temperature data collection, see the website here: http://www.esrf.fr/UsersAndScience/Experiments/MX/About_our_beamlines/ID14-2/HC1b http://scripts.iucr.org/cgi-bin/paper?S090744490

Re: [ccp4bb] Refining against images instead of only reflections

2010-01-27 Thread Colin Nave
James > Two-headed side chains or TLS will cause > potentially interpretable DS features I think the point here (probably the one you are making) is that if crystallographers produce a pseudo rigid body motion (or static disorder) model described by TLS parameters then it would make specific predi

Re: [ccp4bb] reforigin on 2FKA

2010-01-27 Thread Francois Berenger
Ian Tickle wrote: Francois, the possible non-equivalent alternate origins for F432 are: 1 0. 0. 0. 2 0.2500 0.2500 0.2500 3 0.5000 0.5000 0.5000 4 0.7500 0.7500 0.7500 It correspond to what is found at the end of James Holton's origins.com script htt

Re: [ccp4bb] reforigin on 2FKA

2010-01-27 Thread Ian Tickle
Francois, > However, from what you say, I understand that only 2x3 possible > origins with each coordinate being 0 or .5 should be accepted by > reforigin. No, 4x4 (i.e. the original 4 non-equivalent + 3x4 equivalent to these), specifically: 1 0. 0. 0. 2 0.2500 0.2500

Re: [ccp4bb] Crystal rescue

2010-01-27 Thread Ezra Peisach
MiTeGen (www.mitegen.com) sells a RT device - plastic capillary to put over loop... I do not know how well it would work for a long data collection - but people here have used it to evaluate their crystals Ezra On 1/27/2010 3:58 AM, Flip Hoedemaeker wrote: Zhiyi, You can use a thin cap

Re: [ccp4bb] Crystal rescue

2010-01-27 Thread Clayton, Gina Martyn
MiTeGen have instructions on their website for using their system. In practice I usually put a little silicon grease at the base of the capillary as sometimes the capillaries fall off plus you need reasonable steady hand eye coordination to put the capillary over the loop...I have found MiTeGen R

Re: [ccp4bb] Rfree and thin shells

2010-01-27 Thread Mark J. van Raaij
Dear Al, Refmac by default divides reflexions in 20 shells ("bins") - this can mean a few of them do not contain a thin Rfree shell. When this happens I add "bins 10" to the refmac com-file, or, in CCP4i, instead of "run", do "run and view com file" and add "bins 10" to the file before conti

Re: [ccp4bb] Crystal rescue

2010-01-27 Thread Mark J. van Raaij
in my opinion one should always first check RT diffraction and we use the Mitegen plastic cap over the loop. We find the solutions slowly dry out (6-18 hours), which can be enough to get a useful RT dataset on the rotating anode. If you like, the crystal can also be recovered after RT diffrac

[ccp4bb] SPMP 2.0 - new release of Selvita Protein Modeling Platform

2010-01-27 Thread Mateusz GaƂuszka
Dear All, We are pleased to announce the release of a major new upgrade (version 2.0) of Selvita Protein Modeling Platform. Selvita (www.selvita.com) is a biotechnology company based in Krakow, Poland. One of the company's primary areas of expertise are Molecular Modeling and Computer Assisted D

[ccp4bb] PhD student position in Structural Biology

2010-01-27 Thread Clemens Steegborn
PhD student position in Structural Biology We are currently looking for a highly motivated Ph.D. student for our laboratory at the Dept. of Biochemistry at University Bayreuth, Germany. Our work involves biochemical and structural studies on cellular signalling systems with relevance to aging mech

Re: [ccp4bb] reforigin on 2FKA

2010-01-27 Thread James Holton
Francois Berenger wrote: It correspond to what is found at the end of James Holton's origins.com script http://bl831.als.lbl.gov/~jamesh/pickup/origins.com so I guess it should be correct. Uhhh... He also says how he found them: # TABLE OF ALLOWED ORIGIN SHIFTS These origin shifts were determ

Re: [ccp4bb] reforigin on 2FKA

2010-01-27 Thread Ian Tickle
... and I was assuming that since it was clear that there are omissions for F222 and F23 on the CCP4 'alternate origins' page, that James' page was 100% correct! But I think we have both made the same mistake of assuming that F222, F23 and F432 all behave identically as far as origin shifts are co

Re: [ccp4bb] reforigin on 2FKA

2010-01-27 Thread Ian Tickle
Correction: my apologies, I see now that the table of Cheshire groups that I referred to originally came from: Hirshfeld (1968), Acta Cryst. A24, 301-311. I got it from Jorge: it's still good to know that it has Jorge's seal of approval! Cheers -- Ian > -Original Message- > From: owner

Re: [ccp4bb] reforigin on 2FKA

2010-01-27 Thread Peter Zwart
Hi, If you go to http://cci.lbl.gov/cctbx/explore_symmetry.html fill out any space group (F432), and search for: Additional generators of Euclidean normalizer to get Number of structure-seminvariant vectors and moduli: 1 VectorModulus (1, 0, 0) 2 The seminvariants for F432 a

Re: [ccp4bb] Help with MR in P21

2010-01-27 Thread wu donghui
Two cents are added here. First, try P2 as somethimes systematic absence along b axis is misleading due to weak diffraction or pseduo translation. Second, try P1. Good luck, Donghui On Tue, Jan 26, 2010 at 1:50 AM, Michele Lunelli wrote: > Dear all, > > I am trying to solve a structure at 2.

Re: [ccp4bb] Crystal rescue

2010-01-27 Thread Ho Leung Ng
Hi Zhiyi, I think the easiest way is to mount your crystal in an air-impermeable, viscous oil like Paratone in a loop. Of course, your crystals may not tolerate oil. ho

Re: [ccp4bb] Refining against images instead of only reflections

2010-01-27 Thread John Badger
Colin, Your point: "I think the point here (probably the one you are making) is that if crystallographers produce a pseudo rigid body motion (or static disorder) model described by TLS parameters then it would make specific predictions of diffuse scatter. These predictions could be used to test th

Re: [ccp4bb] Refining against images instead of only reflections

2010-01-27 Thread Ethan Merritt
On Wednesday 27 January 2010, John Badger wrote: > Colin, > > Your point: > "I think the point here (probably the one you are making) is that if > crystallographers produce a pseudo rigid body motion (or static > disorder) model described by TLS parameters then it would make specific > predictions