[ccp4bb] [Fwd: Re: [ccp4bb]: self rotation function matrix & NCS matrix]

2007-08-22 Thread weikai
Hi Eleanor and others: This is a little too late to follow up on this thread. But here is a similar question concerning MR and self-rotation. Without going into the translational part of MR, is it possible to tell the orientation of a 2-fold axis directly from the cross-rotation peaks? e.g. I ha

Re: [ccp4bb] mosflm and APS BM17

2007-08-22 Thread Jan Abendroth
Hi all, thanks a lot for all the responses! As anticipated, the solution is rather simple - the origin of the beam: denzo refines to: x=82.6 y=80.3 mosflm reads from header: x=80.0 y=84.0 - bad indexing etc mosflm works with: x=82.6 y=80.3 No swapping of x and y between denzo and mosflm in this cas

Re: [ccp4bb] crystal with precipitation

2007-08-22 Thread Lisa A Nagy
Oh, there is do much you can do! Lots of alternatives: 1. Decrease or increase the protein concentration (with a corresponding increase or decrease of precipitant. 2. Use a temperature gradient. 3. Set up in a capillary with liquid-liquid diffusion 4. SEED! #3 or #4 are your best bets, probably.

[ccp4bb] crystal with precipitation

2007-08-22 Thread shivesh kumar
Dear all I am trying to crystallize a 7kDa protein using MPD as a precipitant at 16C.I have got small florets at 55-65% of MPD in 3-4 days.The problem is that the drop is precipitating in one day only and the crystals are coming with precipitation.I have added 5% glycerol and 100mM of Nacl as an ad

[ccp4bb] area detector dark current/background correction

2007-08-22 Thread Klaas Decanniere
Hi, I am looking for information on techniques to do dark current/background correction on CCD images. I have found some information of the nonius website (http://www.nonius.nl/KappaCCD/manuals/collect/inside/dark.html) but I was hoping to find more. For instance, I seem to remember a technique

Re: [ccp4bb] [COOT] how to join the broken strand to the other whole molecular

2007-08-22 Thread Antony Oliver
In Coot - turn on the "Cell & Symmetry..." option (in the Draw menu) for your molecule, in order to visualise the other molecules within your crystal. Then use "Save Symmetry Coordinates..." (in the File menu). Click on the isolated bit of your structure that is closest to the rest of your molecul

Re: [ccp4bb] Wasp web server

2007-08-22 Thread Ian Tickle
Something else you need to be aware of when using WASP, even if the symmetry contact problem isn't an issue, e.g. as a work-around for that you could generate a PDB file containing a complete unit cell with a small border of say 3.5 Ang around it - I've no idea if the server does that for you.

Re: [ccp4bb] mosflm and APS BM17

2007-08-22 Thread Harry Powell
Hi I'd guess from the input file that the beam centre may be defined in a different reference frame to that which Mosflm expects in the image header; other possibilities are that the distance, wavelength, or something else (!) is wrong. Indexing is critically dependent on having the beam cent