Re: [ccp4bb] membrane protein and phase separation

2013-08-01 Thread Noinaj, Nicholas (NIH/NIDDK) [F]
Pascal, Not personally observed this myself, but just wondering, as a control, have you tried setting trays with just the buffer+detergent (no PDC)? And if so, do you see the same behavior or not? Also, do you see phase separation in all drops or just a majority? Do the drops that exhibit th

[ccp4bb] updated fragment library web-site and lower pricing due to NIH cuts

2013-08-01 Thread Vicki Nienaber
Dear CCP4, Sorry for the off-topic post but we wanted to make the community aware that we are running a significant sale on our fragment library 1 to help offset the cuts to NIH due to the sequester. Library 1 is our first pass library, is a good stand-alone library and comes as a screening ki

[ccp4bb] membrane protein and phase separation

2013-08-01 Thread Pascal Egea
Dear All, I have a question tailored for the membrane protein and detergent folks. We are purifying a membrane protein that associates into an homoligomeric pore and we have been successfully preparing it in two detergents: FC-12 or a mild lipid. The two Protein Detergent Complexes look very homog

Re: [ccp4bb] X-rays gas scattering picture needed

2013-08-01 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Pietro, would this not look like a frame from your home source with no crystal mounted - unless you do not have access to a source where you can quickly collect an exposure in the absence of a crystal, but from your email address I assume this is

[ccp4bb] X-rays gas scattering picture needed

2013-08-01 Thread Pietro Roversi
Dear all, together with two fellow crystallographers, I am writing a pamphlet to introduce schoolchildren to X-ray crystallography. For the introductory chapter, we would need a picture of X-rays scattered by air. Or by any gas for that matter. I have tried Google images without much luck. Can

[ccp4bb] Announcement: wwPDB Workshop on mmCIF/PDBx for Programmers, 20/21 Nov-13, Cambridge (UK)

2013-08-01 Thread Gerard DVD Kleywegt
wwPDB Workshop on mmCIF/PDBx for Programmers What, why and how? -- The world of the PDB will be changing rapidly and profoundly over the next few years. A major change will involve the transition from PDB to mmCIF/PDBx as the principa

[ccp4bb] July 2013 Computational Crystallography Newsletter

2013-08-01 Thread Nigel Moriarty
Folks The latest edition of the Computational Crystallography Newsletter is available at http://phenix-online.org/newsletter The table of contents is listed below. Articles *cctbx* tools for transparent parallel job execution in Python. III. Remote access *phenix.ensemble_refinement*: a test s

Re: [ccp4bb] Spots not getting indexed properly in protein-DNA complex

2013-08-01 Thread Vandna Kukshal
Hi , Seems to me that crystal packing is not good thats why mosaic diffraction, this might be due to DNA so you can increase diffraction quality by using 1 or 2 nucleotide sticky end DNA for crystallization which can help in crystal packing . Vandna Kukshal Postdoctral Research Associate De

Re: [ccp4bb] Off-topic: Crystallographic Symmetry Applications Available?

2013-08-01 Thread Chen Zhao
Thank you all for your helps, It seems that either COOT with modified PDB file or PDBSET is able to do most of the tricks for me. And thank Edward for sharing you useful files! I have to do a little bit more homework on xtaldraw though. Chen On Thu, Aug 1, 2013 at 9:17 AM, Edward A. Berry wrote

Re: [ccp4bb] Spots not getting indexed properly in protein-DNA complex

2013-08-01 Thread Bosch, Juergen
Hi Appu, nothing really to worry about if you process your data with XDS or d*trek using 3D profile fitting. You still should be able to get something useful out of this data. If you look at 90.png (I'm attaching a zoomed area of your image), you see your crystal is either split or you had two c

Re: [ccp4bb] Spots not getting indexed properly in protein-DNA complex

2013-08-01 Thread Nicolas Foos
Dear Appu, one direction of your cristal has very anistropic diffraction. I think your cristal has grown like multi-layer. The problem is probably due to the DNA. If the different "layer" of your cristal are not very well aligned, you have this type of problem. In my opinion, you can try to

Re: [ccp4bb] Spots not getting indexed properly in protein-DNA complex

2013-08-01 Thread Toth, Eric
That looks like a garden variety mosaic/kinda-crappy crystal. Without being there, it's impossible to tell if it was morphology (e.g. cracks and divots, etc.), crystal handling, or just bad luck. The bottom line is you need better data. The good news is that those crystals diffract to a reasonab

Re: [ccp4bb] Off-topic: Crystallographic Symmetry Applications Available?

2013-08-01 Thread Edward A. Berry
It's not ideal but we have been using a program called XtalDraw on windows for this, to display the different lattices and to build up the content of the unit cell from a small molecule of 2 or 3 atoms by applying the different space group symmetries. The students can edit the coordinates file (n

Re: [ccp4bb] Off-topic: Crystallographic Symmetry Applications Available?

2013-08-01 Thread Mark Brooks
Tim has the more modern answer, but PDBSET http://www.ccp4.ac.uk/html/pdbset.html is quite simple and scriptable. If I recall correctly, the SYMGEN keyword may be of use. >From the example in the documentation: Expand dimer to tetramer, rename chains, transform #!/bin/cs

Re: [ccp4bb] frosted crystals during storage in pucks

2013-08-01 Thread James Holton
In our experience, "dry shipper" dewars will "fail" for two reasons: 1) the vacuum gets compromized 2) the "sponge" that soaks up the liquid nitrogen gets contaminated with water Hot and cold cycling can cause the vacuum pump-out valve (that sticky-out thingy that always seems to be in the way

Re: [ccp4bb] Off-topic: Crystallographic Symmetry Applications Available?

2013-08-01 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Chen Zhao, if I understand correctly, you can use coot: It displays the unit cell based on the CRYST1 card present in some PDB file, and can read in and display the PDB file and also show the symmetry equivalents. It also writes out the coordinat