Re: [ccp4bb] membrane protein optimization
Hi Frank, unfortunately it is very common with membrane protein crystals to get "stuck" with diffraction quality around 20A. From what you describe you could consider the following: a) revise the detergent you solubilize your MP with (e.g. use OG instead of DDM), and consider to change to another (shorter) detergent that might allow tighter crystal packing b) engineer your MP,mutate charged residues to alanine (check function!) c) try homolog protein d) try to crystallize in lipid cubic phase Best of luck! Susanne On Oct 23, 2013, at 9:22 AM, crystalboy wrote: > Hi CCP4BB Forks, > > In recently I got a membrane protein crystal in the quite normal > membrane protein crystallization conditions as other persons reported, > like PEG400 16-19%, pH 6.0-7.5, with 50 mM MgCl2 (in my case) by using > sitting drop method. These crystals are around 50-100 uM. They look > like trapezoid crystal. My problem is all of my crystals have not > diffraction in home source X-ray and just poor diffraction at > Synchrotron (lower than 20 A). My crystals like to appear on the > surface of the drop. Look like my crystals are quite light. I had > tried to use a needle to touch them. Unlike other protein crystal, my > crystal looks like quite "soft". When I touch it, it didn't crack, but > was bend or mashed. I had tried to do additive screen and detergent > screen. It seems they are not useful. > > Do anyone have good ideas to optimization these crystals? Thanks for > your suggestions. > > Frank > <20130917020056875.jpg> Dr. Susanne Ressl Otto Hahn Fellow of the Max-Planck Society Stanford University School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: +1-650-736-1715
[ccp4bb] curved cylindrical helices in PyMOL?
Dear ccp4bb-people, I would like to depict my protein with curved cylindrical helices using PyMOL. (I know and use bobscript "rod fitted" for this purpose and like it.) Anyway, I wonder if anybody has a script or knows how to tell PyMOL to follow the curvature of helices in the cylindrical cartoon representation? Many thanks in advance. Best wishes, Susanne ******** Susanne Ressl MPI Biophysics Department Structural Biology Max-von-Laue Strasse 3 60438 Frankfurt Tel:+49-69-6303-3052 or +49-69-6303-3037
Re: [ccp4bb] cross-section view of (protein) molecules in pymol?
Dear Jacob, for Fig.3b we defined the plane of the section and filled a copy of it with the grey colour in Coraldraw (Photoshop can do this as well) then we superposed the grey pattern of the sliced section on top of the original section...anyway, this is not the most straight forward way to do. Just some days ago I found a very nice and easy script on the Pymol wiki, which makes exactly this nice sliced image and I would have been happy if I would have known this script some time ago... Here is the link (it is not brain intense ;) just follow the script): http://www.pymolwiki.org/index.php/Gallery At this point, many thanks to the person who posted the script on the Pymol wiki!! Cheers, Susanne Susanne Ressl Department Structural Biology MPI Biophysics Frankfurt Max von Laue Str. 3 D-60438 Frankfurt am Main Tel: +49 69 6303 3052 On Mar 13, 2009, at 7:02 PM, Jacob Wong wrote: Dear all, http://www.nature.com/nature/journal/v458/n7234/fig_tab/nature07819_F3.html Just came across this figure Fig. 3b) and would like to know what is the general and easiest way to make things like this, as a "non- brainer". Thank you, -Jacob
