[ccp4bb] Ligand present in only one monomer in NCS

Hello, I am solving a structure of an enzyme, which crystallises as a dimer. We have pretty good evidence that this operates as a dimer in vitro, also. We have an inhibitor of this enzyme, which we are keen to visualise by X-ray methods. We seem to have very strong density in which we can model

[ccp4bb] Difference Map images

Hello, I was wondering what people used to generate difference map images of, say, a ligand in their structures? e.g. Figure 2a here http://journals.iucr.org/f/issues/2009/05/00/tt5012/tt5012.pdf Cheers, Andy

Re: [ccp4bb] Difference Map images

Jon Wright wri...@esrf.fr: There seems to be a clue in the text? Models were displayed and figures were produced with PyMOL (Delano, 2002), which you can read at the end of section 2 Materials and Methods. ANDY DODDS wrote: Hello, I was wondering what people used to generate difference map

[ccp4bb] Taking account of Density modification in Refmac

My basic question is how do you get refmac to take account of denisty modfication of the mtz file. Do you have to explicitly tell it to do this? Is it done by inputting hendrickson-lattman coefficients or something? cheers Andy

Re: [ccp4bb] Taking account of Density modification in Refmac

for your structure. As far as I know you can ask refmac to take experimental phases into account. What exactly are you trying to do? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 17 Apr 2009, ANDY DODDS wrote: My

Re: [ccp4bb] how to purify protein in its native form

recently I have had much success stopping pesky proteins sticking to my SEC columns by sticking 10% galactose in my buffer. cheers andy 2009/4/16 conancao conan_...@hotmail.com: Hi: I have seen some protocols(IMPACT from New England Lab etc.) which can overexpress protein with a tag then

Re: [ccp4bb] DM and MR

Hi James, I usually use DM in teh CCP4 suite to do DM. It gives you options to do solvent flattening, Histogram matching and NCS averaging. If you compare the FOM to the DMFOM in the mtz files, you can usually see and improvement in the score. That is usually all I bother my arse to look at.

Re: [ccp4bb] DM and MR

I have to use refmac for licencing reasons, sadly, unless someone can recommend an entirely free refinement program to anyone including industry/people in limbo etc. Actually, I was just thinking. In the new MTZ files (which helpfully I dont have on me) there are new values with 'DM' added to

Re: [ccp4bb] protein folds

The original poster may be interested in this paper from Phil Bourne's lab a few years ago which looked at the contribution of folds (among other things) by the Protein Structure Initiative, particularly Fig 5 and table 1. http://helix-web.stanford.edu/psb04/bourne.pdf The Status of Structural

[ccp4bb] Getting Molprobity to run using WinCoot

Dear all, I am trying to use the molprobity server with WinCoot 0.6-pre-1. I have followed the instructions here http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot-faq.html and believe I have put probe and reduce into the right places and pointed to them in the coot.py script. however, when I

[ccp4bb] tutorial / pipeline for ligand fitting, refinement?

Hello, does anyone know of a tutorial which lays out some sort of pipeline, hopefully using CCP4 packages, to fit and refine a small molecule ligand please? cheers andy

[ccp4bb] definition of I Sigma I

Hi, does anyone have a definition of I Sigma I please. Any definitions that i have found are not very informative for novices. thanks andy

[ccp4bb] resuspending precipitated protein

Hello, following on from a previous topic about precipitating protein, but I believe a distinct caveat of this warranting a separate thread, I would like to know people's experiences in trying to get precipitated protein back into solution? Is there a way or are there many ways? Any experiences

[ccp4bb] Using DM for density averaging.

Hello, I have a dimer with ligands present in the binding sites (1 per monomer). The electron density in one of the monomers is pretty poor compared to the other, so I was hoping to use DM to try and average the densities. I am having problems telling DM the NCS operators. How would you go

[ccp4bb] thermofluor - Thermal Shifts - Tm and Delta Tm

the buffer is, but reading further we have observed several examples where, the Tm is raised, but yet the Delta-Tm indicates a destabilizing affect. How can this be so? Any references regarding a good explanation of Delta-Tm would be great. thanking you Andy Dodds