[ccp4bb] Publication ethics Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

Dear Colleagues, I have followed this thread with great interest. It reminds me of the Open Commission Meeting of the Biological Macromolecules Commission in Geneva in 2002 at the IUCr Congress. Ie at which it was concluded that protein coordinates and diffraction data would not be provided to

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

Dear Jeremy, Thank you for the attached cartoon, most warmly welcome by all those in need of a displacement activity in this gruesomely cold and rainy month of April. Oh those terrible French! I know them, I am one of them ;-) . I found the Wikipedia entry on the subject

[ccp4bb] commercially available proteins

Hi all, Sorry for the very off topic problem. I'm looking for a loading control for my westerns (doing in vitro assays). Due to separation/antibody specificity issues, I need super good separation between 70 and 100 kDa, oftentimes running those markers all the way to the bottom of the gel. If

Re: [ccp4bb] commercially available proteins

How about plain old BSA ? Jürgen On Apr 26, 2012, at 1:29 PM, Peter Hsu wrote: Hi all, Sorry for the very off topic problem. I'm looking for a loading control for my westerns (doing in vitro assays). Due to separation/antibody specificity issues, I need super good separation between 70 and

[ccp4bb] Refmac and sigma value

Dear All: I use Refmac5 to refine my structure model. When I set the sigma value to 0.3 (as recommended from tutorial), the resulted model has many red-bars by coot validation (geometry, rotamer, especially, Temp Facotr). I then lower the sigma value to 0.1, the resulted model is much improved

Re: [ccp4bb] Refmac and sigma value

Hi, Alex: Which sigma do you mean? The one for automatic weight, not for Jelly-body refinement. I did not turn the Jelly-body refinement on. Thanks Ros On Thu, Apr 26, 2012 at 4:08 PM, aaleshin aales...@burnham.org wrote: Hi Uma, Which sigma do you mean? The one for Jelly-body

Re: [ccp4bb] detergent crystal?

Those don't look like DDM crystals I've seen, but the diffraction pattern does not look much like protein diffraction either. Which things from the picture did you shoot--the rods/needles? Jacob On Fri, Apr 27, 2012 at 5:07 AM, 于洪军 hongju...@moon.ibp.ac.cn wrote: Hi, I am trying to screen

Re: [ccp4bb] detergent crystal?

Hi, For me it is detergent crystals or other stuff that is not quite important in this case. As you showed the resolution is quite low. I suggest you need to repeat again again again. You may go to PEG200. In our case, it is very difficult to reproduce membrane protein crystals. Good luck!

Re: [ccp4bb] negative density at some places in the side chain of residues

Alaksa, 1) What rmsd / sigma are you contouring your density at ? i.e. are you down in the noise or are you at a reasonable value for your Fo-Fc map? 2) It looks like some of your side-chains appear to have more than one conformation - it's fairly easy in Coot to position and model both.

Re: [ccp4bb] content calculation in phaser

Hello All, Follow up on the problem. With some help from Randy Read, it was discovered that the sequence file had four chains designated which was causing the problem. I found out later from the researcher whose project this is that the structure they were using had 4 copies in the

Re: [ccp4bb] detergent crystal?

Generally speaking it is quite hard to crystallize DDM since it is so soluble (20% in water). You most likely have protein crystals (of course containing a lot of detergent as well) that are just not ordered, presumably because most or all of the lattice contacts are mediated by detergent and

Re: [ccp4bb] detergent crystal?

Hi Hongjun, The 'spherulites' could be DDM crystals. The rods/needles DO NOT seem like DDM crystals. A carefully done SDS-PAGE could clarify further. Alternatively, you could use the sample buffer (no protein) against the same crystallization reagent to find out. Veer. Veer Sandeep