[ccp4bb] Faculty Position, Structural Biology, University at Buffalo

The Department of Structural Biology at the University at Buffalo, part of the Jacobs School of Medicine and Biomedical sciences, is recruiting for faculty positions in the department at UB. This is a great opportunity to be a part of the growth here in Buffalo. New York State, SUNY, and UB are

[ccp4bb] COOT: Rotate/Translate Fragment tool

When using the COOT (0.9.8.5 EL) on a Mac, the behavior appears to have changed for manually rotating a fragment (Rotate/Translate Zone/Chain Molecule tool) When activated, the pop-up window allows me to use the sliders to rotate or translate. That works as advertised. However, I used to be abl

[ccp4bb] Research Scientist at Hauptman-Woodward Institute

Please see the posting below for an independent investigator at the Hauptman-Woodard Institute. Please direct any questions or applications to the opportun...@hwi.buffalo.edu email address. Best wishes, Andrew -- Andrew M. Gulick, Ph.D. ---

[ccp4bb] Research Scientist at Hauptman-Woodward Institute, Buffalo, USA

Please see the posting below for an independent investigator at the Hauptman-Woodard Institute. Please direct any questions or applications to the opportun...@hwi.buffalo.edu email address. Best wishes, Andrew -- Andrew M. Gulick, Ph.D. - Hauptman-Woodward Institu

Re: [ccp4bb] precipitation after storage

We routinely use a P200 to pipette drops of protein directly into a small Dewar of liquid nitrogen. The protein forms small BB's with a volume of approximately 30 micro-L each. Pipette slowly, allowing the drops to freeze solid before adding the next one. The frozen BB's can be picked up with fo

Re: [ccp4bb] Cys-Lysine Side chain Interaction

Hello John, We had just such an issue a year or so ago and I posed the same question to the BB. The density that I observed, and the CCP4bb discussion, can be found at: http://labs.hwi.buffalo.edu/gulick/cyslys.html http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg06092.html I was advi

Re: [ccp4bb] Identifying an unknown ligand

My money is on: Dithiothreitol or dithioerythritol. Any chance they are in there? If not and you believe this copurified with your protein, than I'd guess erythritol or threitol. (I didn't bother trying to gauge the stereochemistry from your picture) Cheers Andy On 4/2/09 1:38 PM, "Abhinav K

Re: [ccp4bb] generating omit maps

Let me also follow up on this point. I also agree that the ligand should be added very late in the refinement/model-building procedure. I also encourage people in my group to create a subdirectory "BEFORE_LIGANDS" into which they put the current PDB and map (or mtz) files prior to adding the ligan

Re: [ccp4bb] Problem with crystallization of Se-Met labeled protein

Consider also the possibility that your SeMet protein differs from the native protein by something other than the sulfur --> selenium. Growing your cells in different conditions may induce different host proteins that could modify your protein. (Often we use rich media for native protein productio

[ccp4bb] Density Joining Cysteine and Lysine Side chains

Greetings. I'm wondering if anyone has ever seen something like this. I have a 2.1 A data set (synchrotron data) that is nearing completion. I see density that appears to join a cysteine side chain to a lysine (30 residues away from each other in primary sequence). There is a picture of the densit

Re: [ccp4bb] Tag, you're in! Flag, V5, etc

If circumstances require a C-terminal tag, the intein system from New England Biolabs has worked very well for us. The pTYB1 plasmid encodes a fusion between your protein of interest, a viral intein (think "protein intron") and a chitin binding domain. The fusion adsorbs to a chitin resin and all

Re: [ccp4bb] How to refine a structure with ATP and AMP and pyrophosphate sharing the same density in CCP4i?

In the best case, you would know something about the enzyme bound equilibrium constant between the two ligand mixtures (see, for example, TM Larsen et al Biochemistry 35, 4349). That would give you a good sense of how to model the occupancies of the active site ligands. Unfortunately, in many ca

[ccp4bb] carving up maps (was re: pymol help)

I'd be curious to know if there is any consensus in the community with using the "carve" command for showing maps. I have never felt comfortable showing density within a cutoff radius of a particular residue or--even worse--a ligand, and felt the figures should display the extraneous bits as well.

[ccp4bb] Coot and Density Fit Analysis

Can someone tell me what the number is that appears with each residue above the bar in the COOT Density Fit Analysis graph? I have a structure with good data (resolution=2.3A, Rmerge=5%) but a high Wilson B of ~60. The structure refines reasonably well; we've gotten the Rfactor to 18% and Rfree

[ccp4bb] Sorting on residue number in Coot

I am building a new structure that was partially fit with RESOLVE. Various lengths of chain are properly numbered (where RESOLVE identified a match) and the unplaced polyalanine peptides are numbered 801-806, 811-823, 831-835, etc... When I have identified the correct sequence for a stretch of