Re: [ccp4bb] Maps look different from auto-mtz vs EDS vs FFT in Coot or CCP4MG.

Dear Kendall, I would suggest you to run a simulated annealing omit map around the region you are interested. The model bias will be reduced and you will get a more clear answer. Ciao, Joao Joao M. Dias Ollmann Saphire Lab The Scripps Research Institute 10550 North Torrey Pines Rd. IMM-2 La J

[ccp4bb] removal of sulfate ion from the active site

Hi all, I have crystals of the apo enzyme growing from 1.7M ammonium sulfate condition. After soaking with 10mM ligand (substrate analog) which has a phosphate group, the ligand did not enter the active site of the enzyme because of the competition of sulfate ion and phosphate group. So I am wond

[ccp4bb] Maps look different from auto-mtz vs EDS vs FFT in Coot or CCP4MG.

I¹d like help in interpreting some mystery density in a structure. I¹m writing a paper about soaking the apo-estrogen receptor with different ligands. The apo structure is already released, as pdb code 2B23. The question is whether there is a mystery molecule in the pocket of the apo receptor. If

Re: [ccp4bb] another quick question...

James, The "stars" are atoms in a residue that are no longer within recognizable bonding distances of other atoms. Somewhere along the way these residues were mangled to the point that some atoms are no longer within bonding distance of each other. (In Refmac, for example, this can happen if the X

[ccp4bb] experiences on fluidigm topaz system

Dear All, We would be interested in the communitys experiences/opinions about the usefulness of the TOPAZ system, benefits/problems, how much you feel it helps having one around vs price etc., as an addition to the regular vapour diffusion/batch screen done with a robot (e.g. the cartesian). T

[ccp4bb] another quick question...

Good day all, In COOT, when I view my coordinate pdb file with my ccp4 map file (using "Auto-open mtz"), I have a couple residues for which only a part of the peptide chain is visible. E.g. for a Lys, only the terminal nitrogens at the end of the R-group chain are visible as bonds. The other par

[ccp4bb] new version of MR pipeline BALBES

Dear all, A new version of an automatic molecular pipeline system - BALBES is now available. It can be downloaded from: www.ysbl.york.ac.uk/~fei/balbes The new options in this system are: 1) Use of user defined external PDB library 2) Use of a single PDB file as an input model for Molecular r

[ccp4bb] SUMMARY: His-His H-bond

Dear All, As usual the bulletin board has been enormously helpful. To remind you here was my original post: We have solved a structure that has an intersubunit His-His H-bond (ND1---NE2). The protein most likely undergoes conformational changes that involve the making and breaking of H-bonds at t

Re: [ccp4bb] can glucose covalently bond to the guanidino nitrogen of arginine?

Dear Michael, I did a quick check of the bonds found between GLC/BGC (alpha-D and beta-D-glucoses) and Arginine using the MSDSite service at http://www.ebi.ac.uk/msd-srv/msdsite/ From the left panel if you choose Ligand Bonds and put in GLC|BGC in the ligand box and ARG in the residue box, th

[ccp4bb] Fw: temporary position - GlaxoSmithKline - protein crystallography laboratory

Crystallisation support scientist - GlaxoSmithKline - Harlow. A temporary (seven month) position is available to work in the protein crystallisation laboratory in GlaxoSmithKline, Harlow. JOB DESCRIPTION. Assist structural biologists in setting up high throughput protein crystallisation exper

[ccp4bb] Postdoctoral position in Cambridge

I post this advertisement on behalf of Dr Ben Luisi. ___ Job Advertisement: A postdoctoral position is available in the laboratory of Ben Luisi in the Department of Biochemistry, University of Cam