[ccp4bb] [Second Notice] BioSAXS2019 workshop at SSRL/SLAC

Second Notice: Dear all, We are glad to announce the BioSAXS2019, a workshop on biological small-angle X-ray scattering at Stanford Synchrotron Radiation Lightsource (SSRL). When: December 2-5, 2019 Where: SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA The SSRL Structural

Re: [ccp4bb] Occupancy refinement of overlapping electron density of a residue and ligand

Hi Nestor, I think the reason for Arg side chain to curl up is because I refined ligand and Arg side chain with occupancy refinement, and the Arg moved away from the density, most likely due to 'repulsion' from ligand. The other question is: Is it possible that the H-bonds stay very

[ccp4bb] lysine methylation in E. coli?

Dear CCP4 community, I am hoping that someone here might know the answer to this as I cannot find anything concrete in my literature search. I have recently received a mass spec result indicating that a recombinant protein expressed in /E. coli/ is heavily lysine methylated. I would like

[ccp4bb] Fwd: CCP4i2 London Road Show

Reminder One week to London CCP4i2 Road show.  Places still available. *CCP4 i2 Road Show, London* There will be a CCP4 Road Show for use of the i2 interface on Tuesday 12th November, at Birkbeck College. *Time:* 14:00 - 16:00 for the main workshop with about an hour afterwards for those

Re: [ccp4bb] lysine methylation in E. coli?

It happens. Ef-Tu is methylated on a single lysine Also LafV is a putative methylase in E. Coli but its effects were not studied in detail. Salmonella methylates flagellin which is how lysine methylation was discovered - and E.coli is a kissing cousin so... Artem On Tue, Nov 5, 2019, 12:31

Re: [ccp4bb] why does Coot ignore CONECT?

Hi Pavel I work with peptide-scaffold chimeras on a daily basis. Initially, I tried to include the scaffolds as HETATM and use JLigand to create the links between the scaffolds and the natural amino acids. This procedure however is rather fussy and by now I build the chimera in silico, using

Re: [ccp4bb] Introducing Dials User Interface for CCP4

On 05/11/2019 09:53, Fuentes-Montero, Luis (DLSLtd,RAL,LSCI) wrote: Hi FH, It looks to me like an installation issue, I am CCing you to the rest of the CCP4BB with hope to find anyone who knows what to do: Guys: Does anybody faced the following error message before? *undefined symbol:

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

Hi Michael, I believe you are looking at the anisotropic B factor. 8 A2 is very low, you are all good. The Wilson B is given by Truncate if I'm not mistaking. Best regards Vincent Le 04/11/2019 à 00:18, Michael Jarva a écrit : Hi CCP4BB, I have some unusual crystal diffraction data I'd

Re: [ccp4bb] Introducing Dials User Interface for CCP4

Hi FH, It looks to me like an installation issue, I am CCing you to the rest of the CCP4BB with hope to find anyone who knows what to do: Guys: Does anybody faced the following error message before? undefined symbol: PyUnicodeUCS2_DecodeUTF8 Thanks in advance, Luiso.

Re: [ccp4bb] Occupancy refinement of overlapping electron density of a residue and ligand

Dear HK, If you believe that R120 only adopts one conformation then you should not refine the occupancies of the side chain atoms. It makes no physical sense to have occupancies less than one for these atoms, but occupancy equal to one for the rest of the protein (unless you believe the side

[ccp4bb] Postdoctoral position available at the Basque Centre for Biophysics (Bilbao, SPAIN)

Dear colleagues, We are currently looking for a postdoctoral researcher to join our lab. Please see below for details: *OFFER* – Postdoctoral Position (Two years) *DEADLINE: *4th of February, 2020 at 17:00 h CET or until position is filled. *WHERE* – Basque Centre for Biophysics

Re: [ccp4bb] Occupancy refinement of overlapping electron density of a residue and ligand

Dear HK, No that's not quite correct - 'occupancy group alts complete' means that both R120 and the ligand are constrained so that their occupancies sum to unity. In contrast, 'occupancy group alts incomplete' means that the occupancies of R120 and the ligand will not be constrained to sum to

[ccp4bb] Occupancy refinement of overlapping electron density of a residue and ligand

Dear all, I have problem with occupancy refinement by Refmac5 for an overlapping electron density of part of residue (an arginine) and part of ligand (tetracyclic compound) (attached figures in Dropbox with a link as shown below).