[ccp4bb] Joint CCP-EM & CCP-BioSim Workshop on EM & MD @University of Leeds

Just a reminder that there are still places available... We are proud to announce a pair of workshops held at the University of Leeds exploring the crossover between EM and MD. http://www.ccpem.ac.uk/training/leeds_em_md_2017/leeds_em_md.php (1) Computation for Biomolecular Cryo-Electron

Re: [ccp4bb] Protein or DNA crystals

Hi Joseph, Could you post the UV fluorescence image? Oftentimes, UV absorbing objects that do not fluoresce (such as nucleic acid crystals) show up dark against a brighter background in UV fluorescence. V. Nagarajan JANSi On 6/19/2017 7:20 AM, Joseph Ho wrote: Dear all: I would like to

[ccp4bb] Protein or DNA crystals

Dear all: I would like to seek your opinion on our crystal hits. We are working on protein/dsDNA complex. By changing different protein and DNA (14-22bp) constructs, we recently got some hits from commercial screens using sitting drop vapor diffusion (very small xtals). The precipitant is PEG and

Re: [ccp4bb] Protein or DNA crystals

Dear Joseph, I think, you already did the most classical test to determine what is in your crystal. Maybe you can try a destructive approach by washing the crystal prior to put them in Agarose gel do a short run and color with ethydium bromide. Simpler, you can also melt the crystal after

[ccp4bb] ccp4 7.0 update 041

Dear All update 041 contains * rdkit 2017_03_02 * acedrg - update for new rdkit * ccp4i2 - update for new rdkit and acedrg * ccp4mg - update for new rdkit * coot - update for new rdkit Next up dials 1.6.1 All the best CCP4 core team

Re: [ccp4bb] Protein or DNA crystals

Hi Joseph, Are you having trouble getting bigger crystals. You said you shot them, and they are not salt. Do they diffract at all? If they are diffracting to any extent, you could optimize the crystallization condition to get better, bigger crystals and shoot them. A simple way of growing fewer,

Re: [ccp4bb] Protein or DNA crystals

Dear Kumar you said 'shot from other conditions': we do not know then if you shot these crystals or not. Else: - DNA should give you an X pattern, most of the time. - protein should give you at least low resolution pattern, or faint rings if it is powder pattern like - salt should give you

Re: [ccp4bb] REFMAC? COOT? and TER records

Hi Eleanor, From PDB format 3.3: * Every chain of ATOM/HETATM records presented on SEQRES records is terminated with a TER record. * The TER records occur in the coordinate section of the entry, and indicate the last residue presented for each polypeptide and/or nucleic acid chain for which

[ccp4bb] AW: [ccp4bb] Unknown Ligand Density

Dear Nick, I would contact some MassSpec people and ask if they could find out the mass of your mystery ligand. I would also carefully look at the neighboring protein. It might be an alternate conformation of a partially disordered loop. Finally, I would check literature to see if a natural

[ccp4bb] REFMAC? COOT? and TER records

These do seem to multiply wonderfully in the PDB output files and sometimees to have have strange effects/ affects in COOT? As I understand there should be a TER record after a protein chain? but not after a ligand. Dont know about carbohydrate chains. Eleanor The correspondence about N linked

Re: [ccp4bb] N-linked glycosylation check

Hi Jan, I do the same thing, but it would be nice if there was a consistent target. I noticed that the targets (and their sigmas) used by the PDB validation software don't fully coincide with the 'ideal' values from their own Chemical Component Dictionary. How are supposed to correct the

[ccp4bb] PDBe API webinar 4th July 2017

Dear CCP4BB On Tuesday 4th July 2017 at 3.30pm British Summer Time PDBe will be presenting a webinar on using our REST API service. In this webinar we will introduce the PDBe REST API service and show you how to access macromolecular structural data programmatically. This webinar is part

Re: [ccp4bb] N-linked glycosylation check

Hi Chris, Not a direct answer to your question, but I notice that there are two TER records for the same residue. We've been noticing a lot of problems with leftover TER records. Any idea where they came from? It probably won't help, but try deleting those. Cheers, Robbie > -Original

Re: [ccp4bb] N-linked glycosylation check

On 19/06/17 09:54, Chris Ulens wrote: I am looking to get feedback from others who have recently built and refined bond lengths and angles of an N-linked glycosyl chain in Refmac. I observed in Coot that the bond between O3 of BMA303 and C1 of MAN304 does show while the bond between O6 of

Re: [ccp4bb] REFMAC? COOT? and TER records

Thank you Robbie. I guess ligands do not (or should not) appear in SEQRES therefore should not have a TER record. Eleanor On 19 June 2017 at 11:04, Robbie Joosten wrote: > Hi Eleanor, > > From PDB format 3.3: > * Every chain of ATOM/HETATM records presented on