Re: [ccp4bb] Open position - data management in biophysics

Dear PI s, and senior scientists' involved in recruitment, Why do so many (especially postdoc) positions these days indicate: > Readiness for high workload > able to work independently but also effectively and collaboratively with > other lab member > Candidates should have a documented

Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

Dear Flemming, On 8/21/19, Flemming Goery wrote: > I find the message in my original e-mail has changed, perhaps by hackers, What do u mean by 'hackers' BTW!!! > > Dear all: > A has sought a job in the lab of B. B invited A for a interview with a PPT > oral presentation, as requested A has

[ccp4bb] covalent link to aa

Dear all, I have a structure where CYS is bound to OCA (octanoic acid). I started with Jligand and created a CYS-OCA covalent link. It then output a CIF file (verified looks OK). Add the LINK record to PDB file: LINK SG CYS A 161 C1 OCA A 902CYS-OCA

Re: [ccp4bb] buying a cluster

Hi Graeme, I suspect that this conclusions depends very closely on (i) the shape of > the problem and (ii) the extent to which the binary has been optimised for > the given platform. > > I do hope some of these info are analyzed and either published or at least put at ccp4 wiki. I am pretty sure

Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

Hi Raquel, Are u using a compressed filesystem? I recently moved everything including /home directory to ZFS - which gave ~ 1.4X compression for old adsc images. Remember vaguely, years before, James suggested to use aufs/unionfs. You could even enable data-deduplication to save redundant

[ccp4bb] Polder or FEM

Dear Pavel, By coincidence today I was looking at a soak-dataset and got totally confused with FEM (map) and Polder now. I am working on a dataset that processed it at 2.7A (in summer with XDS) and there was weak density for (OCA-Octanoic acid) when looked with FEM. This week, I retried it with

[ccp4bb] Assumptions on protein activity (again)

Dear all Thanks to for all the responses. I would continue my question for getting more advice. I expressed a dimeric multi-protein (600 KDa). This protein was purified (affinity chromatography) in 4 different common buffers and run with the same SEC-buffer. We observe clear single

[ccp4bb] Assumptions on protein purification

Dear all, Not directly a ccp4 question. I am working on a multi-domain protein with multiple catalytic centres. Purifying in gel-filtration (Äkta) with different buffers gives a clear distinct peak indicating pure protein. We could even crystallise it and determine 3D structure to about 2.5 A.

[ccp4bb] size exclusion columns

Dear all, We are looking for a size exclusion chromatography column (silica-based) for protein purification prior to a MALS-detector. We looked for (www.waters.com BEH-450), Sepax (Unix-C 300) and Phenomex (BioZen SEC-3). Any 'column' tips or recommendations when dealing with large proteins

[ccp4bb] unit cell is double between 2 forms

Dear all, we crystallized a small protein, that gives crystals P2 with cell Cell 53.16 65.73 72.8990 110.94 90 (has 3 molecules in the asymmetric unit). Tested with pointless. Does not give any other possibility. The other crystal form of the same protein, similar

[ccp4bb] double cell dimensions between P2 and C2

Dear all, >From a small protein, gives crystals P2 with cell Cell 53.16 65.73 72.8990 110.94 90 (has 3 molecules in the asymmetric unit). Tested with pointless. Does not give any other possibility. Another crystal if the same protein, similar conditions: C2 Cell 109.14

[ccp4bb] ccp4 website not secure

If anyone from CCP4 website has noticed that... Your connection is not secure The owner of www.ccp4.ac.uk has configured their web site improperly. To protect your information from being stolen, Firefox has not connected to this web site. (https warning message)

[ccp4bb] to fix angle between ligand and residue atoms

Dear ccp4-ers, I have a data set at 2.8 A. There is clear *continuous* density for a ligand + residue. I used the LINK record to connect the S-gamma-atom from Cys to C1-atom of ligand OCA. My biochemistry collaborator says that CB-SG-C1-O1 should be approximately planar. However, during

Re: [ccp4bb] Electronic Laboratory Notebook

Hi Sebastiano, I posted the same question recently (in April). Just removed the names and email ids for confidentiality (as some needs that). SUMMARY - I think biovia (aka accelrys) have a version, although I’ve never used it, so I don’t know how good it is. Blair Johnston (Strathclyde)

[ccp4bb] add ligand solution onto drop directly SUMMARY

Thanks for the responses. Yes, my crystal did survive and I can see density for my ligand. Summary: 1. If the crystal survives, it’s fine. These are just different ways of exposing the crystal to the ligand and do what works. The only issue will be if you don’t see electron density for the ligand

[ccp4bb] add ligand solution onto drop directly

Dear all, I wondered if it is OK to pipette ligand soln (X-CoA) *directly* to the drop with crystal (1:1 ratio of protein:precipitant 2µl) instead of dissolving it in precipitant solution and transferring the crystal to this ligand containing precipitant solution. The crystals survive this as I