Re: [ccp4bb] Off topic - fluorescence plate reader in cold room or cold box

Dear Markus, I've had to solve this exact issue in the past. Putting a 'simple' (nothing is simple these days, everything has some kind of AI or other evil gnomes in it) spectrofluorimeter into the cold room *should* be OK. Caveat #1: I don't know if this will work with your specific device Cavea

Re: [ccp4bb] Presence of negative density in Sim Omit map

Happy to do it! All the best,JP On Friday, July 26, 2024 at 12:28:22 PM CDT, Renuka Kadirvelraj wrote: Hi John,Thanks again for helping us! Regarding the map after placing missing residues and refinement: you are correct, both the negat

Re: [ccp4bb] Off topic - fluorescence plate reader in cold room or cold box

I think you are right, in the final equilibrium all the moisture would condense on the (evaporator?) coils, and there should be provision for them to drip into a reservoir outside. However each time the door opens and humid air is admitted, there will be condensation everywhere. If you leave th

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hi John, Thanks again for helping us! Regarding the map after placing missing residues and refinement: you are correct, both the negative and positive densities have gone away from the loop. Thanks, Renu - Renu Kadirvelraj, Ph.D. Research Scientist A42

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hi Renu, how do the maps look (2Fo-Fc and Fo-Fc) after you run a standard refinement in Phenix with the missing residues in place? If the negative density disappears in the Fo-Fc then there is not necessarily a problem. Of course the positive density should also go away in the Fo-Fc map since i

[ccp4bb] Off topic - fluorescence plate reader in cold room or cold box

Dear All, apologies for the off-topic question. I am facing the problem of running enzyme activity assays at low temperature (close to 4C would be ideal) in a fluorescence plate reader. Before I get labeled in our department as "the one who voids warranties" and destroys our beloved plate reader, I

[ccp4bb] Rolling call open for MX beamline P11, PETRA III, DESY

Dear all, We would like to inform you that the rolling call for proposals for beamtime at MX beamline P11, PETRA III is open. Proposals to beamlines participating in the rolling procedure can be submitted exclusively via this new access route. Submission is possible at any time without a deadl

[ccp4bb] Fully funded postdoc positions available

Dear members of the structural biology community, I am looking for postdoctoral researchers and would be grateful if you could bring the following position to the attention of potential candidates. Thanks, Albert   Postdoc positions in the laboratory of Albert Weixlbaumer available at the IGBM

[ccp4bb] DLS/CCP4 data analysis workshop 2024

We are pleased to announce that applications are now open for the 11th joint Diamond-CCP4 Workshop on MX data collection and structure solution! Bringing together leading experts in the field of MX to teach best practice in data collection and analysis, this course is aimed at PhD students, postdoc

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hi Eleanor,   I had basically the same question that I asked in phenixbb recently, the answer was also that the reason for red blobs is the solvent mask. In phenix there is mosaic modelling available that deals with the red blobs: https://onlinelibrary.wiley.com/doi/full/10.1002/pro.4909 Best,

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hi Eleanor, My understanding about negative holes in difference maps is that it is down to incorrectly modelled bulk solvent. I have seen this in structures where there are voids inside a protein that are perhaps in reality empty, but get modelled as bulk solvent, and so you get a negative diff