Re: [ccp4bb] Should we still keep copies of all raw data?

Dear Frank, CERN does save all its data. It also hosts the Zenodo science data archive. The Square Kilometre Array has decided to save processed data rather than its raw data as they have concluded that isn't possible. Best wishes, John Emeritus Professor John R Helliwell DSc > On 13 Jul 2018,

Re: [ccp4bb] Should we still keep copies of all raw data?

Hi Frank on the same lines: do we keep our crystals after frying them? Or do molecular biologists keep their agarose gels? Hummm... evolution and technologies do progress. Yet, I would support keeping images, just as you may (but really will most likely never) want to re-process those with

Re: [ccp4bb] Should we still keep copies of all raw data?

I'm proud to have raw images backed up from as far back as my graduate days. Unfortunately I don't have the tape drives to read any of them. It's not only backing up the data but also backing up the backup capability and being able to read the data. I remember a wonderful discussion on this

Re: [ccp4bb] Should we still keep copies of all raw data?

Sergei, all, I for one would always recommend saving data - not least as this is the basis for your science and you may need to revisit it later, perhaps before or after publication. Re: (a) I know we’re all working on improving the methods but they are still have scope for improvement (b)

Re: [ccp4bb] Should we still keep copies of all raw data?

Are the LHC researchers that analyse the detector readout on the fly without ever storing the data also guilty of malpractice? Hardcore. Just a few more years, a few more Eiger detectors, a few more serial beamlines, a few more clusters and clouds, and a few more DIALS-style programmers,

Re: [ccp4bb] Wavelength mismatch during PDB deposition

Dear Robbie, Thank you for the prompt response. I have verified my PDB file for remark 200 and 3, but I couldn't find the wavelength information. For refinement REFMAC 5.8.0230 was used from CCP4i. I have tried to convert it into mmCIF using AIMLESS and MOLREP log with PDB_extract. Then I

Re: [ccp4bb] Should we still keep copies of all raw data?

Dear John, I certainly agree with your point. This would indeed be an argument to keep copies of all datasets -- even though we are not any likely to look at them ever again, beyond 1% of the more difficult cases. Regards, Sergei Prof. Sergei V. Strelkov Laboratory for Biocrystallography

Re: [ccp4bb] Creating map volume of custom size

I use CCP4 mapmask to exted the map some Å beyond the asymmetric unit in order to see the density at crystal contacts Dr. Matthias Barone AG Kuehne, Rational Drug Design Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany Phone: +49

Re: [ccp4bb] Creating map volume of custom size

I think the CCP4 program map rot will do this Phil > On 13 Jul 2018, at 10:16, melanie.voll...@diamond.ac.uk > wrote: > > Hello everyone, > > > I have a question about manipulating map files. > > > I want to use my map derived from X-ray diffraction and create a standard > volume for it,

Re: [ccp4bb] Should we still keep copies of all raw data?

Dear Sergei, Re “all”. As a researcher my perspective is that one’s funding agency requirement for a data management plan will be the core of what you would need to follow. Your employer may have additional policies and requirements placed on you as an employee. Eg the UK funding agency EPSRC

[ccp4bb] Should we still keep copies of all raw data?

Dear All, I believe this question may be of some interest. In the past, we always stored all raw data ever collected by the lab. With the recent advances, such as (a) automated/on-the-fly processing offered by some (European) synchrotrons, and (b) an ongoing discussion on centralized raw

[ccp4bb] Creating map volume of custom size

Hello everyone, I have a question about manipulating map files. I want to use my map derived from X-ray diffraction and create a standard volume for it, say 300A3. This is to be able to create slices of equal dimensions along all three directions of the electron density stored in the map

Re: [ccp4bb] Wavelength mismatch during PDB deposition

Hi Santhosh, The seems to be the result of a rounded value in the SF file and a truncated value in the PDB. I suppose that the PDB file you are depositing actually does have the wavelength (it lives in REMARK 200, but depending on which refinement program you used it may also be in REMARK 3,

[ccp4bb] Wavelength mismatch during PDB deposition

Dear all, I got an issue after submitting my structure to PDB. The exact message is as follows... 1. Wavelength mismatch (pdb= 0.9794 : sf= 0.9795)! Please provide the correct wavelength value used for the structure determination. The data I have collected at the synchrotron with

Re: [ccp4bb] PDBe Scientific Programmer / Bioinformatician

The deadline for applications to this post has been extended until the 22nd July 2018. Regards John From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of John Berrisford Sent: 21 May 2018 13:57 To: CCP4BB@JISCMAIL.AC.UK Subject: