Hi Eleanor, I’m glad it’s not just me then. I too tried the grepping option, but my recollection was that that didn’t go too well either. It doesn’t help that I’m not very comfortable with MMCIF format yet… Also, I forgot to mention, but was just reminded that you can change “Output calculated riding hydrogens to file” to “No” in the Output tab of REFMAC, but it still writes them to the MMCIF! Without wishing to start a lengthy email discussion, can’t we just have the option to write an MMCIF without hydrogens from REFMAC?
Dave ------------------------------- Prof. David M. Lawson Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk From: Eleanor Dodson <eleanor.dod...@york.ac.uk> Sent: 09 February 2021 13:15 To: David Lawson (JIC) <david.law...@jic.ac.uk> Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file? I took this up with pdbe but what with lock down and all I am not too sure what the decision was ( or whether there was one) maybe you could start a chat to the pdbe lot Our code was d- 1292109592. It was a mess - tony Wilkinson was depositing the data from the labs, I had been doing refinement from home so we didn’t have a proper deposition directory. And then they grumbled about hydrogens with zero occupancy. I grepped them out of the Mcciff file but it isn’t the best silution On Tue, 9 Feb 2021 at 12:29, David Lawson (JIC) <david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk>> wrote: Hi All, By default, when you run REFMAC5 run through CCP4I2, it uses riding hydrogens during refinement. It then writes out a PDB file without the hydrogens and an MMCIF file that retains these hydrogens. In the latter, you end up with mostly hydrogens with unit occupancy and a few with zero occupancy. Upon further investigation it seems the latter are mostly polar hydrogens, but some sit at the end of side-chains that have been truncated (I don’t want restart the discussion about whether you should or should not truncate side-chains). As a result, if you use the latter for deposition, which is the only option if you use the CCP4I2 “New Deposition Task”, you run into trouble. So my question is: how can I stop REFMAC from writing the hydrogens to the MMCIF file (I also don’t want to restart the discussion about whether you should or should not deposit hydrogens)? The alternative is that I revert to using the more tedious option of the pdb_extract server since that works with a PDB file. Thanks in advance, Dave ------------------------------- Prof. David M. Lawson Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
