Yes, I agree.. garish? Rob Nichols?? Can you email this to them directly? E
On Tue, 9 Feb 2021 at 13:28, David Lawson (JIC) <david.law...@jic.ac.uk> wrote: > 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> > 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 > > > > > ------------------------------ > > 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/
