Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]
Thanks both! Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, 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 -Original Message- From: CCP4 bulletin board On Behalf Of Charles Ballard - STFC UKRI Sent: Wednesday, August 9, 2023 3:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7] In answer to Paul, should be available soon. Targeting Monday. -Original Message- From: CCP4 bulletin board On Behalf Of Paul Emsley Sent: 09 August 2023 15:31 To: ccp4bb Subject: Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7] On 09/08/2023 10:54, David Lawson (JIC) wrote: > Hi Paul, > > Just wondering where we are with this fix. The blog is generally the place to turn for this sort of thing. Having said that, I missed the post about 0.9.8.9! But I have added one for 0.9.8.91 (that revision fixed the missing peptide omega graph and fixes "Replace Residue" (needed for the upcoming Summer School)). As to if/when that gets added to CCP4, that is up to Charles. > Is it safe to apply the latest CCP4 updates? Isn't it always? Paul. > > Many thanks > > Dave > > --- > > Prof. David M. Lawson > Department of Biochemistry and Metabolism, 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 > > > -Original Message- > From: CCP4 bulletin board On Behalf Of Paul > Emsley > Sent: Tuesday, July 18, 2023 5:11 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space > refinement is broken in 0.9.8.7] > > On 18/07/2023 03:55, Mark Saper wrote: >> I reported this problem to Paul and to the group at least 2-3 months ago. > Your email didn't arrive. > > Just to be clear, Coot's real space refinement is not (was not) broken, the > problem is that the version of Coot distributed by CCP4 and the version of > the monomer library distributed by CCP4 were not compatible. > >> It affects protein as well as [nucleic] acid. I never heard back >> from Paul if a fix was in progress. > Keitaro Yamashita alerted me to the problem in a timely fashion and an update > to Coot was added and documented in early June. > > > [To Charles in particular] My commitments will be out of the way at > the end of the week and I hereby commit to making the 0.9.8.9 release > early next week. > > > Paul. > > ## > ## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > > ## > ## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > > > -- > CAUTION: This email originated from outside of the LMB. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > .-owner-ccp...@jiscmail.ac.uk-. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]
In answer to Paul, should be available soon. Targeting Monday. -Original Message- From: CCP4 bulletin board On Behalf Of Paul Emsley Sent: 09 August 2023 15:31 To: ccp4bb Subject: Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7] On 09/08/2023 10:54, David Lawson (JIC) wrote: > Hi Paul, > > Just wondering where we are with this fix. The blog is generally the place to turn for this sort of thing. Having said that, I missed the post about 0.9.8.9! But I have added one for 0.9.8.91 (that revision fixed the missing peptide omega graph and fixes "Replace Residue" (needed for the upcoming Summer School)). As to if/when that gets added to CCP4, that is up to Charles. > Is it safe to apply the latest CCP4 updates? Isn't it always? Paul. > > Many thanks > > Dave > > --- > > Prof. David M. Lawson > Department of Biochemistry and Metabolism, 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 > > > -Original Message- > From: CCP4 bulletin board On Behalf Of Paul > Emsley > Sent: Tuesday, July 18, 2023 5:11 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space > refinement is broken in 0.9.8.7] > > On 18/07/2023 03:55, Mark Saper wrote: >> I reported this problem to Paul and to the group at least 2-3 months ago. > Your email didn't arrive. > > Just to be clear, Coot's real space refinement is not (was not) broken, the > problem is that the version of Coot distributed by CCP4 and the version of > the monomer library distributed by CCP4 were not compatible. > >> It affects protein as well as [nucleic] acid. I never heard back >> from Paul if a fix was in progress. > Keitaro Yamashita alerted me to the problem in a timely fashion and an update > to Coot was added and documented in early June. > > > [To Charles in particular] My commitments will be out of the way at > the end of the week and I hereby commit to making the 0.9.8.9 release > early next week. > > > Paul. > > ## > ## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > > ## > ## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > > > -- > CAUTION: This email originated from outside of the LMB. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > .-owner-ccp...@jiscmail.ac.uk-. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]
On 09/08/2023 10:54, David Lawson (JIC) wrote: Hi Paul, Just wondering where we are with this fix. The blog is generally the place to turn for this sort of thing. Having said that, I missed the post about 0.9.8.9! But I have added one for 0.9.8.91 (that revision fixed the missing peptide omega graph and fixes "Replace Residue" (needed for the upcoming Summer School)). As to if/when that gets added to CCP4, that is up to Charles. Is it safe to apply the latest CCP4 updates? Isn't it always? Paul. Many thanks Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, 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 -Original Message- From: CCP4 bulletin board On Behalf Of Paul Emsley Sent: Tuesday, July 18, 2023 5:11 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7] On 18/07/2023 03:55, Mark Saper wrote: I reported this problem to Paul and to the group at least 2-3 months ago. Your email didn't arrive. Just to be clear, Coot's real space refinement is not (was not) broken, the problem is that the version of Coot distributed by CCP4 and the version of the monomer library distributed by CCP4 were not compatible. It affects protein as well as [nucleic] acid. I never heard back from Paul if a fix was in progress. Keitaro Yamashita alerted me to the problem in a timely fashion and an update to Coot was added and documented in early June. [To Charles in particular] My commitments will be out of the way at the end of the week and I hereby commit to making the 0.9.8.9 release early next week. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ -- CAUTION: This email originated from outside of the LMB. Do not click links or open attachments unless you recognize the sender and know the content is safe. .-owner-ccp...@jiscmail.ac.uk-. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]
Hi Paul, Just wondering where we are with this fix. Is it safe to apply the latest CCP4 updates? Many thanks Dave --- Prof. David M. Lawson Department of Biochemistry and Metabolism, 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 -Original Message- From: CCP4 bulletin board On Behalf Of Paul Emsley Sent: Tuesday, July 18, 2023 5:11 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7] On 18/07/2023 03:55, Mark Saper wrote: > I reported this problem to Paul and to the group at least 2-3 months ago. Your email didn't arrive. Just to be clear, Coot's real space refinement is not (was not) broken, the problem is that the version of Coot distributed by CCP4 and the version of the monomer library distributed by CCP4 were not compatible. > It affects protein as well as [nucleic] acid. I never heard back from > Paul if a fix was in progress. Keitaro Yamashita alerted me to the problem in a timely fashion and an update to Coot was added and documented in early June. [To Charles in particular] My commitments will be out of the way at the end of the week and I hereby commit to making the 0.9.8.9 release early next week. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] FW: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]
Hi The current version of coot in ccp4 (on osx and linux) is 0.9.8.8, since update 12 in June Charles -Original Message- From: CCP4 bulletin board On Behalf Of Paul Emsley Sent: 18 July 2023 17:11 To: ccp4bb Subject: [ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7] On 18/07/2023 03:55, Mark Saper wrote: > I reported this problem to Paul and to the group at least 2-3 months ago. Your email didn't arrive. Just to be clear, Coot's real space refinement is not (was not) broken, the problem is that the version of Coot distributed by CCP4 and the version of the monomer library distributed by CCP4 were not compatible. > It affects protein as well as [nucleic] acid. I never heard back from > Paul if a fix was in progress. Keitaro Yamashita alerted me to the problem in a timely fashion and an update to Coot was added and documented in early June. [To Charles in particular] My commitments will be out of the way at the end of the week and I hereby commit to making the 0.9.8.9 release early next week. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] Monomer Library [was Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7]
On 18/07/2023 03:55, Mark Saper wrote: I reported this problem to Paul and to the group at least 2-3 months ago. Your email didn't arrive. Just to be clear, Coot's real space refinement is not (was not) broken, the problem is that the version of Coot distributed by CCP4 and the version of the monomer library distributed by CCP4 were not compatible. It affects protein as well as [nucleic] acid. I never heard back from Paul if a fix was in progress. Keitaro Yamashita alerted me to the problem in a timely fashion and an update to Coot was added and documented in early June. [To Charles in particular] My commitments will be out of the way at the end of the week and I hereby commit to making the 0.9.8.9 release early next week. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
