Re: [ccp4bb] nearestcell
Dear all, a short summary: - SAUC and the Phenix tool worked well. - SIMBAD was also pointed out to me, but it stops with an error message both in my local CCP4 installation and in "CCP4 online". - The https://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi alternative to http://www.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi does not respond - "othercell" is also useful but for other purposes, and it is in CCP4 thanks to all who responded so quickly! Kay On Wed, 27 Dec 2023 18:38:15 +, Kay Diederichs wrote: >Dear all, > >I seem to remember a tool called "nearestcell", a command-line equivalent of >the Oxford Nearest-Cell web server which appears to be offline. >However I cannot locate that tool in CCP4 nor elsewhere. Can anyone point me >to it or give alternatives, please? (I did try the PDB's advanced search but >it is not made for this purpose) > >Thanks, and a happy and successful 2024 to everybody! > >Kay > > > >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] nearestcell
That is a live link to sauc, but I have not updated the database from the PDB in a while. Let me know if there is an urgent need for an update, Otherwise I am planning one for March. I normally build the database from COD and the PDB, but if CCDC wishes, we can add the CSD to the mix. For the longer term, would anybody be willing to provide an institutional home? Regards, Herbert On Wed, Dec 27, 2023 at 1:47 PM Mike S wrote: > Hi Kay, > > http://flops.arcib.org:8084/sauc-1.1.1/ > > similar to the nearest-cell server, which seems to change its link and is > harder to find (or stale link) > https://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi > > HTH, > Mike > > On Wed, Dec 27, 2023 at 1:39 PM Kay Diederichs < > kay.diederi...@uni-konstanz.de> wrote: > >> Dear all, >> >> I seem to remember a tool called "nearestcell", a command-line equivalent >> of the Oxford Nearest-Cell web server which appears to be offline. >> However I cannot locate that tool in CCP4 nor elsewhere. Can anyone point >> me to it or give alternatives, please? (I did try the PDB's advanced search >> but it is not made for this purpose) >> >> Thanks, and a happy and successful 2024 to everybody! >> >> Kay >> >> >> >> 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 > 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] nearestcell
Hi Kay, http://flops.arcib.org:8084/sauc-1.1.1/ similar to the nearest-cell server, which seems to change its link and is harder to find (or stale link) https://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi HTH, Mike On Wed, Dec 27, 2023 at 1:39 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Dear all, > > I seem to remember a tool called "nearestcell", a command-line equivalent > of the Oxford Nearest-Cell web server which appears to be offline. > However I cannot locate that tool in CCP4 nor elsewhere. Can anyone point > me to it or give alternatives, please? (I did try the PDB's advanced search > but it is not made for this purpose) > > Thanks, and a happy and successful 2024 to everybody! > > Kay > > > > 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] nearestcell
Hi Kay, to address "(...) not elsewhere (...)", in Phenix GUI go to Tools then down to "Search PDB symmetry...". I've never used it myself nor do I know who added it in Phenix but from the description it looks like what you're looking for. Let us know if you have any problems with it. All the best, Pavel On Wed, Dec 27, 2023 at 10:39 AM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Dear all, > > I seem to remember a tool called "nearestcell", a command-line equivalent > of the Oxford Nearest-Cell web server which appears to be offline. > However I cannot locate that tool in CCP4 nor elsewhere. Can anyone point > me to it or give alternatives, please? (I did try the PDB's advanced search > but it is not made for this purpose) > > Thanks, and a happy and successful 2024 to everybody! > > Kay > > > > 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] nearestcell
Are you thinking of "othercell" ? On 12/27/2023 10:38 AM, Kay Diederichs wrote: Dear all, I seem to remember a tool called "nearestcell", a command-line equivalent of the Oxford Nearest-Cell web server which appears to be offline. However I cannot locate that tool in CCP4 nor elsewhere. Can anyone point me to it or give alternatives, please? (I did try the PDB's advanced search but it is not made for this purpose) Thanks, and a happy and successful 2024 to everybody! Kay 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] nearestcell
Dear all, I seem to remember a tool called "nearestcell", a command-line equivalent of the Oxford Nearest-Cell web server which appears to be offline. However I cannot locate that tool in CCP4 nor elsewhere. Can anyone point me to it or give alternatives, please? (I did try the PDB's advanced search but it is not made for this purpose) Thanks, and a happy and successful 2024 to everybody! Kay 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/
