I dont expect anyone to install these in the interface, and indeed if COOT told you the symmetry operators in a comprehensive way the distang style searches would be almost redundant .. But sometimes it helps to have textual information.. clearer andeasier to record than graphical messages.. E
On Tue, 7 Jul 2020 at 17:42, Christian Roth <christianroth...@gmail.com> wrote: > I understand that one is used to the programs one is familiar with and > Eleanor especially is very fond of these things, but there are several > things which can be done for example in Coot (symmetry coordinates etc) . > It is just another way to do it. I had the chance and pleasure to work for > a while with the programmers of some of these programs in one building and > such decisions are not taken lightly. But one cannot support all programs > and write for every program interfaces or even keep two interfaces alive. > There are just not enough people and money to do that. Also most scientific > programmers don't get paid to keep the things just running. Would it be > better to have also programmers to keep legacy up to date and write and > update GUI's, maybe? But again someone needs to pay for that. > Just my 2 cents. > > Cheers > Christian > > > On Tue, Jul 7, 2020 at 6:30 PM Oganesyan, Vaheh < > vaheh.oganes...@astrazeneca.com> wrote: > >> … and how all these changes being justified? >> >> >> >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> * On Behalf Of *Eleanor >> Dodson >> *Sent:* Tuesday, July 7, 2020 12:25 PM >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* Re: [ccp4bb] Accessing full list of programs in CCP4I2 >> >> >> >> Yes - there are things I use all the time which are not part of the >> CCP4I2 list >> >> pdbset to generate symmetry equivalents or find the centre of mass etc >> etc >> >> coordconv to turn orthogonal coordinates to fractional - after all we are >> crystallographers and need to relate models to unit cells.. >> >> distang to do a quick check on crystal contacts.. >> >> nd there must be more.. >> >> Eleanor >> >> >> >> On Tue, 7 Jul 2020 at 17:16, Palm, Gottfried <p...@uni-greifswald.de> >> wrote: >> >> For occasions like Laus, it would be useful to further on have access to >> the >> CCP4 v7.0 Program Documentation, >> >> even if the programs are not updated as Christian explained. >> >> I was for instance looking for translating coordinates as in pdbset, but >> couldn't find a replacement in the ccp4i2 gui. >> >> Greetings >> >> Gottfried >> >> >> >> >> On Tuesday, 07-07-2020 at 18:00 Lau Kelvin wrote: >> >> Ah I see! Great I can run it that way >> >> >> >> And yes, Eleanor, after I realized that list was gone, I was panicking >> that there are some random things I used to do with those programs would no >> longer be possible. Good to know that the command line versions are still >> there in the 7.1 distro. >> >> >> >> Best, >> >> >> >> Kelvin >> >> >> >> -- >> Kelvin Lau >> >> https://people.epfl.ch/kelvin.lau >> >> >> Protein production and structure core facility - PTPSP >> EPFL SV PTECH PTPSP >> AI 2146 (Bâtiment AI) >> Station 19 >> CH-1015 Lausanne >> Switzerland >> Email: kelvin....@epfl.ch <kelvin....@epfl.ch> >> Phone: +41 21 69 30267 <+41%2021%2069%C2%A030267> >> >> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267> >> >> >> >> >> >> On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" < >> CCP4BB@JISCMAIL.AC.UK on behalf of christianroth...@gmail.com> wrote: >> >> >> >> ....yes Eleanor is right. command line still works.[image: :-)] >> >> fft is also in 7.1 distribution. >> >> >> >> >> >> >> >> On Tue, Jul 7, 2020 at 3:43 PM Eleanor Dodson <eleanor.dod...@york.ac.uk> >> wrote: >> >> Oh Lau - how I miss that list! >> >> But if you just run fft online it is still distributed..wombat:Downloads >> eleanor$ >> >> >> >> fft hklin .... mapout .... >> >> LABIN FP= and so on.. >> >> >> >> >> >> On Tue, 7 Jul 2020 at 14:22, Christian Roth <christianroth...@gmail.com> >> wrote: >> >> Hi Kelvin, >> >> well fft as single program is kind of not longer supported as is not >> ccp4i. In i2 internally, as well in communication with mg or coot, >> everything is done using map coefficients. >> >> Their are two options: >> >> First via i2: Use the unusual map coefficients Task and choose not to >> compare maps, but to generate the map coefficients plus a map (button is in >> Advanced tab) the standard grid parameters can be changed, but are actually >> optimized already. >> >> Second just save the map out of Coot (Export map) >> >> >> >> To avoid redundancy, the old fft task was discontinued. i2 works with >> coefficients, which generates smaller files and Coot provides all the >> functions to generate the map and is its own gui. >> >> >> >> Hope that explains a bit why things are how they are now. >> >> >> >> Cheers >> >> Christian >> >> >> >> On Tue, Jul 7, 2020 at 1:56 PM Lau Kelvin <kelvin....@epfl.ch> wrote: >> >> Hi Christian, >> >> >> >> I was in particular looking for the fft program (I couldn’t find that >> using the method you described) just to convert an mtz into a .map. Before >> in version 7.0 I could just browse all programs, now it seems like I cannot >> do that (other than using the filter, and some seem to be missing) >> >> >> >> At the end I just used mtz2map in phenix. >> >> >> >> -- >> Kelvin Lau >> >> https://people.epfl.ch/kelvin.lau >> >> >> Protein production and structure core facility - PTPSP >> EPFL SV PTECH PTPSP >> AI 2146 (Bâtiment AI) >> Station 19 >> CH-1015 Lausanne >> Switzerland >> Email: kelvin....@epfl.ch <kelvin....@epfl.ch> >> Phone: +41 21 69 30267 <+41%2021%2069%C2%A030267> >> >> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267> >> >> >> >> >> >> On 06.07.20, 13:34, "Christian Roth" <christianroth...@gmail.com> wrote: >> >> >> >> Hi Kelvin, >> >> not quite sure if I understand you correctly, but if you press the Task >> Manager button you get on the right sight a list of topics (import data, >> Molecular Replacemnt etc.) each point can be open up like a file tree to >> see all programs or pipelines available. You can search with the search >> field (Filter) on top for specific program names. >> >> Does that help? >> >> >> >> Cheers >> >> Christian >> >> >> >> On Mon, Jul 6, 2020 at 1:15 PM Lau Kelvin <kelvin....@epfl.ch> wrote: >> >> Hello, >> >> >> >> I am looking for a way to find the list of programs accessible using the >> new 7.1 CCP4I2 interface? Is this still possible or do I have to revert >> back to version 7.0? >> >> >> >> Best regards, >> >> >> >> Kelvin >> >> >> >> -- >> Kelvin Lau >> >> https://people.epfl.ch/kelvin.lau >> >> >> Protein production and structure core facility - PTPSP >> EPFL SV PTECH PTPSP >> AI 2146 (Bâtiment AI) >> Station 19 >> CH-1015 Lausanne >> Switzerland >> Email: kelvin....@epfl.ch <kelvin....@epfl.ch> >> Phone: +41 21 69 30267 <+41%2021%2069%C2%A030267> >> >> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267> >> >> >> >> >> ------------------------------ >> >> 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 >> >> >> ------------------------------ >> >> 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 >> >> >> ------------------------------ >> >> 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 >> >> ------------------------------ >> >> 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 > ######################################################################## 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/
