… 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<mailto: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<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<mailto:kelvin....@epfl.ch> Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494<tel:+41%2021%2069%C2%A030267> On 07.07.20, 15:51, "CCP4 bulletin board on behalf of Christian Roth" <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of christianroth...@gmail.com<mailto:christianroth...@gmail.com>> wrote: ....yes Eleanor is right. command line still works.[:-)] fft is also in 7.1 distribution. On Tue, Jul 7, 2020 at 3:43 PM Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto: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<mailto: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<mailto: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<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<mailto:kelvin....@epfl.ch> Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494<tel:+41%2021%2069%C2%A030267> On 06.07.20, 13:34, "Christian Roth" <christianroth...@gmail.com<mailto: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<mailto: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<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<mailto:kelvin....@epfl.ch> Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494<tel:+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<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<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<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<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<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<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/
