James - could you send me a few examples to add to the documentation? Lockdown means I cant easily access my own examples - all trapped on the lab desktop.. Eleanor
On Mon, 7 Jun 2021 at 17:18, James Holton <[email protected]> wrote: > I wrote a script for auto-generating occupancy refinement relationships > for refmac. It is perhaps not as sophisticated as what phenix does > internally, but it gets common things right, like if you have a 2-headed > side chains or partial-occupancy metals. > > https://bl831.als.lbl.gov/~jamesh/scripts/refmac_occupancy_setup.com > > It is a csh/awk shell script. You run it with the name of your input pdb > file on the command line and it dumps the refmac keywords to a file > called refmac_opts_occ.txt and to the terminal. If you want every > "hetatm" atom to be refined put "allhet" as a second command-line argument. > > You can then perhaps copy-and-paste this to the relevant GUI window. > > -James Holton > MAD Scientist > > On 6/7/2021 3:35 AM, Marina Gárdonyi wrote: > > Hi, > > > > I didn't know that I can also enter keywords without a file! That is a > > good note, thank you!! > > > > Best regards, > > Marina > > > > Zitat von Jon Cooper <[email protected]>: > > > >> Hello, the keywords can be entered in refmac gui (in one of the > >> dropdown things), so you don't need a file, as such, but it's useful > >> to keep a record. > >> > >> Sent from ProtonMail mobile > >> > >> -------- Original Message -------- > >> On 5 Jun 2021, 16:39, Marina Gárdonyi wrote: > >> > >>> Hello everyone, > >>> > >>> I am trying to refine structures with Refmac. > >>> > >>> The problem is that nobody from my working group is familiar with this > >>> programm. They are using Phenix exclusively. > >>> > >>> That's why I need your help. I would like to refine the occupancy. I > >>> know that I need a keyword file for this, but I have no idea how to > >>> create such a keyword file. > >>> > >>> Can someone maybe send me a sample file? I think that would help me. I > >>> have found essential keywords, but I don't know how to build up such a > >>> file. > >>> > >>> Thank you very much in advance! > >>> > >>> Best regards, > >>> Marina > >>> > >>> -- > >>> Marina Gárdonyi > >>> > >>> PhD Student, Research Group Professor Dr. Klebe > >>> > >>> Department of Pharmaceutical Chemistry > >>> > >>> Philipps-University Marburg > >>> > >>> Marbacher Weg 6, 35032 Marburg, Germany > >>> > >>> Phone: +49 6421 28 21392 > >>> > >>> E-Mail: [email protected] > >>> > >>> http://www.agklebe.de/ > >>> > >>> > ######################################################################## > >>> > >>> > >>> 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/ > > > > > > > > ######################################################################## > > 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/ > ######################################################################## 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/
