Re: [COOT] what python command to mutate with stub ?
Scott, I do this all the time too using key bindings. The way I have it set up, a lower case s chops back the side chain of the residue you are centred on and upper case S puts it back: (add-key-binding Delete Sidechain s (lambda () (using-active-atom (delete-residue-sidechain aa-imol aa-chain-id aa-res-no aa-ins-code 0 (add-key-binding Fill Partial Sidechain S (lambda () (let ((active-atom (active-residue))) (if (not active-atom) (format #t No active atom~%) (let ((imol (list-ref active-atom 0)) (chain-id (list-ref active-atom 1)) (res-no(list-ref active-atom 2)) (ins-code (list-ref active-atom 3)) (atom-name (list-ref active-atom 4)) (alt-conf (list-ref active-atom 5))) (fill-partial-residue imol chain-id res-no ins-code)) Enjoy! Dave --- Dr. David M. Lawson Biological Chemistry Dept., John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Fax: +44-(0)1603-450018 NOTE NEW EMAIL ADDRESS: Email: david.law...@jic.ac.uk Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm -Original Message- From: Scott Classen [mailto:sclas...@lbl.gov] Sent: 22 January 2014 23:12 To: COOT@JISCMAIL.AC.UK Subject: what python command to mutate with stub ? Hello Cootaholics I'd like to add a custom button (or key binding, or both) that will do a simple mutate, keep the residue type the same, and trim it back to the beta carbon. This would be the same as the stub function in the Simple Mutate dialogue box. I am finding that I repeat this action often and would like to make it quicker and easier. Can someone help me out with the proper python command? Thanks, Scott
[COOT] what python command to mutate with stub ?
Hello Cootaholics I'd like to add a custom button (or key binding, or both) that will do a simple mutate, keep the residue type the same, and trim it back to the beta carbon. This would be the same as the stub function in the Simple Mutate dialogue box. I am finding that I repeat this action often and would like to make it quicker and easier. Can someone help me out with the proper python command? Thanks, Scott smime.p7s Description: S/MIME cryptographic signature
Re: [COOT] what python command to mutate with stub ?
The function you want is delete_residue_sidechain() http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#delete_002dresidue_002dsidechain For keybindings, pythonics (old version), please see (Kill Sidechain): http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Bernhards_key_bindings_for_coot.py HTH B Hello Cootaholics I'd like to add a custom button (or key binding, or both) that will do a simple mutate, keep the residue type the same, and trim it back to the beta carbon. This would be the same as the stub function in the Simple Mutate dialogue box. I am finding that I repeat this action often and would like to make it quicker and easier. Can someone help me out with the proper python command? Thanks, Scott -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
