Re: [COOT] Default B-factor for new residues
In the meantime, adding something like this to whatever custom python extensions file you use seems to do the trick: def set_new_atom_b_fac_to_mean(): mol_id=active_residue()[0] mean_b=average_temperature_factor(mol_id) set_default_temperature_factor_for_new_atoms(mean_b) add_simple_coot_menu_menuitem(menu, Set Bfac for new atoms to mean B for active mol,lambda func: set_new_atom_b_fac_to_mean())
Re: [COOT] Default B-factor for new residues
This is fixed in r5695 (B-factors of side chain atoms having default B that is). Setting (refining?!) B-factors more intelligently is on the list, but requires a bit more sophistication than just adapting it from neighbouring residues (who says these are right(ish)?!). B On 16/05/2015 22:23, Oliver Clarke wrote: Also, on the same topic - the default B-factor for new atoms only seems to apply to add terminal residue... when a new sidechain is added, it defaults to a B-factor of 20. I think the same parameter should probably apply in both instances? Oliver -- *** Dr. Bernhard Lohkamp Associate Professor/Docent 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 --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] Default B-factor for new residues
Thanks for fixing that Bernhard! I agree that maybe setting the B-factor based on adjacent residues might be a bit risky, so Eleanor's suggestion of setting it based on the average B for the molecule or chain sounds like a good interim solution. That value is unlikely to be wrong, at least after the first couple of cycles of refinement, and seems likely to be closer to the true B-factor than an arbitrary value. It would also only need to be updated at the time the user first loads the molecule - probably no need to update on the fly as the average B won't change much On a completely unrelated note, as of the last couple of nightlies I have noticed that I am now unable to resize my Coot window (on Mac, OS X 10.10.3). Not a big deal, but if anyone has any suggestions on how to fix I would be most grateful. Cheers, Oliver.
Re: [COOT] Default B-factor for new residues
At least it would be good to set new residues to the overall B value. Eleanor On 17 May 2015 at 17:57, Bernhard Lohkamp bernhard.lohk...@ki.se wrote: This is fixed in r5695 (B-factors of side chain atoms having default B that is). Setting (refining?!) B-factors more intelligently is on the list, but requires a bit more sophistication than just adapting it from neighbouring residues (who says these are right(ish)?!). B On 16/05/2015 22:23, Oliver Clarke wrote: Also, on the same topic - the default B-factor for new atoms only seems to apply to add terminal residue... when a new sidechain is added, it defaults to a B-factor of 20. I think the same parameter should probably apply in both instances? Oliver -- *** Dr. Bernhard Lohkamp Associate Professor/Docent 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 --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [COOT] Default B-factor for new residues
Also, on the same topic - the default B-factor for new atoms only seems to apply to add terminal residue... when a new sidechain is added, it defaults to a B-factor of 20. I think the same parameter should probably apply in both instances? Oliver
