Re: [COOT] symmetry related molecules
No idea why this is happening to you, but before analysing symmetry stuff it sometimes helps ro use PISA to generate the best assembly for your 2 molecules in the asymmetric unit. All the symmetry search things only use a limited number of unit cell translations Eleanor On 18 May 2015 at 05:45, Joel Tyndall joel.tynd...@otago.ac.nz wrote: Oops, meant to say its 2 molecules per asymmetric unit J *From:* Mailing list for users of COOT Crystallographic Software [mailto: COOT@JISCMAIL.AC.UK] *On Behalf Of *Joel Tyndall *Sent:* Monday, 18 May 2015 4:11 p.m. *To:* COOT@JISCMAIL.AC.UK *Subject:* symmetry related molecules Hi all, I have a structure that we have almost completed (2.66 A ) and the space group is P1, R factor is around 0.20940.25. When I turn on cell symmetry to see related symmetry molecules, there are cases that some related molecules can be seen and a specific case where there is an intersection of 3 related molecules and one is missing. There is clear density for this but only one of the 2 symmetry molecules are displayed. When the symmetry related molecules are generated in Pymol, it is there and when that specific one is read into Coot it fills the density appropriately. There is no overlap crossover what-so-ever but there are numerous contacts. Is there something I am missing? J _ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293
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] symmetry related molecules
Hi folks, Thanks to all who responded, the workaround appears that you can add a command (in windows) using: Calculate Scripting python and run set_symmetry_shift_search_size(2) Then when you generate the symmetry related molecules they are all there. Whilst it doesn't solve the problem it's a great workaround Thanks J From: Joel Tyndall Sent: Monday, 18 May 2015 4:45 p.m. To: Joel Tyndall; COOT@JISCMAIL.AC.UK Subject: RE: symmetry related molecules Oops, meant to say its 2 molecules per asymmetric unit J From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Joel Tyndall Sent: Monday, 18 May 2015 4:11 p.m. To: COOT@JISCMAIL.AC.UKmailto:COOT@JISCMAIL.AC.UK Subject: symmetry related molecules Hi all, I have a structure that we have almost completed (2.66 A ) and the space group is P1, R factor is around 0.20940.25. When I turn on cell symmetry to see related symmetry molecules, there are cases that some related molecules can be seen and a specific case where there is an intersection of 3 related molecules and one is missing. There is clear density for this but only one of the 2 symmetry molecules are displayed. When the symmetry related molecules are generated in Pymol, it is there and when that specific one is read into Coot it fills the density appropriately. There is no overlap crossover what-so-ever but there are numerous contacts. Is there something I am missing? J _ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293
