Aha, Last night it happened to me too (in fact I saw 3 copies of my message to you/list). Strange. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, August 8, 2023 12:22 PM To: ��� ���� <bshaanan@bgu.ac.il> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Advice on handling cofactor-protein electrostatic interactions Hi Boaz, (apologies if you get this multiple times, the chimerax-users list was rejecting my earlier replies for some unknown reason) If you use Coulombic it will automatically calculate the charges, as in my example of 1qs0 with the TPP residue. I.e. you don't have to do it in a separate step first, and in fact it may be better if you do not: if you use Add Charge first, it will also add hydrogens and make the surface a lot bumpier. If you just use Coulombic the hydrogens are added only on a temporary copy that is in memory, not on your model, and the coloring will be applied to the smoother molecular surface without hydrogens. You just need to substitute the cofactor residue name for ":tpp" in my example, if it is not TPP. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 8, 2023, at 7:09 AM, Boaz Shaanan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thanks a lot for the detailed reply and (as always) very helpful suggestions. I'll experiment first with the Chimerax coulombic surfaces and trick to include the cofactor. This sounds attractive, certainly for the TDP case as a starting point. As for derivatives of TDP, which are already included in the pdb, I guess I should follow the 'Add Charges' guide, right?
Thanks again.
Boaz