Hi Boaz, Addendum to (2). Actually there are options to the "save" command with which you can do this without having to delete anything beforehand. See the "atoms" and/or "skipAtoms" options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#mol2> Maybe you were looking at the File... Save dialog, which does not currently expose those options when the Mol2 file type is chosen. Best, Elaine
On Sep 12, 2023, at 11:10 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Boaz, (1) I thought we'd answered this before and actually, you were the one who asked! See this previous reply about setting an option in Surface Color to show value in a pop-up on mouseover
<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
Of course, the shape of the surface will also be different between when the cofactor is on the inside of it and on the outside of it.
(2) as long as you have a saved copy of the entire thing, just delete the part you don't want before saving.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 12, 2023, at 9:25 AM, Boaz Shaanan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Your advice on using the Coulomb surface +vcofactor works fine, thanks. I have a few more questions though: • I'm trying to figure out the difference between the Coulomb surface with and w/o the coafactor but I'm not sure I see a difference. Is there an option to 'walk' with the mouse on the surface to probe the actual values (as in the surface generates by the volume viewer)? • Writing out the displayed model coordinates in mol2 format does not give an option write out a selected displayed group (e.g. cofactors) as in the case of .pdb. I guess this has to do with mol2 format but is it not possible to add such an option?
Thanks,
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: בעז שאנן <bshaanan@bgu.ac.il> Sent: Tuesday, August 8, 2023 12:25 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Advice on handling cofactor-protein electrostatic interactions
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: בעז שאנן <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
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