[Chimera-users] building on functional groups
jjsqrd at bellsouth.net
Wed Oct 22 05:00:09 PDT 2014
Thank you Elaine. I appreciate it.
I have been able to acetylate the lysine residues but now I am having difficulty in eliminating the charge. I noticed that each hydrogen on a normal epsilon amino group of lysine is assigned +0.34 charge. It would obviously be less than +1 and when I try and assign it +0 it basically is not capable of conducting the calculation. I will continue to read and work on it.
On Tuesday, October 21, 2014 1:18 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
I should have added an "etc." … the steps I mentioned still wouldn't be the whole acetyl group!
On Oct 21, 2014, at 11:06 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Jesse,
> You can manually build onto your structure atom-by-atom using Build Structure (in menu under Tools… Structure Editing). It's not the most friendly builder, but once you play around with it for a while, you can see how the general process works. Basically to build outward you use the "Modify Structure" tab, with cycles of hydrogen addition and then changing a hydrogen to some other atom type. You would add hydrogens (could do with AddH the first time around… this tool is also in the Structure Editing section), then change one hydrogen to a carbon of the proper hybridization type, then add hydrogens again, then change one of the hydrogens on the carbon to an oxygen of the proper hybridization type.
> See the following (or click Help on the tool dialog)
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Oct 21, 2014, at 10:55 AM, JESSE JAYNES <jjsqrd at bellsouth.net> wrote:
>> I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse
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