[Chimera-users] Help Coordinating Metal Atom to an Amino Acid (Cysteine)

[Elaine Meng]

Hi Sydney,
We do not have funding or manpower for individual, in-depth consulting on your research project, sorry.  As you have found out, part of getting a PhD is delving into a lot of different experimental and/or computational tools and trying to solve the many problems that inevitably arise, which may require learning more than you had intended.

Chimera minimization is meant to be simple and easy to use, in turn using some tools that are not developed by our group (Antechamber, MMTK, etc.), but it is not comprehensive nor will it cover all kinds of molecules.

Changing atom and residue names does not necessarily involve coding -- it could just be text-editing a saved PDB file and reading it back in. I don't write code either, but text-editing a PDB can be quite simple if you look at the format description, e.g. the simplified intro in the Chimera User Guide:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>

I don't know if changing the atom/residue names would fix whatever issues you are having, however.

Another idea is when building the structure, to start with a known PDB file that already has the desired metal-binding geometry (or at least similar) and then delete the parts you don't want and modify the others.

Best regards,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Aug 1, 2022, at 11:28 AM, Sydney Marchi via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello Chimera Software Developers,
> 
> I am having a lot of trouble coordinating a metal atom (using Zinc in place of Cr) to the nitrogen, oxygen, and potentially sulfur atom on cysteine. The two main problems that I am having are getting the geometry I need, which is octahedral, where the metal is also coordinated to two-three water molecules as well as eventually the N-7 of guanine. I am trying to build and minimize the Zn-Cysteine model first though before incorporating it into a DNA oligo. I can't seem to get the geometry I need but beside from that, I have tried to minimize the structure using Amber with an undesired geometry just to test if it will run, and it doesn't let me. I have read the reply log and I believe this is due to the atom labeling on cysteine being the issue. But changing the atoms names is a coding problem, and I don't know anything about coding. I tried building cysteine on my own as a potential fix in place of using the prebuilt model but ran into the same problem where it would not minimize my structure. I need this model for my dissertation, so any help would be greatly appreciated. I can attach any files that you may need, set up a zoom meeting, whatever is easiest for you. I know this is probably not the most conventional use for this software, but I really need to figure this out, and I don't have enough knowledge to tinker with it on my own anymore. Thank you for any feedback.
> 
> Best Regards,
> 
> Sydney Marchi
> PhD Candidate, Chemistry
> Office: Shelby Hall, 3043
> University of Alabama