[Chimera-users] Problem with minimizing structure

Renee Arias rarias72 at gmail.com
Thu Jul 26 11:58:21 PDT 2018

Hi Eric,

I gave your advice a try with the following steps:

First, I just deleted residue 88, which was giving me problems in the first
Fetch 2VB2
del H
Then added them back with Tools, Structure Editing, AddH
Minimize structure, kept default steps, etc
Memorize options chosen in subsequent dialogs
Unchecked "Add hydrogens"

And I got a structure that looked like this, which obviously not correct.
The original structure starts with the copper out in the middle,
coordinated by the Mets and the His. For some reason it moves the copper
over to the histidine, and then distorts the histidine in a strange way. Do
you know what I could be doing wrong here?

[image: image.png]
Thanks a lot for your help,


On Thu, Jul 26, 2018 at 11:16 AM Renee Arias <rarias72 at gmail.com> wrote:

> Thanks so much! I will give it a try!
> On Thu, Jul 26, 2018 at 11:14 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> Forgot to mention that one easy way to delete all hydrogens is with the
>> command “del H” (Favorites→Command Line).
>> —Eric
>> On Jul 26, 2018, at 11:13 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> Hi Renee,
>> For standard residues, Chimera simply looks up the Amber atom type and
>> partial charge (both needed for minimization) in a table based on the
>> atom’s name.  Obviously for this to work the atom needs to have the
>> appropriate PDB-standard name.  There is no ‘H1’ atom in standard PDB GLN
>> residues.
>> Typically the easiest way to remedy this, since you are about to minimize
>> the structure anyway, is to delete the existing hydrogens and let Chimera
>> add them back during the minimization prep — which will ensure they have
>> the correct names in most cases.  The one case I can think of where that
>> doesn’t work is if there are *backbone* heavy atoms missing in a
>> residue.  In that situation it may be best to delete the residue entirely.
>> —Eric
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>> On Jul 25, 2018, at 4:03 PM, Renee Arias <rarias72 at gmail.com> wrote:
>> Hello all,
>> I am having a problem with the minimizing structure function in Chimera.
>> I am just trying to change a single residue on a very small protein (88
>> residues), but I keep getting the error: No MMTK name for atom "H1" in
>> standard residue "GLN". Previous message boards seem to just point to bug
>> fixes in Chimera, but I am running the newest version available for Windows
>> 10.
>> I would appreciate any help!
>> Thanks so much,
>> Renee
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