[Chimera-users] issue with heme minimization

[Rio Aquarius]

Hello again!
Oh, I got it. So, just two steps are necessary for cleaning heme from all
extra H. I try to get an universal protocol for any protein with heme.
Indeed I don't know if the Fe ion must be in the heme plane, but one expert
of crystallography who works with this protein believes that it must be so.
But you are right, even though I delete all extra H, it doesn't help to
keep the Fe ion in the heme plane. It's so sad. But thank you very much,
Elaine, for your kind help and detailed explanation.

пн, 14 сент. 2020 г. в 23:59, Elaine Meng <meng at cgl.ucsf.edu>:

> Hello,
>
> HEM[FE] is for specifying the net charge of the Fe ion only.
> HEM[non-FE] is for specifying the net charge of the rest of the heme
> residue (the other atoms except Fe).
>
> I don't think you needed to do any of the protocol (including defattr) in
> that previous post, because when I open your structure, delete hydrogens
> and add them back, commands
>
> delete H
> addh
>
> ....I don't see any extra hydrogens on the ring N.  The reason the other
> person used the defattr file was to fix atom types so that they wouldn't
> get extra hydrogens.
>
> I tried minimizing just the heme/Fe from your structure (without the
> protein to make the test faster) and it still did not go exactly into the
> plane.
>
> However:
>
> (1) are you sure the iron is supposed to be in the plane of the heme?  I
> see some experimental structures where the ion is not in the plane. I'm
> sure it depends what ligands are binding the metal, etc.
>
> (2) even if it supposed to be in the plane, you may be expecting too much
> fine detail from a simple molecular mechanics  calculation as done by
> Chimera.  To model small changes from metal oxidation state, you may need
> to use some kind of quantum-mechanical calculation instead (or in addition
> to) molecular mechanics, and this cannot be done with Chimera. In Chimera
> the iron ion is just a ball that does not change size no matter what charge
> value you put on it, and the charge does not get delocalized no matter what
> other atoms are around the atom.
>
> Elaine
>
> > On Sep 14, 2020, at 11:42 AM, Rio Aquarius <rioxel at gmail.com> wrote:
> >
> > On the last step of this protocol I need to specify net charges. Does
> HEM[FE] mean the charge of the Fe atom or the charge of the heme in state
> with Fe? But I guess it means the charge of the Fe atom. If it is so can I
> specify in such a way reduced (Fe+2) and oxidized (Fe+3) states of the heme?
> >
> > пн, 14 сент. 2020 г. в 21:13, Elaine Meng <meng at cgl.ucsf.edu>:
> > Hello,
> > You can put it wherever your computer allows it.  In first image, the
> error is that the file was not found, so you must have not given the same
> place where you actually put it.
> >
> > In the second image, it is just a warning message (not an error) that
> the Render by Attribute dialog will not be shown, but as far as I can tell
> it did already read the file and assign the attribute correctly.  In that
> case, you can just ignore the warning and continue with your calculations.
> >
> > 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 14, 2020, at 11:05 AM, Rio Aquarius <rioxel at gmail.com> wrote:
> > >
> > > Thank you for your kind reply. Could you help me a little more? Where
> must the heme.defattr file be, when I use the 'defattr' command? I have
> tried to put it in the root directory, but it didn't work and I got such a
> message:
> > > <изображение.png>
> > >
> > > I have also tried to open this file using the tool 'Define Attribute'
> in Tools/Structure Analysis/, but got such a message:
> > > <изображение.png>
> > >
> > >
> > > пн, 14 сент. 2020 г. в 19:07, Elaine Meng <meng at cgl.ucsf.edu>:
> > > The heme.defattr file is a link from the URL you already found:
> > >
> > > >
> https://www.cgl.ucsf.edu/pipermail/chimera-users/2019-July/015972.html
> > >
> > > In the lower part of that page, the link to the defattr file is
> > >
> > > URL: <
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190715/ecb1dce6/attachment.obj
> >
> > >
> > > ...and you just need to click that and then save it as a plain text
> file.  You can rename that plain text file heme.defattr if you want.
> > >
> > > 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, 2020, at 9:53 AM, Rio Aquarius <rioxel at gmail.com> wrote:
> > > >
> > > > Hi,
> > > > I have an issue with heme minimization, Fe atom leaves a heme plane.
> I saw at least one user had the same issue and got help to solve it (
> https://www.cgl.ucsf.edu/pipermail/chimera-users/2019-July/015972.html).
> I could try the protocol described there, but I don't have the heme.defattr
> file. I hope you can help me with it too. I have attached a pdb file with
> this issue.
> > > > <CYP51_min300.pdb>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200915/2539c508/attachment.html>