[Chimera-users] issue with heme minimization
Rio Aquarius
rioxel at gmail.com
Mon Sep 14 11:42:21 PDT 2020
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>
>
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