[Chimera-users] issue with heme minimization

[Elaine Meng]

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>