[Chimera-users] saving new position of the model (map saving)

[Dmitry Semchonok]

Dear Elaine,

Yes indeed the command works.

So what I did:

Vop add #0                     then I turned one manually and then

vop resample #0 onGrid #1

Volume viewer: save map as….

But when I open the created and rotated map it is still in the top view (and not in the rotated orientation)……

I definitely did a mistake. 

Could you please prompt?

Thank you

Sincerely,
Dmitry



Sent from Mail for Windows 10

From: Elaine Meng
Sent: Thursday, May 10, 2018 9:09 PM
To: Dmitry Semchonok
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] saving new position of the model (map saving)

Hi Dmitry,
You need to specify two maps, the one you are sampling and the one whose grid you are sampling on, e.g.

vop resample #0 onGrid #1

This means map #1 with the desired grid must already exist.  As mentioned in that link, you could create it with “vop new”

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new>

You can show outline boxes indicating axis orientation with the data display options in Volume Viewer or “volume” command, and move models separately by  specifying model to move with the “models” option of “turn” (or “roll”) or with the mouse after freezing some models by unchecking their “A”ctive buttons in the Model Panel.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 10, 2018, at 11:56 AM, Dmitry Semchonok <semchonok at gmail.com> wrote:
> 
> Dear Elaine,
>  
> Thank you for your answer.
>  
> I read the last link
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting
>  
> but I still can not save the map
>  
> <F8EED359A67845868DD4F80A9DAF3499.png>
>  
> If I put onGrid I get this
>  
> <B7696E2A55B04A298BEB09E32A85BDF2.png>
>  
> Could you please briefly tell how to make it work?
>  
> Thank you.
>  
>  
> Sincerely,
> Dmitry
>  
>  
> Sent from Mail for Windows 10
>  
> From: Elaine Meng
> Sent: Thursday, May 10, 2018 5:59 PM
> To: Dmitry Semchonok
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] saving new position of the model
>  
> Dear Dmitry,
> For atomic models, of course: you can just specify saving transformed coordinates in the Save PDB or Save Mol2 dialog (or “write” command).
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>
>  
> The rotating could be done by hand with the mouse or with commands “turn” or “roll."
>  
> However, I’m guessing you probably mean a map since that is more complicated.  As explained in the “Saving Maps After Fitting” link below, you would generally have to resample the map onto a different grid that has the axes oriented how you want:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>
>  
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                      
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>  
> > On May 10, 2018, at 8:34 AM, Dmitry Semchonok <semchonok at gmail.com> wrote:
> >
> > Dear colleagues,
> > Is there a way to rotate the model and than save it with a new x y z?
> > Thank you
> > Sincerely,
> > Dmitry
>  
>  
> <F8EED359A67845868DD4F80A9DAF3499.png><B7696E2A55B04A298BEB09E32A85BDF2.png>


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