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@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@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@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>
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@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@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@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@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>
Hi Dmitry, Oh, I guess I see what you mean. X,Y, and Z will still be the same X,Y, and Z… just the data itself would be rotated. I do not know it you can actually save into a different set of axes, as everything just transforms the data, including “vop permuteAxes”. Maybe our density-map expert will have further ideas. Sorry I misunderstood you, Elaine
On May 10, 2018, at 12:51 PM, Dmitry Semchonok <semchonok@gmail.com> wrote:
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@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@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@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@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>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I don’t understand the problem. You should understand that density map file formats do not have a rotation transformation in the file so the only way to rotate them is to resample them as Elaine pointed out. If you want to save the orientation you can save a Chimera session file, but of course that can only be opened in Chimera. Tom
On May 10, 2018, at 1:52 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dmitry, Oh, I guess I see what you mean. X,Y, and Z will still be the same X,Y, and Z… just the data itself would be rotated. I do not know it you can actually save into a different set of axes, as everything just transforms the data, including “vop permuteAxes”. Maybe our density-map expert will have further ideas. Sorry I misunderstood you, Elaine
On May 10, 2018, at 12:51 PM, Dmitry Semchonok <semchonok@gmail.com> wrote:
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@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@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@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@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>
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Dmitry Semchonok -
Elaine Meng -
Tom Goddard