Hi All, I would like to know how to extend an e-density map in y or z direction. Here is my case: The DNA structure that was refined in shelx. Model #0 is DNA and the e-density map is model #1. When I used vop cover #1 atom #0, the electron density covers the molecule along two axes, and for the third axis it covers partly. How to extend the e-density map in a particular axis? Thank you! -- ------------------------------------------------------------------- Pradeep Pallan
Hi Pradeep, Maybe your xray density map is not a full asymmetric unit so the whole unit cell cannot be reconstructed from it. Or maybe the symmetry operators aren’t in the map file so it is only using unit cell translations. Can’t be sure what the problem is without access to the specific data files. Tom
On May 19, 2017, at 11:37 AM, Pradeep Pallan wrote:
Hi All,
I would like to know how to extend an e-density map in y or z direction. Here is my case:
The DNA structure that was refined in shelx. Model #0 is DNA and the e-density map is model #1. When I used vop cover #1 atom #0, the electron density covers the molecule along two axes, and for the third axis it covers partly. How to extend the e-density map in a particular axis?
Thank you! --
------------------------------------------------------------------- Pradeep Pallan _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
The problem was the map file had symmetry operators using lowercase x,y,z in the symmetry operators in the CCP4 file header and Chimera only parses uppercase X,Y,Z. When I open your map I see in the Chimera reply log the following warning Unable to parse symmetry operators of dnaxraydata.map x, y, z x+1/2, -y+1/2, -z -x, y+1/2, -z+1/2 -x+1/2, -y, z+1/2 Since it can’t read the 4 symmetry operators the vop cover command only uses unit cell translational symmetry. I see using “volume #0 dumpHeader true” a comment in the map header saying “From clipper Xmap”. So I guess that software writes lowercase x, y, z. I’ve changed Chimera to accept upper or lower case symmetry operators. This will be in tonight’s Chimera daily build. Thanks for reporting the problem. Tom
On May 19, 2017, at 4:48 PM, Tom Goddard wrote:
Hi Pradeep,
Maybe your xray density map is not a full asymmetric unit so the whole unit cell cannot be reconstructed from it. Or maybe the symmetry operators aren’t in the map file so it is only using unit cell translations. Can’t be sure what the problem is without access to the specific data files.
Tom
On May 19, 2017, at 11:37 AM, Pradeep Pallan wrote:
Hi All,
I would like to know how to extend an e-density map in y or z direction. Here is my case:
The DNA structure that was refined in shelx. Model #0 is DNA and the e-density map is model #1. When I used vop cover #1 atom #0, the electron density covers the molecule along two axes, and for the third axis it covers partly. How to extend the e-density map in a particular axis?
Thank you! --
------------------------------------------------------------------- Pradeep Pallan _______________________________________________ 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
Thank you, Tom. Pradeep On Mon, May 22, 2017 at 12:24 PM, Tom Goddard <goddard@sonic.net> wrote:
The problem was the map file had symmetry operators using lowercase x,y,z in the symmetry operators in the CCP4 file header and Chimera only parses uppercase X,Y,Z. When I open your map I see in the Chimera reply log the following warning
Unable to parse symmetry operators of dnaxraydata.map x, y, z x+1/2, -y+1/2, -z -x, y+1/2, -z+1/2 -x+1/2, -y, z+1/2
Since it can’t read the 4 symmetry operators the vop cover command only uses unit cell translational symmetry. I see using “volume #0 dumpHeader true” a comment in the map header saying “From clipper Xmap”. So I guess that software writes lowercase x, y, z. I’ve changed Chimera to accept upper or lower case symmetry operators. This will be in tonight’s Chimera daily build. Thanks for reporting the problem.
Tom
On May 19, 2017, at 4:48 PM, Tom Goddard wrote:
Hi Pradeep,
Maybe your xray density map is not a full asymmetric unit so the whole unit cell cannot be reconstructed from it. Or maybe the symmetry operators aren’t in the map file so it is only using unit cell translations. Can’t be sure what the problem is without access to the specific data files.
Tom
On May 19, 2017, at 11:37 AM, Pradeep Pallan wrote:
Hi All,
I would like to know how to extend an e-density map in y or z direction. Here is my case:
The DNA structure that was refined in shelx. Model #0 is DNA and the e-density map is model #1. When I used vop cover #1 atom #0, the electron density covers the molecule along two axes, and for the third axis it covers partly. How to extend the e-density map in a particular axis?
Thank you! --
------------------------------------------------------------------- Pradeep Pallan _______________________________________________ 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
-- ------------------------------------------------------------------- Pradeep Pallan
participants (2)
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Pradeep Pallan -
Tom Goddard