HI- We are using chimera to fit xxx model into rho map. I'd like to fit rho map into xxx model. That is, rotate and translate my map to coincide with a fixed orientation of the model. Of course, then I can average rho1, rho2 etc. We can get around the "map" part of the "fit (button1) to map (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem. But how do we write out the new rotated version of the rho map when we are done fitting? Thanks.
Hi Michael, Saving a rotated map requires resampling it at new grid positions because none of the map formats include an option for specifying a rotation in the header. However, with resampling there is some loss of resolution because interpolation is required to get the values at the new grid point locations. That is why we normally recommend saving the rotated PDB instead when the goal is to have a PDB and map that fit together. However, if you are going to average maps they may need to be resampled onto a consistent grid anyway. Resampling a map onto the grid of another map can be done with "vop resample" as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ vop.html#resample> For example, vop resample #0 onGrid #1 [other-options] You would want to figure out which map's grid you want to do the final averaging on and use the fewest resamplings as possible to achieve that, for minimal loss of data quality. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 16, 2009, at 1:27 PM, Michael Schmid wrote:
HI- We are using chimera to fit xxx model into rho map. I'd like to fit rho map into xxx model. That is, rotate and translate my map to coincide with a fixed orientation of the model. Of course, then I can average rho1, rho2 etc. We can get around the "map" part of the "fit (button1) to map (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem. But how do we write out the new rotated version of the rho map when we are done fitting? Thanks.
Hi- We tried this vop resample #0 onGrid #14 And got Invalid model specifier syntax:"resample" On 9/17/09 4:51 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Michael, Saving a rotated map requires resampling it at new grid positions because none of the map formats include an option for specifying a rotation in the header. However, with resampling there is some loss of resolution because interpolation is required to get the values at the new grid point locations. That is why we normally recommend saving the rotated PDB instead when the goal is to have a PDB and map that fit together.
However, if you are going to average maps they may need to be resampled onto a consistent grid anyway. Resampling a map onto the grid of another map can be done with "vop resample" as described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ vop.html#resample>
For example, vop resample #0 onGrid #1 [other-options]
You would want to figure out which map's grid you want to do the final averaging on and use the fewest resamplings as possible to achieve that, for minimal loss of data quality. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 16, 2009, at 1:27 PM, Michael Schmid wrote:
HI- We are using chimera to fit xxx model into rho map. I'd like to fit rho map into xxx model. That is, rotate and translate my map to coincide with a fixed orientation of the model. Of course, then I can average rho1, rho2 etc. We can get around the "map" part of the "fit (button1) to map (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem. But how do we write out the new rotated version of the rho map when we are done fitting? Thanks.
Hi Michael, It depends on what version you are using. What I showed was for newer versions. If you are using an older version the "resample" goes after the model number. To see the documentation for the version you are using, use the command help vop Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 17, 2009, at 3:35 PM, Michael Schmid wrote:
Hi- We tried this vop resample #0 onGrid #14
And got Invalid model specifier syntax:"resample"
On 9/17/09 4:51 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Hi Michael, Saving a rotated map requires resampling it at new grid positions because none of the map formats include an option for specifying a rotation in the header. However, with resampling there is some loss of resolution because interpolation is required to get the values at the new grid point locations. That is why we normally recommend saving the rotated PDB instead when the goal is to have a PDB and map that fit together.
However, if you are going to average maps they may need to be resampled onto a consistent grid anyway. Resampling a map onto the grid of another map can be done with "vop resample" as described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ vop.html#resample>
For example, vop resample #0 onGrid #1 [other-options]
You would want to figure out which map's grid you want to do the final averaging on and use the fewest resamplings as possible to achieve that, for minimal loss of data quality. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 16, 2009, at 1:27 PM, Michael Schmid wrote:
HI- We are using chimera to fit xxx model into rho map. I'd like to fit rho map into xxx model. That is, rotate and translate my map to coincide with a fixed orientation of the model. Of course, then I can average rho1, rho2 etc. We can get around the "map" part of the "fit (button1) to map (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem. But how do we write out the new rotated version of the rho map when we are done fitting? Thanks.
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Hi Michael, Elaine's suggestion to use the "vop resample" command is just what you need. You can also create the map from the model using the Chimera molmap command which is equivalent to the EMAN pdb2mrc program (I looked at how the pdb2mrc code defines the parameters when I implemented molmap). For example molmap #0 5 will create a 5 Angstrom resolution map from atomic model #0. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html You can also add different maps in Chimera using the "vop add" command and then if you want an average you can divide by the number of maps with the "vop scale" command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html Tom -------- Original Message -------- Subject: [Chimera-users] Fit MAP to MODEL From: Michael Schmid To: chimera-users Date: 9/16/09 1:27 PM
HI- We are using chimera to fit xxx model into rho map. I'd like to fit rho map into xxx model. That is, rotate and translate my map to coincide with a fixed orientation of the model. Of course, then I can average rho1, rho2 etc. We can get around the "map" part of the "fit (button1) to map (button2)" by running pdb2mrc to turn xxx model into xxx map. No problem. But how do we write out the new rotated version of the rho map when we are done fitting? Thanks.
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participants (3)
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Elaine Meng -
Michael Schmid -
Thomas Goddard