Hi, I would like to radially clip a density map. There are nice ways to do radial coloring, but I haven't found anything that allows a similar cropping (preferably with capping). Is there an easy way to do this? I do not want to erase the density, but rather be able to see the surface at varying radii, just as you can do with planes. (At the moment, I can only run v1.4). Thank you, Kelly
Hi Kelly, As far as I know there is no spherical clipping capability in Chimera other than using Volume Eraser to erase outside the sphere. However, you could do almost the same thing by creating spherical or icosahedral surfaces of progressively larger (or smaller) radii and coloring them by the density values in the map. See for example the movie at the very bottom of our animation gallery: <http://www.cgl.ucsf.edu/chimera/animations/animations.html> See the "shape" command for creating spherical or icosahedral surfaces, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> also Icosahedron Surface tool <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/icosahedron/icosahe...> and "scolor" for coloring the surface by density values, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html> also Surface Color tool <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor...> 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 Mar 15, 2011, at 1:29 PM, Kelly Dryden wrote:
Hi, I would like to radially clip a density map. There are nice ways to do radial coloring, but I haven't found anything that allows a similar cropping (preferably with capping). Is there an easy way to do this? I do not want to erase the density, but rather be able to see the surface at varying radii, just as you can do with planes. (At the moment, I can only run v1.4). Thank you, Kelly
Hello chimera users/developers, Can someone change the bfactors for a group of selected residues and save a pdb file with the new bfactors in chimera? I would like to use these values as constraints for simulations in NAMD. I could use VMD, but it selects only atoms and not entire residues. Any suggestions will be greatly appreciated. Thanks, Austin-
Hi Austin, The bfactor is an atom attribute, and you can change attribute values (or create new attributes) with the command "settatr" for one value at a time, or by creating an attribute definition file for setting multiple values at a time. The attribute definition file is in a simple column-separated text format: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> and is loaded with the Define Attribute tool or the command "defattr". If you were just going to use this attribute in Chimera, you could create a new one with an arbitrary name rather than naming it "bfactor" and overwriting the existing values. However, if you need it to be in the bfactor column when saving the PDB, using the name "bfactor" would be the way to go. Attribute values can be used in many ways such as to define an atom selection (e.g. only atoms with bfactor less than some cutoff, only residues with a certain hydrophobicity), and can be shown with colors, radii, etc. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...> 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 Mar 16, 2011, at 9:01 AM, Austin B. Yongye wrote:
Hello chimera users/developers, Can someone change the bfactors for a group of selected residues and save a pdb file with the new bfactors in chimera?
I would like to use these values as constraints for simulations in NAMD. I could use VMD, but it selects only atoms and not entire residues.
Any suggestions will be greatly appreciated. Thanks, Austin-
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Just to clarify, while each use of the "setattr" command only sets *to* a single value, it can set multiple atoms' bfactors to that value. For example, setattr a bfactor 12.0 :8-15 would set bfactor = 12.0 for all atoms in residues 8-15. Elaine On Mar 16, 2011, at 9:44 AM, Elaine Meng wrote:
Hi Austin, The bfactor is an atom attribute, and you can change attribute values (or create new attributes) with the command "settatr" for one value at a time, or by creating an attribute definition file for setting multiple values at a time. The attribute definition file is in a simple column-separated text format:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
and is loaded with the Define Attribute tool or the command "defattr". If you were just going to use this attribute in Chimera, you could create a new one with an arbitrary name rather than naming it "bfactor" and overwriting the existing values. However, if you need it to be in the bfactor column when saving the PDB, using the name "bfactor" would be the way to go.
Attribute values can be used in many ways such as to define an atom selection (e.g. only atoms with bfactor less than some cutoff, only residues with a certain hydrophobicity), and can be shown with colors, radii, etc.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...>
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 Mar 16, 2011, at 9:01 AM, Austin B. Yongye wrote:
Hello chimera users/developers, Can someone change the bfactors for a group of selected residues and save a pdb file with the new bfactors in chimera?
I would like to use these values as constraints for simulations in NAMD. I could use VMD, but it selects only atoms and not entire residues.
Any suggestions will be greatly appreciated. Thanks, Austin-
Hi Elaine, Thanks a lot for the responses. This command worked: setattr a bfactor 12.0 :8-15 Thanks! Austin- --- On Wed, 3/16/11, Elaine Meng <meng@cgl.ucsf.edu> wrote:
From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Setting bfactors To: "Austin B. Yongye" <ybausty@yahoo.com> Cc: "UCSF Chimera Mailing List" <chimera-users@cgl.ucsf.edu> Date: Wednesday, March 16, 2011, 10:02 AM Just to clarify, while each use of the "setattr" command only sets *to* a single value, it can set multiple atoms' bfactors to that value. For example,
setattr a bfactor 12.0 :8-15
would set bfactor = 12.0 for all atoms in residues 8-15.
Elaine
On Mar 16, 2011, at 9:44 AM, Elaine Meng wrote:
Hi Austin, The bfactor is an atom attribute, and you can change attribute values (or create new attributes) with the command "settatr" for one value at a time, or by creating an attribute definition file for setting multiple values at a time. The attribute definition file is in a simple column-separated text format:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
and is loaded with the Define Attribute tool or the command "defattr". If you were just going to use this attribute in Chimera, you could create a new one with an arbitrary name rather than naming it "bfactor" and overwriting the existing values. However, if you need it to be in the bfactor column when saving the PDB, using the name "bfactor" would be the way to go.
Attribute values can be used in many ways such as to define an atom selection (e.g. only atoms with bfactor less than some cutoff, only residues with a certain hydrophobicity), and can be shown with colors, radii, etc.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...>
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 Mar 16, 2011, at 9:01 AM, Austin B. Yongye wrote:
Hello chimera users/developers, Can someone change the bfactors for a group of selected residues and save a pdb file with the new bfactors in chimera?
I would like to use these values as constraints for simulations in NAMD. I could use VMD, but it selects only atoms and not entire residues.
Any suggestions will be greatly appreciated. Thanks, Austin-
participants (3)
-
Austin B. Yongye -
Elaine Meng -
Kelly Dryden