Hi All, I am using latest Chimera v1.6. I want to show the backbone carbonyl oxygen of one of the residue. The backbone is in ribbon representation. Also, how to make dotted line representation of the missing residues joining two domains of the same chain. Thanks. James
Hi James, By default, showing ribbon automatically hides backbone atoms (peptide N,CA,C,O), but you can enable showing them at the same time with the command "ribbackbone." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html> Example commands: ribbackbone display #0:38@O You can draw a line between any two atoms, but only a straight line. Actually when you open a file from the PDB of a protein with a missing segment, it will automatically draw a dashed line (for example, PDB 1www), but maybe there is something about your input file that prevents that from happening. If there is not already a line, a couple of ways to add one are: (a) measure distance between the two atoms, then in Distances tool (under Tools... Structure Analysis) set label to "None"... there are several ways to measure the distance, as described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances> (b) use PseudoBond Reader (under Tools... Depiction) to read in a text file describing the atom pair(s) you want to draw lines between. Format is described in that page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html> Then to further control display settings of the line, Ctrl-click to select it, then click the magnifying glass in the lower right corner of the Chimera window to show the Selection Inspector, and then inspect "pseudobond" and "pseudobond group" to change various settings. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html> 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 2, 2012, at 9:10 PM, james09 pruza wrote:
Hi All, I am using latest Chimera v1.6. I want to show the backbone carbonyl oxygen of one of the residue. The backbone is in ribbon representation. Also, how to make dotted line representation of the missing residues joining two domains of the same chain. Thanks. James
Dear Dr. Elaine, Thanks for the information. I will check that out. One more thing, How to show the ball and stick representation. By default, there are three spheres. I am selecting all of them and Actions - Atoms and Bonds - Ball and stick. Nothing happens. Any clue. Thanks. James On Sat, Mar 3, 2012 at 12:35 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi James, By default, showing ribbon automatically hides backbone atoms (peptide N,CA,C,O), but you can enable showing them at the same time with the command "ribbackbone." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html>
Example commands: ribbackbone display #0:38@O
You can draw a line between any two atoms, but only a straight line. Actually when you open a file from the PDB of a protein with a missing segment, it will automatically draw a dashed line (for example, PDB 1www), but maybe there is something about your input file that prevents that from happening. If there is not already a line, a couple of ways to add one are: (a) measure distance between the two atoms, then in Distances tool (under Tools... Structure Analysis) set label to "None"... there are several ways to measure the distance, as described here: < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
(b) use PseudoBond Reader (under Tools... Depiction) to read in a text file describing the atom pair(s) you want to draw lines between. Format is described in that page: < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...
Then to further control display settings of the line, Ctrl-click to select it, then click the magnifying glass in the lower right corner of the Chimera window to show the Selection Inspector, and then inspect "pseudobond" and "pseudobond group" to change various settings. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
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 2, 2012, at 9:10 PM, james09 pruza wrote:
Hi All, I am using latest Chimera v1.6. I want to show the backbone carbonyl oxygen of one of the residue. The backbone is in ribbon representation. Also, how to make dotted line representation of the missing residues joining two domains of the same chain. Thanks. James
Hard to say without knowing your specific data and exactly what you did to reach that state. Normally you would see the bonds of whatever atomic data you have displayed, in whatever representation you are using. But maybe there is something weird about your file and the atoms aren't bonded. You could doublecheck whether the bonds exist by displaying all atoms, for example by using Presets... interactive 2 (all atoms). You may want to save the session first, if you have already spent time displaying and coloring things how you want. If bonds are missing, they can be added with Build Structure (under Tools... Structure Editing) or the command "bond." Elaine On Mar 3, 2012, at 11:29 AM, james09 pruza wrote:
Dear Dr. Elaine,
Thanks for the information. I will check that out. One more thing, How to show the ball and stick representation. By default, there are three spheres. I am selecting all of them and Actions - Atoms and Bonds - Ball and stick. Nothing happens. Any clue.
Thanks. James
On Sat, Mar 3, 2012 at 12:35 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi James, By default, showing ribbon automatically hides backbone atoms (peptide N,CA,C,O), but you can enable showing them at the same time with the command "ribbackbone." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html>
Example commands: ribbackbone display #0:38@O
You can draw a line between any two atoms, but only a straight line. Actually when you open a file from the PDB of a protein with a missing segment, it will automatically draw a dashed line (for example, PDB 1www), but maybe there is something about your input file that prevents that from happening. If there is not already a line, a couple of ways to add one are: (a) measure distance between the two atoms, then in Distances tool (under Tools... Structure Analysis) set label to "None"... there are several ways to measure the distance, as described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances> (b) use PseudoBond Reader (under Tools... Depiction) to read in a text file describing the atom pair(s) you want to draw lines between. Format is described in that page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html>
Then to further control display settings of the line, Ctrl-click to select it, then click the magnifying glass in the lower right corner of the Chimera window to show the Selection Inspector, and then inspect "pseudobond" and "pseudobond group" to change various settings. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
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 2, 2012, at 9:10 PM, james09 pruza wrote:
Hi All, I am using latest Chimera v1.6. I want to show the backbone carbonyl oxygen of one of the residue. The backbone is in ribbon representation. Also, how to make dotted line representation of the missing residues joining two domains of the same chain. Thanks. James
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, I have couples of sticks in the ribbon, want to show the carbonyl oxygen of only one. What is happening is with the command ribbackbone #0:110.A@O all the main-chain atoms of sticks comes up. If there is only residues110 shown in stick, its fine. Also, the sticks are not following the ribbon tracing. I appreciate your help. James On Sat, Mar 3, 2012 at 2:29 PM, james09 pruza <james09xtal@gmail.com> wrote:
Dear Dr. Elaine,
Thanks for the information. I will check that out. One more thing, How to show the ball and stick representation. By default, there are three spheres. I am selecting all of them and Actions - Atoms and Bonds - Ball and stick. Nothing happens. Any clue.
Thanks. James
On Sat, Mar 3, 2012 at 12:35 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi James, By default, showing ribbon automatically hides backbone atoms (peptide N,CA,C,O), but you can enable showing them at the same time with the command "ribbackbone." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html>
Example commands: ribbackbone display #0:38@O
You can draw a line between any two atoms, but only a straight line. Actually when you open a file from the PDB of a protein with a missing segment, it will automatically draw a dashed line (for example, PDB 1www), but maybe there is something about your input file that prevents that from happening. If there is not already a line, a couple of ways to add one are: (a) measure distance between the two atoms, then in Distances tool (under Tools... Structure Analysis) set label to "None"... there are several ways to measure the distance, as described here: < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
(b) use PseudoBond Reader (under Tools... Depiction) to read in a text file describing the atom pair(s) you want to draw lines between. Format is described in that page: < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...
Then to further control display settings of the line, Ctrl-click to select it, then click the magnifying glass in the lower right corner of the Chimera window to show the Selection Inspector, and then inspect "pseudobond" and "pseudobond group" to change various settings. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
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 2, 2012, at 9:10 PM, james09 pruza wrote:
Hi All, I am using latest Chimera v1.6. I want to show the backbone carbonyl oxygen of one of the residue. The backbone is in ribbon representation. Also, how to make dotted line representation of the missing residues joining two domains of the same chain. Thanks. James
Hi James, The command ribbackbone merely enables the simultaneous display of both ribbon and backbone atoms. You would still use display/~display to control which of those backbone atoms are shown, for example: ~disp @o disp :110.a@o As explained here, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset> the default ribbon is smoothed and does not go exactly through the atom positions. That is why by default they aren't shown at the same time. However, if you want ribbon that goes through the exact CA atom positions, use the cardinal spline instead of the default B-spline, for example: ribspline cardinal Then the ribbon is not as pretty, however. There are some smoothing options for a compromise, as described in the help page elicited by command "help ribspline" 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 3, 2012, at 12:15 PM, james09 pruza wrote:
Hi, I have couples of sticks in the ribbon, want to show the carbonyl oxygen of only one. What is happening is with the command ribbackbone #0:110.A@O all the main-chain atoms of sticks comes up.
If there is only residues110 shown in stick, its fine. Also, the sticks are not following the ribbon tracing. I appreciate your help.
James
participants (2)
-
Elaine Meng -
james09 pruza