[Chimera-users] how to show backbone carbonyl oxygen

james09 pruza james09xtal at gmail.com
Sat Mar 3 12:15:59 PST 2012


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 at 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.


On Sat, Mar 3, 2012 at 2:29 PM, james09 pruza <james09xtal at 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 at 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 at 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
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