i have to measure distance b/w Iron and HEM group in Chimera Software but i cant do that. can somebody help me to do this?
Hi Misbah,
Try the following procedure to measure between two atoms:
1) Click atom1 by left button of mouse with control key.
2) Click atom2 by left button of mouse with control and shift keys.
3) Open the Structure Measurements panel (Tools -> Structure Analysis -> Distances)
4) Click "Create" button to show the distance between the atoms.
5) To deselect atoms, click background with control key.
Unfortunately, UCSF Chimera is not able to mesure distance between groups or group-to-atom. In such case, you can first calculate centroids of groups on the Structure Measurements panel, and do distance between the centroids manually, for instance, using Excel.
It is a very interested question ,see
Article RRDistMaps: A UCSF Chimera tool for viewing and comparing pr...
how we can calculate centroids b/w groups?? do we do this mannually??
Yoshinobu Ishikawa
Hi again,
You can select only atoms, not group, in measuring distance in Chimera.
You should learn how to know centroid of selected atoms or a group by the following link:
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes
You can calculate distance between centroids (for instance, (0.000 0.000 0.000) and (1.000 1.000 1.000)) by sqr{(1.000-0.000)^2 + (1.000-0.000)^2 + (1.000-0.000)^2}.
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