Hi Boaz, As far as we know, and in our testing, the ribbons are behaving normally in these newer versions. Some possibilities as to what is happening:

(A) a different scaling scheme is being used than the default. Open Tools... Depiction... Ribbon Style Editor, then under Ribbon Scaling, make sure it is set to "Chimera default" and then click OK or Apply (without anything selected) If someone had made different scalings before and saved them, one of those might have been in use rather than the default. Those are saved in the preferences file.

(B) secondary structure assignments: are the helices known to be helices? One way to check is to use the command select helix and see if the areas you believe to be helices are selected. (I'm assuming you are viewing a protein, not nucleic acids) You can change assignments (a) manually (by selecting the desired parts, then clicking the button reporting what is selected on the bottom right corner of the Chimera window to open the Selection Inspector, Inspect "Residue" instead of "Atom," setting "in helix" to "true" and "in strand" to "false") OR (b) by running ksdssp with different parameters (open Model Panel, which is under Favorites, then make sure the line for your protein is chosen, change from "frequently used" to the "infrequently used" list, click "compute SS" and set parameters as desired)

A final possibility if these methods (a,b) do not make what you want into a helix is that there are some atom-naming or PDB format problems that prevent the coordinates from being recognized correctly as peptide/ protein.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

On Aug 30, 2005, at 2:21 AM, Boaz Shaanan wrote:

Hello,

I the latest snapshots (Windows 2143 and linux 2154) helices show up as thin worms when I ask for 'ribbons' under action (they used to look like nice ribbons in previous releases). I found the tools/ depiction/ribbons display and managed somehow to change the look of the ribbons (still, they looked nicer before) but failed to change the look of the helices. Where can I do this now ?

Thanks,

     Boaz

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