hi Tom, Perfect! I got the desired surface with the separate curves. Thank you so much for the great tools and helps! Jinghua On Wed, 21 Oct 2009, Tom Goddard wrote:

Hi Jinghua,

You should not connect the rings in the two planes. Just draw two separate rings or curves. I use the place markers while dragging setting. It will automatically close a loop when you get near the start point. If you don't want closed loops then clear the selection before drawing a second curve so the two curves won't be connected.

Tom

-------- Original Message -------- Subject: Re: [Chimera-users] how to create surface from volume tracer path From: jinghua To: Tom Goddard Date: 10/21/09 12:28 PM

...

hi Tom,

Thank you so much for your reply. Have fun in France!

I have tried several different build of chimera with the same result as attached. What are your mouse options during tracing? Is there special sequence to go from one plane to the next plane?

Best wishes,

Jinghua

On Wed, 21 Oct 2009, Tom Goddard wrote:

...

Hi Jinghua,

The volume tracer capability to stitch loops drawn in parallel planes to form tube surfaces uses some strange heuristics that don't always produce a good result. I'd have to see the case where you have trouble to understand it. I just tried making a tube, see attached photo, and it worked ok in a Chimera daily build from a few days ago.

I am at a workshop until the middle of next week so may not reply to email for a while.

Tom

-------- Original Message -------- Subject: [Chimera-users] how to create surface from volume tracer path From: jinghua To: chimera-users Date: 10/21/09 10:48 AM

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When I try to create a tube by tracing two planes, the surface it makes is more like a cone. Do I need connect all the markers from two different planes?

Thank you for your help!

Jinghua

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Hi Jinghua, I don't know any way to make the smooth ribbon "broken." You can draw a straight line between any pair of atoms (with Pseudobond Reader or by creating a distance measurement) and control how that line is drawn (solid, dashed, etc.), but if you wanted a curved dashed line, you would have to add that with some other program like Photoshop after saving the image. You might try making the ribbon for one of the conformations transparent, as shown in the image here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html

Example command: color 0.8,0,0.4,0.4,r #0:20-48.b where the color is defined with red,green,blue,opacity numbers and the ",r" means ribbons only for residues 20-48 in chain B of model 0. 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 Dec 15, 2009, at 7:38 PM, jinghua@ucsd.edu wrote:

To differentiate two conformations of a small loop, does anyone know how to draw one of the loop (a smooth C alpha trace) as broken line?

Thank you for your kind help!

Jinghua

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Oh, that was tricky. I guess you could just hide (undisplay) the ribbon for every other residue too! Elaine On Dec 16, 2009, at 10:22 AM, jinghua@ucsd.edu wrote:

hi Elaine,

Thank you for your advice! I tried a clumsy way to select every other residue and change its color. Some one might have more elegant ways.

Best wishes,

Jinghua