How to set transparency on surfaces during morphing? I start out with 95% but end up with 0%. The morphing works well though. Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.
Hi Krishnan, I could not reproduce this problem. I tried ChimeraX 1.4 and a newer daily build, both preserved surface transparency when the morph (atomic or map) was played back. Example commands for atomic morph: open 2gbp open 2fw0 mm #2 to #1 morph #1,2 surf #3 trans 50 Now the surface is 50% transparent, and when I play back the morph with the slider, it stays transparent. Similarly when I created a map morph (with "volume morph") the transparency was preserved when I played back the morph. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 26, 2022, at 1:26 PM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
How to set transparency on surfaces during morphing? I start out with 95% but end up with 0%. The morphing works well though.
Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals
Hi Krishnan, If you use "volume morph" then it interpolates the map color and transparency from the first map to the second. So if the first map is 95% transparent and the second is 0% transparent that would match what you saw. You can use the "interplateColors false" option to the volume morph command if you don't want it interpolating color and transparency, or make the second map 95% transparent. See the documentation for volume morph https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#morph Tom
On Sep 26, 2022, at 1:48 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Krishnan, I could not reproduce this problem. I tried ChimeraX 1.4 and a newer daily build, both preserved surface transparency when the morph (atomic or map) was played back. Example commands for atomic morph:
open 2gbp open 2fw0 mm #2 to #1 morph #1,2 surf #3 trans 50
Now the surface is 50% transparent, and when I play back the morph with the slider, it stays transparent.
Similarly when I created a map morph (with "volume morph") the transparency was preserved when I played back the morph.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 26, 2022, at 1:26 PM, Krishnan Raman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
How to set transparency on surfaces during morphing? I start out with 95% but end up with 0%. The morphing works well though.
Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals
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participants (3)
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Elaine Meng -
Krishnan Raman -
Tom Goddard