Hi, I’m trying to generate a square surface between 4 markers to trace an atomic plane. I’ve created a marker file (attached) with the positions of the 4 atoms and when I select all markers and use the Volume Tracer tool to generate the surface, I see it show up in the Model Panel but it is not visible (see screen shot - I’m trying this in a random PDB file to test). The Volume Tracer tool also says “No surface” despite the Traced surface showing up in the Model Panel. I notice that there is no color next to the traced surface as well. It’s likely something silly I’m missing but I would appreciate help with this. Thanks. DH Destin Heilman, Ph.D (he/him/his) Professor of Chemistry and Biochemistry Chair, Undergraduate Studies Director, UMass MQP Project Center Department of Chemistry and Biochemistry Worcester Polytechnic Institute 100 Institute Road, Worcester MA 01609-2280 Goddard Hall 103B Office: 508-831-5396 Lab: 508-831-5386 [cid:787efcd6-e2fa-4b91-a11d-7b66c303cbed@prod.exchangelabs.com]
Hi Destin, Thanks for including an image, which helps to diagnose the issue. To create a surface, you must first link the markers into a "path" ... e.g. turn on "link consecutively selected markers" in the Mouse menu of Volume Tracer, and then go around selecting the markers in turn so that links (e.g. stick bonds) are drawn to make the quadrilateral outline of where the surface will be. Then select all the markers and click Create in the Surfaces feature of the Volume Tracer tool. See "Volume Tracer" documentation for creating surfaces: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#surfaces> Tested in Chimera 1.16 release. I made 4 markers, selected them and tried making a surface, and this only worked to make the surface (although the model is created either way, as you reported) when the markers were linked into a path first. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 12, 2022, at 9:17 AM, Heilman, Destin via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi,
I’m trying to generate a square surface between 4 markers to trace an atomic plane. I’ve created a marker file (attached) with the positions of the 4 atoms and when I select all markers and use the Volume Tracer tool to generate the surface, I see it show up in the Model Panel but it is not visible (see screen shot - I’m trying this in a random PDB file to test). The Volume Tracer tool also says “No surface” despite the Traced surface showing up in the Model Panel. I notice that there is no color next to the traced surface as well. It’s likely something silly I’m missing but I would appreciate help with this. Thanks.
DH
Destin Heilman, Ph.D (he/him/his) Professor of Chemistry and Biochemistry Chair, Undergraduate Studies Director, UMass MQP Project Center Department of Chemistry and Biochemistry
Worcester Polytechnic Institute 100 Institute Road, Worcester MA 01609-2280
Goddard Hall 103B Office: 508-831-5396 Lab: 508-831-5386
<Screen Shot 2022-08-12 at 12.10.39 PM.png> <markers.cmm>
participants (2)
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Elaine Meng -
Heilman, Destin