Hi specialists, I have a problem when adjusting the level of a map. If the level > 0, it seemed OK, but when it is less than 0, it showed a solid box. This is different from EMAN2. In EMAN2, the threshold less than 0 also works. I'm not sure whether the defining of level is the same as the threshold in EMAN2. Or is there any other way to show the density of a map as in EMAN2 with threshold less than 0? Some snapshots of the visualization in both programs are attached to the post. Thank you! regards, Jianhao
Hi Jianhao, You have to untick the “cap high values at box faces” to see surfaces bellow 0 threshold. You can find this option in Volume Viewer -> Features -> Surface and Mesh options at the bottom of the panel. Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288 On 1 Dec 2017, at 4:43 , C.J. <biocjh@gmail.com<mailto:biocjh@gmail.com>> wrote: Hi specialists, I have a problem when adjusting the level of a map. If the level > 0, it seemed OK, but when it is less than 0, it showed a solid box. This is different from EMAN2. In EMAN2, the threshold less than 0 also works. I'm not sure whether the defining of level is the same as the threshold in EMAN2. Or is there any other way to show the density of a map as in EMAN2 with threshold less than 0? Some snapshots of the visualization in both programs are attached to the post. Thank you! regards, Jianhao <7a.png><7b.png><10a.png><10b.png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you very much! regards, Jianhao 2017-12-01 17:28 GMT+08:00 Gabor PAPAI <papai@igbmc.fr>:
Hi Jianhao,
You have to untick the “cap high values at box faces” to see surfaces bellow 0 threshold. You can find this option in Volume Viewer -> Features -> Surface and Mesh options at the bottom of the panel.
Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries <https://maps.google.com/?q=1,+rue+Laurent+Fries&entry=gmail&source=g>, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288 <+33%203%2069%2048%2052%2088>
On 1 Dec 2017, at 4:43 , C.J. <biocjh@gmail.com> wrote:
Hi specialists,
I have a problem when adjusting the level of a map. If the level > 0, it seemed OK, but when it is less than 0, it showed a solid box. This is different from EMAN2. In EMAN2, the threshold less than 0 also works. I'm not sure whether the defining of level is the same as the threshold in EMAN2. Or is there any other way to show the density of a map as in EMAN2 with threshold less than 0? Some snapshots of the visualization in both programs are attached to the post. Thank you!
regards, Jianhao <7a.png><7b.png><10a.png><10b.png>__________________________ _____________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/ mailman/listinfo/chimera-users
-- Best regards! C.J.
There’s also a “volume” command “capFaces” option, e.g. volume #3 capFaces false <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dispsurf> Elaine
On Dec 1, 2017, at 2:10 AM, C.J. <biocjh@gmail.com> wrote:
Thank you very much! regards, Jianhao
2017-12-01 17:28 GMT+08:00 Gabor PAPAI <papai@igbmc.fr>: Hi Jianhao, You have to untick the “cap high values at box faces” to see surfaces bellow 0 threshold. You can find this option in Volume Viewer -> Features -> Surface and Mesh options at the bottom of the panel. Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288
On 1 Dec 2017, at 4:43 , C.J. <biocjh@gmail.com> wrote:
Hi specialists, I have a problem when adjusting the level of a map. If the level > 0, it seemed OK, but when it is less than 0, it showed a solid box. This is different from EMAN2. In EMAN2, the threshold less than 0 also works. I'm not sure whether the defining of level is the same as the threshold in EMAN2. Or is there any other way to show the density of a map as in EMAN2 with threshold less than 0? Some snapshots of the visualization in both programs are attached to the post. Thank you! regards, Jianhao
participants (3)
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C.J. -
Elaine Meng -
Gabor PAPAI