Hi,
I am trying to get rid of an improper bond that chimera is displaying between two nearby segments that are actually cleaved. The bond is distorted, creating long CACB bonds if B-spline mode is active. I tried to turn off the auto-chaining, but didn’t work.
Because PYmol can properly display these segments as independent polypetides, I was wondering if there is other adjustment that I can try before manually deleting the bond. The PDB is 1ohf and the bond is between residue 570 and 571.
Cheers,
Hi Tatiana, You could delete the bond with a command, e.g.
~bond :570@c :571@n
Based on the ATOM records and PDB format specifications, they would be considered as connected (consecutive standard residues with same chain ID, no TER, ...), so it should be an unusual case. Chimera doesn't distance-test in these "standard residue" situations.
Best, 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 18, 2013, at 5:52 AM, Tatiana Domitrovic wrote:
Hi, I am trying to get rid of an improper bond that chimera is displaying between two nearby segments that are actually cleaved. The bond is distorted, creating long CACB bonds if B-spline mode is active. I tried to turn off the auto-chaining, but didn’t work. Because PYmol can properly display these segments as independent polypetides, I was wondering if there is other adjustment that I can try before manually deleting the bond. The PDB is 1ohf and the bond is between residue 570 and 571. Cheers,
If you look at the sequence for that chain you can see there is a 34-residue segment missing between residues 570 and 571, which is confirmed in the PDB file REMARK records with:
REMARK 400 ALL CHAINS ARE AUTOCATALYTICALLY CLEAVED BETWEEN RESIDUES REMARK 400 570 AND 571
I guess I find it surprising that they decided to keep the numbering consecutive instead of numbering to account for the missing residues (or possibly changing chain IDs), but that's why Chimera shows a regular bond between those residues instead of a "missing structure" dashed line, and therefore why the ribbon tries to connect the residues.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Dec 18, 2013, at 9:16 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Tatiana, You could delete the bond with a command, e.g.
~bond :570@c :571@n
Based on the ATOM records and PDB format specifications, they would be considered as connected (consecutive standard residues with same chain ID, no TER, ...), so it should be an unusual case. Chimera doesn't distance-test in these "standard residue" situations.
Best, 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 18, 2013, at 5:52 AM, Tatiana Domitrovic wrote:
Hi, I am trying to get rid of an improper bond that chimera is displaying between two nearby segments that are actually cleaved. The bond is distorted, creating long CACB bonds if B-spline mode is active. I tried to turn off the auto-chaining, but didn’t work. Because PYmol can properly display these segments as independent polypetides, I was wondering if there is other adjustment that I can try before manually deleting the bond. The PDB is 1ohf and the bond is between residue 570 and 571. Cheers,
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi,
I am trying to animate some clipping motion in volume data. I only find very simple clipping method using plane.
I'd like to make a movie for clipping motion using prism or 3-D box (the clipping gear gradually moving deeper into volume data).
I have tried mask (by inverse masking) using 3-D box, but it was very inconvenient, and took too much time to make a movie. Are there any other way to make an animation for some fancy clipping?
Many thanks,
Hyeong-Tae ----------------- Hyeong-Tae Jou KIOST
Dear Hyeong-Tae, I'm not the expert in this area, but will try to list the possibilities that I know about. Other people may have better ideas when they return from the holiday break.
(a) single plane or slab perpendicular to viewer, front-back motion ("global clipping") (b) single plane or slab per model, at any angle to viewer ("per-model clipping") … commands and more details here ... http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html
( c) moving orthogonal planes through the data, for example the "Herpes virus slices" movie about halfway down the Animation Gallery page. Example command file is linked there. http://www.rbvi.ucsf.edu/chimera/animations/animations.html
(d) showing the volume values with coloring on a surface, where that surface can grow/shrink, for example the movie at the very bottom of the Animation Gallery, "Rice Dwarf Virus". http://www.rbvi.ucsf.edu/chimera/animations/animations.html Certain shapes of surfaces (sphere, icosahedron, etc.) can be created with the "shape" command, and the surfaces can be colored by volume data value with the "scolor" command. I don't think there is a shape command option to automatically replace a previous shape, so it may be a bit tedious to create new surface, close old surface, color new surface (repeat). It was probably done with python rather than commands, but that is beyond my skills, sorry. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html
Best, 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 26, 2013, at 3:10 PM, "Hyeong-Tae Jou" htjou@kiost.ac wrote:
Hi,
I am trying to animate some clipping motion in volume data. I only find very simple clipping method using plane.
I'd like to make a movie for clipping motion using prism or 3-D box (the clipping gear gradually moving deeper into volume data).
I have tried mask (by inverse masking) using 3-D box, but it was very inconvenient, and took too much time to make a movie. Are there any other way to make an animation for some fancy clipping?
Many thanks,
Hyeong-Tae
Hyeong-Tae Jou KIOST
Ah, I see that the "sop transform" command can be used to grow/shrink an existing surface shape. It's the last example in the "Clipping and Slicing" (bottom) section of the video mini-examples page:
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html
There is also a volume planes animation example.
Elaine
On Dec 26, 2013, at 4:37 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Hyeong-Tae, I'm not the expert in this area, but will try to list the possibilities that I know about. Other people may have better ideas when they return from the holiday break.
(a) single plane or slab perpendicular to viewer, front-back motion ("global clipping") (b) single plane or slab per model, at any angle to viewer ("per-model clipping") … commands and more details here ... http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html
( c) moving orthogonal planes through the data, for example the "Herpes virus slices" movie about halfway down the Animation Gallery page. Example command file is linked there. http://www.rbvi.ucsf.edu/chimera/animations/animations.html
(d) showing the volume values with coloring on a surface, where that surface can grow/shrink, for example the movie at the very bottom of the Animation Gallery, "Rice Dwarf Virus". http://www.rbvi.ucsf.edu/chimera/animations/animations.html Certain shapes of surfaces (sphere, icosahedron, etc.) can be created with the "shape" command, and the surfaces can be colored by volume data value with the "scolor" command. I don't think there is a shape command option to automatically replace a previous shape, so it may be a bit tedious to create new surface, close old surface, color new surface (repeat). It was probably done with python rather than commands, but that is beyond my skills, sorry. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html
Best, 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 26, 2013, at 3:10 PM, "Hyeong-Tae Jou" htjou@kiost.ac wrote:
Hi,
I am trying to animate some clipping motion in volume data. I only find very simple clipping method using plane.
I'd like to make a movie for clipping motion using prism or 3-D box (the clipping gear gradually moving deeper into volume data).
I have tried mask (by inverse masking) using 3-D box, but it was very inconvenient, and took too much time to make a movie. Are there any other way to make an animation for some fancy clipping?
Many thanks,
Hyeong-Tae
Hyeong-Tae Jou KIOST
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine,
Many thanks for your quick reply. I'll try some of your suggestions while waiting for other's ideas. It's holiday season, and I'll take time to get the good solution. I wish you a Happy New Year.
Hyeong-Tae.
-----원본 메시지----- From: Elaine Meng Sent: Friday, December 27, 2013 9:50 AM To: Hyeong-Tae Jou Cc: chimera-users@cgl.ucsf.edu List Subject: Re: [Chimera-users] Movie for various clipping
Ah, I see that the "sop transform" command can be used to grow/shrink an existing surface shape. It's the last example in the "Clipping and Slicing" (bottom) section of the video mini-examples page:
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html
There is also a volume planes animation example.
Elaine
On Dec 26, 2013, at 4:37 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Hyeong-Tae, I'm not the expert in this area, but will try to list the possibilities that I know about. Other people may have better ideas when they return from the holiday break.
(a) single plane or slab perpendicular to viewer, front-back motion ("global clipping") (b) single plane or slab per model, at any angle to viewer ("per-model clipping") … commands and more details here ... http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html
( c) moving orthogonal planes through the data, for example the "Herpes virus slices" movie about halfway down the Animation Gallery page. Example command file is linked there. http://www.rbvi.ucsf.edu/chimera/animations/animations.html
(d) showing the volume values with coloring on a surface, where that surface can grow/shrink, for example the movie at the very bottom of the Animation Gallery, "Rice Dwarf Virus". http://www.rbvi.ucsf.edu/chimera/animations/animations.html Certain shapes of surfaces (sphere, icosahedron, etc.) can be created with the "shape" command, and the surfaces can be colored by volume data value with the "scolor" command. I don't think there is a shape command option to automatically replace a previous shape, so it may be a bit tedious to create new surface, close old surface, color new surface (repeat). It was probably done with python rather than commands, but that is beyond my skills, sorry. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html
Best, 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 26, 2013, at 3:10 PM, "Hyeong-Tae Jou" htjou@kiost.ac wrote:
Hi,
I am trying to animate some clipping motion in volume data. I only find very simple clipping method using plane.
I'd like to make a movie for clipping motion using prism or 3-D box (the clipping gear gradually moving deeper into volume data).
I have tried mask (by inverse masking) using 3-D box, but it was very inconvenient, and took too much time to make a movie. Are there any other way to make an animation for some fancy clipping?
Many thanks,
Hyeong-Tae
Hyeong-Tae Jou KIOST
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Hyeong-Tae,
I am making a movie now where I show a rectangular indentation in the face of an electron microscopy map, and then the indentation gets gradually deeper tunnelling into the density map. This is for a planetarium movie which has a very wide field of view so I fly the view point into this rectangular tunnel so you can see the data on all sides. Making the rectangular indentation is not easy -- I use 9 copies of the same density map, one for each rectangular face of the indentation (5 faces) and 4 rectangular strips to show a hole in the front face of the original map. Then I move these faces with the volume planes command.
I'm not sure if the above example is what you have in mind. Chimera does not have exotic clipping methods -- just planes. You can use box display mode to show 6 faces of a box within a density map using the Orthoplanes feature (volume dialog menu Features / Orthogonal planes).
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volume...
Tom
On Dec 26, 2013, at 3:10 PM, "Hyeong-Tae Jou" wrote:
Hi,
I am trying to animate some clipping motion in volume data. I only find very simple clipping method using plane.
I'd like to make a movie for clipping motion using prism or 3-D box (the clipping gear gradually moving deeper into volume data).
I have tried mask (by inverse masking) using 3-D box, but it was very inconvenient, and took too much time to make a movie. Are there any other way to make an animation for some fancy clipping?
Many thanks,
Hyeong-Tae
Hyeong-Tae Jou KIOST _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (5)
-
Elaine Meng -
Eric Pettersen -
Hyeong-Tae Jou -
Tatiana Domitrovic -
Tom Goddard