high resolution animation in chimera
Dear Chimera Developing team, I am trying to make an animation using chimera. But it looks like that the animation output is poor quality, seems less dpi. How to get a high resolution animation, say 300 dpi, suing chimera? Thank you very much, Shanti Pal ******************************************** Shanti Pal Gangwar, Ph.D Dept of Pharmacology and Toxicology University of Texas Medical Branch Galveston, Texas-77555 Mobile: +1-409-256-8400 Email: spgangwa@utmb.edu
Dear Shanti Pal, You didn’t say if you were using the “movie” command or the Animation tool. In addition to the dpi (pixel width and height) you may also want to consider the image-supersampling and movie quality settings. With the command “movie record” there are options “supersample” and “size” and for “movie encode” there is a “quality” option, with explanations here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#record-opt...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#encode-opt...> In the Animation tool graphical interface, clicking the red recording button shows another dialog with recording options. In that, see Rendering with Chimera, Supersample, and in its Advanced Options, Quality. Although the size is not shown in this dialog you can enter the same “size X,Y” option (where X and Y are the numbers of pixels for width and height) as would be used with the “movie record” command in the area marked “Additional recording options”. <http://www.rbvi.ucsf.edu/home/meng/docs/ContributedSoftware/animation/animat...> If you didn’t specify size, it would be the same as your Chimera window. 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 May 25, 2017, at 12:56 PM, Gangwar, Shanti P. <spgangwa@UTMB.EDU> wrote:
Dear Chimera Developing team, I am trying to make an animation using chimera. But it looks like that the animation output is poor quality, seems less dpi. How to get a high resolution animation, say 300 dpi, suing chimera? Thank you very much, Shanti Pal
Dear Elaine, Thanks for replying. I am using commands to make animations. The commands are given here *windowsize 800 600* *movie encode output movie.avi high quality bitrate 10000* But somehow the resolution of the animation si not coming good, then set the max window size and it looks better than the earlier. Shanti Pal ******************** Shanti Pal Gangwar, Ph.D Dept of Pharmacology and Toxicology University of Texas Medical Branch Galveston, Texas-77555 Email: gangwarspg@gmail.com <Email%3Agangwarspg@gmail.com> On 25 May 2017 at 18:05, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Shanti Pal, You didn’t say if you were using the “movie” command or the Animation tool. In addition to the dpi (pixel width and height) you may also want to consider the image-supersampling and movie quality settings.
With the command “movie record” there are options “supersample” and “size” and for “movie encode” there is a “quality” option, with explanations here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ movie.html#record-options> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ movie.html#encode-options>
In the Animation tool graphical interface, clicking the red recording button shows another dialog with recording options. In that, see Rendering with Chimera, Supersample, and in its Advanced Options, Quality. Although the size is not shown in this dialog you can enter the same “size X,Y” option (where X and Y are the numbers of pixels for width and height) as would be used with the “movie record” command in the area marked “Additional recording options”. <http://www.rbvi.ucsf.edu/home/meng/docs/ContributedSoftware/animation/ animation.html#recording>
If you didn’t specify size, it would be the same as your Chimera window.
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 May 25, 2017, at 12:56 PM, Gangwar, Shanti P. <spgangwa@UTMB.EDU> wrote:
Dear Chimera Developing team, I am trying to make an animation using chimera. But it looks like that the animation output is poor quality, seems less dpi. How to get a high resolution animation, say 300 dpi, suing chimera? Thank you very much, Shanti Pal
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Use a movie file with a “.mp4” suffix to get a modern H.264 video encoding. Every other format in Chimera will produce an archaic video encoding whose quality for a given file size will be much worse. Tom
On May 25, 2017, at 4:12 PM, Shanti Pal Gangwar <gangwarspg@gmail.com> wrote:
Dear Elaine,
Thanks for replying.
I am using commands to make animations.
The commands are given here
windowsize 800 600
movie encode output movie.avi high quality bitrate 10000
But somehow the resolution of the animation si not coming good, then set the max window size and it looks better than the earlier.
Shanti Pal
******************** Shanti Pal Gangwar, Ph.D Dept of Pharmacology and Toxicology University of Texas Medical Branch Galveston, Texas-77555 Email: gangwarspg@gmail.com <mailto:Email%3Agangwarspg@gmail.com>
On 25 May 2017 at 18:05, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Dear Shanti Pal, You didn’t say if you were using the “movie” command or the Animation tool. In addition to the dpi (pixel width and height) you may also want to consider the image-supersampling and movie quality settings.
With the command “movie record” there are options “supersample” and “size” and for “movie encode” there is a “quality” option, with explanations here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#record-opt... <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#record-options>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#encode-opt... <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#encode-options>>
In the Animation tool graphical interface, clicking the red recording button shows another dialog with recording options. In that, see Rendering with Chimera, Supersample, and in its Advanced Options, Quality. Although the size is not shown in this dialog you can enter the same “size X,Y” option (where X and Y are the numbers of pixels for width and height) as would be used with the “movie record” command in the area marked “Additional recording options”. <http://www.rbvi.ucsf.edu/home/meng/docs/ContributedSoftware/animation/animat... <http://www.rbvi.ucsf.edu/home/meng/docs/ContributedSoftware/animation/animation.html#recording>>
If you didn’t specify size, it would be the same as your Chimera window.
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 May 25, 2017, at 12:56 PM, Gangwar, Shanti P. <spgangwa@UTMB.EDU <mailto:spgangwa@UTMB.EDU>> wrote:
Dear Chimera Developing team, I am trying to make an animation using chimera. But it looks like that the animation output is poor quality, seems less dpi. How to get a high resolution animation, say 300 dpi, suing chimera? Thank you very much, Shanti Pal
_______________________________________________ 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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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Just remember that you can use the “size” option of “movie record” as described in my reply if you want a bigger size than your window… it could even be bigger than your computer screen. Elaine
On May 25, 2017, at 4:12 PM, Shanti Pal Gangwar <gangwarspg@gmail.com> wrote:
Dear Elaine, Thanks for replying. I am using commands to make animations. The commands are given here
windowsize 800 600
movie encode output movie.avi high quality bitrate 10000
But somehow the resolution of the animation si not coming good, then set the max window size and it looks better than the earlier. Shanti Pal
On 25 May 2017 at 18:05, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Shanti Pal, You didn’t say if you were using the “movie” command or the Animation tool. In addition to the dpi (pixel width and height) you may also want to consider the image-supersampling and movie quality settings.
With the command “movie record” there are options “supersample” and “size” and for “movie encode” there is a “quality” option, with explanations here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#record-opt...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#encode-opt...>
In the Animation tool graphical interface, clicking the red recording button shows another dialog with recording options. In that, see Rendering with Chimera, Supersample, and in its Advanced Options, Quality. Although the size is not shown in this dialog you can enter the same “size X,Y” option (where X and Y are the numbers of pixels for width and height) as would be used with the “movie record” command in the area marked “Additional recording options”. <http://www.rbvi.ucsf.edu/home/meng/docs/ContributedSoftware/animation/animat...>
If you didn’t specify size, it would be the same as your Chimera window.
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 May 25, 2017, at 12:56 PM, Gangwar, Shanti P. <spgangwa@UTMB.EDU> wrote:
Dear Chimera Developing team, I am trying to make an animation using chimera. But it looks like that the animation output is poor quality, seems less dpi. How to get a high resolution animation, say 300 dpi, suing chimera? Thank you very much, Shanti Pal
Dear all, Is there any example for tetrahedral sulphide bonds. CB-S1B (0.7) |1.8 A CB-S2....S1A*...S3-CB 2A . 2A . 2A . S4 | CB S1 containing Cys adopt alternate conformation (S1A and S1B) with occupies of 0.7 and 0.3. S1A position occupied by Zn ion with ~0.7. Any input will be appreciated. Thanks Yoga ----- Original Message ----- From: "Elaine Meng" <meng@cgl.ucsf.edu> To: "Shanti Pal Gangwar" <gangwarspg@gmail.com> Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Sent: Friday, May 26, 2017 4:48:27 AM Subject: Re: [Chimera-users] high resolution animation in chimera Just remember that you can use the “size” option of “movie record” as described in my reply if you want a bigger size than your window… it could even be bigger than your computer screen. Elaine
On May 25, 2017, at 4:12 PM, Shanti Pal Gangwar <gangwarspg@gmail.com> wrote:
Dear Elaine, Thanks for replying. I am using commands to make animations. The commands are given here
windowsize 800 600
movie encode output movie.avi high quality bitrate 10000
But somehow the resolution of the animation si not coming good, then set the max window size and it looks better than the earlier. Shanti Pal
On 25 May 2017 at 18:05, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Shanti Pal, You didn’t say if you were using the “movie” command or the Animation tool. In addition to the dpi (pixel width and height) you may also want to consider the image-supersampling and movie quality settings.
With the command “movie record” there are options “supersample” and “size” and for “movie encode” there is a “quality” option, with explanations here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#record-opt...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html#encode-opt...>
In the Animation tool graphical interface, clicking the red recording button shows another dialog with recording options. In that, see Rendering with Chimera, Supersample, and in its Advanced Options, Quality. Although the size is not shown in this dialog you can enter the same “size X,Y” option (where X and Y are the numbers of pixels for width and height) as would be used with the “movie record” command in the area marked “Additional recording options”. <http://www.rbvi.ucsf.edu/home/meng/docs/ContributedSoftware/animation/animat...>
If you didn’t specify size, it would be the same as your Chimera window.
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 May 25, 2017, at 12:56 PM, Gangwar, Shanti P. <spgangwa@UTMB.EDU> wrote:
Dear Chimera Developing team, I am trying to make an animation using chimera. But it looks like that the animation output is poor quality, seems less dpi. How to get a high resolution animation, say 300 dpi, suing chimera? Thank you very much, Shanti Pal
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Yoga, What is the question? Do you already have this structure? What are you trying to do with Chimera? Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 26, 2017, at 10:21 AM, Yogavel Manickam <myogavel@icgeb.res.in> wrote:
Dear all, Is there any example for tetrahedral sulphide bonds.
CB-S1B (0.7) |1.8 A CB-S2....S1A*...S3-CB 2A . 2A . 2A . S4 | CB
S1 containing Cys adopt alternate conformation (S1A and S1B) with occupies of 0.7 and 0.3.
S1A position occupied by Zn ion with ~0.7.
Any input will be appreciated.
Thanks Yoga
Dear Elaine, Recently I have determined this sulfide bond motif containing structure and I would like to know that any exiting PDB having this motif. Thanks Yoga ----- Original Message ----- From: "Elaine Meng" <meng@cgl.ucsf.edu> To: "Yogavel Manickam" <myogavel@icgeb.res.in> Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Sent: Friday, May 26, 2017 11:58:56 PM Subject: Re: [Chimera-users] Tetrahedral Sulphide bonds Dear Yoga, What is the question? Do you already have this structure? What are you trying to do with Chimera? Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 26, 2017, at 10:21 AM, Yogavel Manickam <myogavel@icgeb.res.in> wrote:
Dear all, Is there any example for tetrahedral sulphide bonds.
CB-S1B (0.7) |1.8 A CB-S2....S1A*...S3-CB 2A . 2A . 2A . S4 | CB
S1 containing Cys adopt alternate conformation (S1A and S1B) with occupies of 0.7 and 0.3.
S1A position occupied by Zn ion with ~0.7.
Any input will be appreciated.
Thanks Yoga
Dear Yoga, That is not really a Chimera question… maybe you can try searching some structure databases: RCSB PDB search <http://www.rcsb.org/pdb/secondary.do?p=v2/secondary/search.jsp#search_advanc...> There is also the Cambridge Structural Database for small molecules. <https://www.ccdc.cam.ac.uk/> Good luck, Elaine
On May 26, 2017, at 12:44 PM, Yogavel Manickam <myogavel@icgeb.res.in> wrote:
Dear Elaine, Recently I have determined this sulfide bond motif containing structure and I would like to know that any exiting PDB having this motif. Thanks Yoga
----- Original Message ----- From: "Elaine Meng" <meng@cgl.ucsf.edu> To: "Yogavel Manickam" <myogavel@icgeb.res.in> Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Sent: Friday, May 26, 2017 11:58:56 PM Subject: Re: [Chimera-users] Tetrahedral Sulphide bonds
Dear Yoga, What is the question? Do you already have this structure? What are you trying to do with Chimera? Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 26, 2017, at 10:21 AM, Yogavel Manickam <myogavel@icgeb.res.in> wrote:
Dear all, Is there any example for tetrahedral sulphide bonds.
CB-S1B (0.7) |1.8 A CB-S2....S1A*...S3-CB 2A . 2A . 2A . S4 | CB
S1 containing Cys adopt alternate conformation (S1A and S1B) with occupies of 0.7 and 0.3.
S1A position occupied by Zn ion with ~0.7.
Any input will be appreciated.
Thanks Yoga
participants (5)
-
Elaine Meng -
Gangwar, Shanti P. -
Shanti Pal Gangwar -
Tom Goddard -
Yogavel Manickam