[Chimera-users] Tetrahedral Sulphide bonds

Yogavel Manickam myogavel at icgeb.res.in
Fri May 26 10:21:57 PDT 2017

Dear all,
Is there any example for tetrahedral sulphide bonds.

         CB-S1B (0.7)
         |1.8 A
     2A  .   2A
         . 2A

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.


----- Original Message -----
From: "Elaine Meng" <meng at cgl.ucsf.edu>
To: "Shanti Pal Gangwar" <gangwarspg at gmail.com>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at 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.

> On May 25, 2017, at 4:12 PM, Shanti Pal Gangwar <gangwarspg at 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 at 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 at 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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