[chimerax-users] Loading density files

[Elaine Meng]

Hi Tianming,
You would have to try to be absolutely sure, but I don't think it is necessary to give the same names as in the documentation.  However, I would recommend they all have exactly the same names as each other except including xxxx, where xxxx is the index number with same number of digits, e.g. 0001, 0002 ..... 9999 (or whatever your last number is).  Say you named them all mapxxxx.dx in folder ~/Desktop/series/, then you could use something like this command to open them:

open ~/Desktop/series/map*.dx vseries true

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 12, 2022, at 8:46 AM, Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Dr. Meng,
> 
> Yes, this helps. 
>  
> I can open multiple files now, but I cannot open them in the order I want. I rename them with only numbers which corresponds to the frame number of each map, how can I read them in such numbered order? Should I rename all the file exactly as in the vseries says: _stachxxxx_.dx? In which xxxx represents index of frames?
> 
> Best,
> Tianming
> 发件人: Elaine Meng <meng at cgl.ucsf.edu>
> 日期: 星期二, 2022年10月11日 下午5:29
> 收件人: Tianming Qu <tqu at fsu.edu>
> 抄送: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> 主题: Re: [chimerax-users] Loading density files
> 
> Hi Tianming,
> If the maps are on the same grids as each other, i.e. their outline boxes would be the same and they have the same number of grid points with same spacing, they can be opened as a "volume series" -- then you can play the series with the "vseries play" command or interactively using a slider interface shown with "vseries slider":
> 
> Volume series and how to open the files so that they are interpreted as series:
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html__;!!PhOWcWs!yxSAQG3kbRGnwkST8hops7zzv_ki2MvLq6pq-Fee1F6GgKUdW4nrbeYQ2XGAa1bnpL8h8O7zgEqajQ$  >
> 
> You might need to name the files a certain way so that you can specify them in a single "open" command.  See "open" command "vseries" option:
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html*vseries__;Iw!!PhOWcWs!yxSAQG3kbRGnwkST8hops7zzv_ki2MvLq6pq-Fee1F6GgKUdW4nrbeYQ2XGAa1bnpL8h8O5tw59yjA$  >
> 
> For playback after opening, see the "vseries" commands, including "vseries play" and "vseries slider":
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html__;!!PhOWcWs!yxSAQG3kbRGnwkST8hops7zzv_ki2MvLq6pq-Fee1F6GgKUdW4nrbeYQ2XGAa1bnpL8h8O7N3cUCFA$  >
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Oct 11, 2022, at 2:13 PM, Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Dear Chimerax developers:
> >  
> > I have a lot of density files, is there anyway I can load them at the same time and view then like a protein traj?
> >  
> > Best,
> > Tianming