[Chimera-users] Regarding saving image in chimera nogui

[NAGARAJAN]

Hi,

  Thank you for the suggestion. I have installed the headless version and
now it is working. I tried to color the surface based on b-factor using the
following commnad

  "rangecolor bfactor key 2 blue 30 red 50 yellow"

  it is showing the following error "No module named Togl"

  I referred in internet and it seems this module is removed automatically
during updation.

 Any idea how to solve this problem?

Thank you



On Fri, May 11, 2018 at 6:31 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> This line from the “primer” that Elaine mentioned in her later message
> covers the problem you’re having:
>
> Note that if your script creates images then you *must* start the Chimera
> interface unless you've downloaded the "headless" version of Chimera (see
> the download page <http://www.cgl.ucsf.edu/chimera/download.html>).
>
> —Eric
>
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>
>
> On May 11, 2018, at 4:25 PM, NAGARAJAN <nagabioinfostar at gmail.com> wrote:
>
> Hi,
>
>   Thanks for the quick reply. I have previous experience in using Chimera
> GUI but not in nogui.
>
>   The main thing that I dont know is to use those commands in nogui mode.
>
>    For example: for saving image, I have used "runCommand("copy str.png")
> . but it is now working
>
>    Is there any link to get the informations to use commands in nogui mode
>
> Thank you
>
>
>
>
> On Fri, May 11, 2018 at 6:19 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>> Hi,
>> I guess you will be using commands.  Here are commands for your steps
>> 1. open
>> 2. surface
>> 3. color
>> 4, copy
>> Of course, you will have to include more things in those commands,
>> various options, residue numbers, filenames etc. that you should test in
>> the GUI first to make sure they do what you want.  See also the list of
>> commands for anything else you might want to do like rotate (turn)
>> translate (move) zoom (scale) … and click on the link to see each command’s
>> help with information about the command syntax and  possible options.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
>>
>> See also:
>>  getting started with commands
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/
>> getting_started.html>
>>
>>  tips for making nice images
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> > On May 11, 2018, at 4:09 PM, NAGARAJAN <nagabioinfostar at gmail.com>
>> wrote:
>> >
>> > Hi all,
>> >    I have to use chimera --nogui and do the following
>> >
>> >   1. load a structure
>> >   2. make Surface representation
>> >   3. Color surface of selected residues with a selected color
>> >   4. save image
>> >
>> > Any idea how to do the 4 steps in chimera --nogui?
>> > Thank you
>>
>>
>
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