I'm afraid the only bash command I know is: "tcsh"
However, in addition to suggestions so far, I expect this will work:
echo "" | peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
Your peakmax is waiting for options to come in on "standard input". The
vertical bar "|" is a "pipe" that takes the "standard output" of the
first command (echo ""), and re-directs it to the standard input of the
next command. Pipes are a very powerful tool. Save a lot of
cutting-and-pasting. Fortunately, both bash and tcsh recognize "|" in
the same way. Unfortunately, they differ on how to re-direct output to a
file.
Oh, and that magic little "#!" that you put at the start of the first
line of the script is called a "shebang".
-James Holton
MAD Scientist
On 6/8/2021 11:06 AM, Mohamed Ibrahim wrote:
Thanks Paul,
Is it possible to add Ctrl-D to my bash script?
Best regards,
On Tue, Jun 8, 2021 at 8:03 PM Mohamed Ibrahim
<mohamed.ibra...@hu-berlin.de <mailto:mohamed.ibra...@hu-berlin.de>>
wrote:
Thanks Paul,
Is it possible to add Ctrl-D to my bash script?
Best regards,
On Tue, Jun 8, 2021 at 7:51 PM Paul Emsley
<pems...@mrc-lmb.cam.ac.uk <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
>
> I am trying to get the peak values from omit maps. The
peakmax from the GUI works fine. However, I tried to run
> peakmax from the terminal, and it stuck when returning P1.
Same map file works fine, when I use the GUI. Any ideas,
> how to solve this problem?
>
> command used
> peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"
>
Ctrl-D
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