Many thanks, James, for the tips. This one worked also, peakmax MAPIN "mymap.ccp4" XYZOUT "mypeaks_output.pdb" <<- EOF EOF
Best regards, On Thu, Jun 10, 2021 at 5:19 PM James Holton <jmhol...@lbl.gov> wrote: > > 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> 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> >> 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 >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are >>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> >> >> >> -- >> >> * ----------------------------------* >> *Dr. Mohamed Ibrahim * >> *Postdoctoral Researcher * >> >> *Humboldt University * >> *Berlin, Germany * >> *Tel: +49 30 209347931 * >> > > > -- > > * ----------------------------------* > *Dr. Mohamed Ibrahim * > *Postdoctoral Researcher * > > *Humboldt University * > *Berlin, Germany * > > *Tel: +49 30 209347931 * > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > -- *----------------------------------* *Dr. Mohamed Ibrahim * *Postdoctoral Researcher * *Humboldt University * *Berlin, Germany * *Tel: +49 30 209347931 * ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
