The text following the "<<" in Eleanor's and Phil's example is known as a "heredoc" in Unix or Linux-speak (I had been using them for decades before I found out what they're called...). You can replace both "EOF-pmx"s in Phil's example and both "eof"s in Eleanor's with any text you like.
See https://linuxize.com/post/bash-heredoc/. Harry -- Dr Harry Powell > On 8 Jun 2021, at 19:22, Fischmann, Thierry > <000022f7fda0a875-dmarc-requ...@jiscmail.ac.uk> wrote: > > echo “keyword1 arguments\nkeyword2 arguments\n etc. \nEND” | peakmax MAPIN > myfile.ccp4 XYZOUT myfiles_omit_atom.pdb > should work as well > > Thierry > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Philip D. > Jeffrey > Sent: Tuesday, June 8, 2021 2:16 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Problem with peakmax > > EXTERNAL EMAIL – Use caution with any links or file attachments. > Paul was a little too terse, perhaps. > In script form > > peakmax MAPIN myfile.ccp4 XYZOUT myfiles_omit_atom.pdb << EOF-pmx > keywords in here > EOF-pmx > > at least that's what works for me in Csh. Bash proselytizers will correct me > as necessary... > > Phil Jeffrey > Princeton > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Mohamed > Ibrahim <m.essam.ibra...@gmail.com> > Sent: Tuesday, June 8, 2021 2:06 PM > To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > Subject: Re: [ccp4bb] Problem with peakmax > > 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 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, > New Jersey, USA 07033), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
