Thank all, it works perfectly, using the "<< EOF" Best regards, Mohamed
On Tue, Jun 8, 2021 at 8:32 PM CCP4BB < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > 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 > -- *----------------------------------* *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/
