Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Problem with peakmax

2021-06-11 Thread Eleanor Dodson 
As you know Paul I would like COOT to output a list of peaks into a
"coordinate " file..
You can do it laboriously by hand using Add atom at peak position but that
gets tedious...
Eleanor

On Thu, 10 Jun 2021 at 22:14, Edward A. Berry  wrote:

> On 06/10/2021 11:19 AM, James Holton wrote:
> >
> > I'm afraid the only bash command I know is: "tcsh"
>
> I learned csh by studying "elves"
>
> 
>
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Problem with peakmax

2021-06-10 Thread Edward A. Berry 

On 06/10/2021 11:19 AM, James Holton wrote:


I'm afraid the only bash command I know is: "tcsh"


I learned csh by studying "elves"



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Re: [ccp4bb] Problem with peakmax

2021-06-10 Thread Mohamed Ibrahim 
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  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 
>> 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=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
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>>>
>>
>>
>> --
>> ​
>> * ​ --*
>> *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=1
>
>
>

-- 
​
*​--*
*Dr. Mohamed Ibrahim*
*Postdoctoral Researcher   *

*Humboldt University   *
*Berlin, Germany  *

*Tel: +49 30 209347931 *



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Re: [ccp4bb] Problem with peakmax

2021-06-10 Thread Clemens Vonrhein 
On Thu, Jun 10, 2021 at 08:19:01AM -0700, James Holton wrote:
> I'm afraid the only bash command I know is: "tcsh"

I'm using the exact opposite direction ;-)



  To everyone using "echo" (interactively and/or in scripts): be careful
  which command is picked up at any given point. There are shell
  built-in versions of "echo" and then there is /bin/echo. Some
  recognize "\n" and some don't. Some support "-e" flag and some
  don't. A better command might be

printf "THREshold RMS 5.0\n" | peakmax MAPIN "myfile.ccp4" XYZOUT 
"myfiles_omit_atom.pdb"

  or (if no cards are to be used)

peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb" < /dev/null

  or

printf "\n" | peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"

  (not all CCP4 programs support the "END" card").

  If you want to write instantly portable scripts, it might be best to
  have "#!/bin/sh": not all systems will have /bin/bash, /bin/csh or
  /bin/tcsh installed. Of course, /bin/sh might point to /bin/bash, but
  it could also point to /bin/dash (another variant) ... or something
  else entirely (MacOS is known to replace "standard" Linux/UNIX
  commands from time to time, often going from GNU versions to BSD based
  ones - or something else again). With /bin/sh you /should/ be within a
  POSIX sh environment: maybe more limited to other shells, but
  standardized and therefore much more portable since every UNIX-like
  system so far will always have /bin/sh available.



Cheers

Clemens

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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Re: [ccp4bb] Problem with peakmax

2021-06-10 Thread James Holton 


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 
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
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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-- 
​

/*
​
--*/
/*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
*/



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Re: [ccp4bb] Problem with peakmax

2021-06-08 Thread Mohamed Ibrahim 
Thank all,
it works perfectly, using the "<< EOF"

Best regards,
Mohamed

On Tue, Jun 8, 2021 at 8:32 PM CCP4BB <
193323b1e616-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 <
> 22f7fda0a875-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  * 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  on behalf of Mohamed
> Ibrahim 
> *Sent:* Tuesday, June 8, 2021 2:06 PM
> *To:* 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 
> 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=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=1
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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

Re: [ccp4bb] Problem with peakmax

2021-06-08 Thread CCP4BB 
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 
> <22f7fda0a875-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  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  on behalf of Mohamed 
> Ibrahim 
> Sent: Tuesday, June 8, 2021 2:06 PM
> To: 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  
> 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  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=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=1
> 
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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
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Re: [ccp4bb] Problem with peakmax

2021-06-08 Thread Fischmann, Thierry 
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  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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Mohamed Ibrahim 
mailto:m.essam.ibra...@gmail.com>>
Sent: Tuesday, June 8, 2021 2:06 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto: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 
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 
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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--
​
​
--
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:
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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
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Re: [ccp4bb] Problem with peakmax

2021-06-08 Thread Eleanor Dodson 
peakmax MAPIN "myfile.ccp4" XYZOUT "myfiles_omit_atom.pdb"  <
wrote:

> 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  on behalf of Mohamed
> Ibrahim 
> *Sent:* Tuesday, June 8, 2021 2:06 PM
> *To:* 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 
> 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=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:
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>
> --
>
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>



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Re: [ccp4bb] Problem with peakmax

2021-06-08 Thread Philip D. Jeffrey 
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  on behalf of Mohamed Ibrahim 

Sent: Tuesday, June 8, 2021 2:06 PM
To: 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 
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 
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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--
​
​
--
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



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Re: [ccp4bb] Problem with peakmax

2021-06-08 Thread Mohamed Ibrahim 
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 
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 
> 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=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 *



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Re: [ccp4bb] Problem with peakmax

2021-06-08 Thread Paul Emsley 
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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[ccp4bb] Problem with peakmax

2021-06-08 Thread Mohamed Ibrahim 
Dear All,

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"

Thank you!

-- 
*--*
*Dr. Mohamed Ibrahim*
*Postdoctoral Researcher   *

*Humboldt University   *
*Berlin, Germany  *

*Tel: +49 30 209347931 *



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