Not found when open XCrySDen

Asked by dinesh on 2014-08-26

mm@mm:~/Downloads/xcrysden-1.5.60$ ./xcrysden

+-----------------------------------------------------------------+
|*****************************************************************|
|* *|
|* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *|
|* = === = === *|
|*---------------------------------------------------------------*|
|* *|
|* Anton Kokalj (<email address hidden>) *|
|* Jozef Stefan Institute, Ljubljana, Slovenia *|
|* *|
|* Copyright (c) 1996--2014 by Anton Kokalj *|
|* *|
|*****************************************************************|
+-----------------------------------------------------------------+

  Version: 1.5.60

  Please report bugs to: <email address hidden>

  TERMS OF USE:
  -------------
  XCRYSDEN is released under the GNU General Public License.

  Whenever graphics generated by XCRYSDEN are used in scientific
  publications, it shall be greatly appreciated to include an explicit
  reference. The preferred form is the following:

  [ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
        Code available from http://www.xcrysden.org/.

XCRYSDEN_TOPDIR=/home/mm/Downloads/xcrysden-1.5.60
XCRYSDEN_SCRATCH=/tmp

./xcrysden: 311: /home/mm/Downloads/xcrysden-1.5.60/bin/xcrys: not found

please help me friends!!!

Question information

Language:
English Edit question
Status:
Answered
For:
Ubuntu update-manager Edit question
Assignee:
No assignee Edit question
Last query:
2014-08-27
Last reply:
2015-03-01

It seems you tried to install XCrySDen using a non-standard method.

According to the following link

http://packages.ubuntu.com/search?suite=trusty&searchon=names&keywords=XCrySDen

the Ubuntu package xcrysden is available in the Ubuntu 14.04 LTS repositories.

Please send us the full Terminal output of the following commands:

apt-cache search xcrysden

cat /etc/lsb-release

uname -a

dinesh (dinesh1910) said : #2

The Output is,
mm@mm:~/Downloads/xcrysden-1.5.60$ apt-cache search xcrysden
v-sim-plugins - Plugins for V_Sim (a 3D visualization package)
mm@mm:~/Downloads/xcrysden-1.5.60$ cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=12.04
DISTRIB_CODENAME=precise
DISTRIB_DESCRIPTION="Ubuntu 12.04.5 LTS"
mm@mm:~/Downloads/xcrysden-1.5.60$ uname -a
Linux mm 3.2.0-68-generic #102-Ubuntu SMP Tue Aug 12 22:04:27 UTC 2014 i686 i686 i386 GNU/Linux
mm@mm:~/Downloads/xcrysden-1.5.60$

> To: <email address hidden>
> From: <email address hidden>
> Subject: Re: [Question #253612]: Not found when open XCrySDen
> Date: Tue, 26 Aug 2014 07:42:00 +0000
>
> Your question #253612 on update-manager in Ubuntu changed:
> https://answers.launchpad.net/ubuntu/+source/update-manager/+question/253612
>
> Status: Open => Needs information
>
> Mark Rijckenberg requested more information:
> It seems you tried to install XCrySDen using a non-standard method.
>
> According to the following link
>
> http://packages.ubuntu.com/search?suite=trusty&searchon=names&keywords=XCrySDen
>
> the Ubuntu package xcrysden is available in the Ubuntu 14.04 LTS
> repositories.
>
> Please send us the full Terminal output of the following commands:
>
> apt-cache search xcrysden
>
> cat /etc/lsb-release
>
> uname -a
>
> --
> To answer this request for more information, you can either reply to
> this email or enter your reply at the following page:
> https://answers.launchpad.net/ubuntu/+source/update-manager/+question/253612
>
> You received this question notification because you asked the question.

This is indeed a tricky question, because there are no binary xcrysden packages for Ubuntu 12.04 LTS, but Ubuntu 12.04 LTS is supported.

Please try this compilation and installation procedure in a Terminal session, which works for me in Ubuntu 14.04 LTS 64-bit :

cd

wget http://www.xcrysden.org/download/xcrysden-1.5.60.tar.gz

tar -zxvf xcrysden-1.5.60.tar.gz

cd xcrysden-1.5.60/

sudo ln -s ~/xcrysden-1.5.60/xcrysden /usr/bin/xcrysden

cp system/Make.sys-semishared Make.sys

sudo apt-get update

sudo apt-get install tcl tcl-dev tk tk-dev itcl3 itk3 itk3-dev tk8.4-dev tk8.4

sudo apt-get install iwidgets4 tcl8.5 tcl8.5-dev tk8.5 tk8.5-dev libtogl-dev

sudo apt-get install libxmu-headers libxmu-dev libxmuu-dev

make all

xcrysden -v

xcrysden --help

Running the following Terminal command ./xcrysden

should give the following Terminal output and also a separate XCrySDen graphical user interface, if the previous compilation steps were 100% successful:

$ ./xcrysden

+-----------------------------------------------------------------+
|*****************************************************************|
|* *|
|* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *|
|* = === = === *|
|*---------------------------------------------------------------*|
|* *|
|* Anton Kokalj (<email address hidden>) *|
|* Jozef Stefan Institute, Ljubljana, Slovenia *|
|* *|
|* Copyright (c) 1996--2014 by Anton Kokalj *|
|* *|
|*****************************************************************|
+-----------------------------------------------------------------+

  Version: 1.5.60

  Please report bugs to: <email address hidden>

  TERMS OF USE:
  -------------
  XCRYSDEN is released under the GNU General Public License.

  Whenever graphics generated by XCRYSDEN are used in scientific
  publications, it shall be greatly appreciated to include an explicit
  reference. The preferred form is the following:

  [ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
        Code available from http://www.xcrysden.org/.

TCL_LIBRARY=/home/ulysses/xcrysden-1.5.60/external/lib/tcl8.5
XCRYSDEN_TOPDIR=/home/ulysses/xcrysden-1.5.60
XCRYSDEN_SCRATCH=/tmp

Running on platform : unix
   Operating system : Linux
Package ImageMagick's convert: /usr/bin/convert
Package ImageMagick's import: /usr/bin/import
Package Mencoder: /usr/bin/mencoder
Package Ppmtompeg: /usr/bin/ppmtompeg
Package Xwd: /usr/bin/xwd
Executing: /home/ulysses/xcrysden-1.5.60/bin/ftnunit

<separate graphical user interface will appear in a separate window>

garu (garu-gebreyesus) said : #4

Dear Mark
I followed your instructions but it isnot working. Here si what I found
/usr/bin/xcrysden: 256: /usr/bin/xcrysden: /home/garu/xcrysden-1.5.60/bin/xcrys: not found
please help

@garu: that's probably because my instructions were not correctly followed. I think you mistyped this command:

sudo ln -s ~/xcrysden-1.5.60/xcrysden /usr/bin/xcrysden

Because of the incorrect link, you first need to run the following command:

sudo rm /usr/bin/xcrysden

Then run the CORRECT command:

sudo ln -s ~/xcrysden-1.5.60/xcrysden /usr/bin/xcrysden

Try copy-paste instead of manual typing to avoid errors like this....

garu (garu-gebreyesus) said : #6

@mark,
I didnt miss type it since i copy and pasted. To be sure,
I did copy and paste, but again it isnot workng. By the way, I am installing it in kubuntu 14.04 Lts.

Can you help with this problem?

Provide an answer of your own, or ask dinesh for more information if necessary.

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