Error Opening xcrysden Software in Linux Terminal - How to Fix?

Hello everyone,

I recently purchased a laptop for my studies and installed Linux on it to run some essential software. One of the programs I need is xcrysden, but I'm encountering an issue whenever I try to open it from the terminal. The error message I receive is:

I'm not sure what's causing this problem or how to resolve it. Has anyone else experienced a similar issue with xcrysden on a cheapest student laptop running Linux? What steps did you take to fix it?

I've already tried reinstalling the software and ensuring all dependencies are installed, but the error persists. Any advice or troubleshooting tips would be greatly appreciated!

Thanks in advance for your help!

Best regards,
Jonathan Jone

Trouble Shooting

If the installation of sources has failed for some reason then read the printed error message. Also read carefully the instructions inside the Make.sys and edit the file according to your needs.

The most often cause of failure is that either some header files were not found or that there are some missing references, which means that the code will have to be linked against additional libraries.

If the failure appeared in compilation of external library, then try to compile this library manually, i.e., do cd external/src/LIB, where LIB is the corresponding library directory, and read the installation instructions therein.

In case of unsolvable problems, first google for help and only then ask for help on XCrySDen mailing list (Subscribe | Archives).

Reference

Also, check install requirements from the same reference above:

?? Why the terminal window has csharp lable. csharp cannot be used in this install according to the docs:

How to Install the Source Package

Software requirements: The compilation of XCrySDen requires C and Fortran compilers and the following libraries (development version): Tcl/Tk, Togl, OpenGL (i.e. Mesa), BWidget, FFTW3, X11 libraries, and few other system libraries.

C != C# (totally different programming languages)

fyi, for reference,
i installed this via apt on a linux mint 20.x host,
video card is an invidia quadro K2200

sudo apt install xcrysden
.....

xcrysden

+-----------------------------------------------------------------+
|*****************************************************************|
|*                                                               *|
|*  XCrySDen -- (X-Window) CRYstalline Structures and DENsities  *|
|*               =         ===         =              ===        *|
|*---------------------------------------------------------------*|
|*                                                               *|
|*    Anton Kokalj (tone.kokalj@ijs.si)                          *|
|*    Jozef Stefan Institute, Ljubljana, Slovenia                *|
|*                                                               *|
|*    Copyright (c) 1996--2019 by Anton Kokalj                   *|
|*                                                               *|
|*****************************************************************|
+-----------------------------------------------------------------+

  Version: 1.6.2

  Please report bugs to: tone.kokalj@ijs.si


  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=/usr/share/xcrysden
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 Ppmtompeg: /usr/bin/ppmtompeg
Package Xwd: /usr/bin/xwd
Executing: /usr/lib/xcrysden/ftnunit
Viewer: mesaWid = .mesa

renders the following

image812×775 34.3 KB

I just did the macos install, on my M1 MacStudio:

Step 1

sudo port install tk libGLU xorg-libX11 xorg-libXmu fftw-3 ImageMagick openbabel

Step 2

sudo port install xcrysden

The above was a long, kinda arduous process installing myriad dependancies!

Then I got some X display errors and ran:

Step 3

sudo port install tk +quartz

Then ran:

Step 4

xcrysden

and this popped up:

What can I do next? haha .... can someone upload some cool molecules to play with?

I want to look at adenosine and the phosphorylations, AMP, ADP and ATP.

Thanks.

Thanks!

A bit confusing. I expected a repository of many molecules so I could easily load one, but did not find any.

Maybe because the last xcrysden update was 2009 or so?

Seems interesting, but mostly antiquated and poorly supported?

The "demo widgets" were not interesting and there were no cool molecules or interesting proteins to load and visualize!

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