Nanoqian

11-15-2025

Fixing Common XCrysDen Errors

Overview

XCrysDen is a program for visualizing molecular structure. It was written during 1996-1999 and has had some updates since then but it is still difficult to run on modern Linux systems.

Common Issues:

1. XCrysDen will not work on Wayland

This is probably because XCrysDen uses direct calls to the X API. You have to use X instead to fix this.

Solution

You will have to switch to a X11 desktop environment. Doing this depends on your system configuration, but this option is usually in the login menu or a config file for your display manager.

2. XCrysDen XSever Error on Startup

This error shows as:



    +-----------------------------------------------------------------+
    |*****************************************************************|
    |*                                                               *|
    |*  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 Ppmtompeg: /usr/bin/ppmtompeg
    Package Xwd: /usr/bin/xwd
    Executing: /usr/lib/xcrysden/ftnunit
    X Error of failed request: BadWindow (invalid Window parameter)
	Major opcode of failed request: 3
	ResourceID in failed request: 0xffffffff
	Serial number of failed request: 937
    X Error of failed request: BadWindow (invalid Window parameter)
	Major opcode of failed request: 3
	ResourceID in failed request: 0xffffffff
	Serial number of failed request: 939
    Error in startup script:
    Couldn't configure togl widget
	while executing
    "togl .mesa  -width          400  -height         400  -ident          .mesa  -rgba           $toglOpt(rgba)           -redsize        $toglOpt(redsize..."
	(procedure "PlaceGlobWin" line 107)
	invoked from within
    "PlaceGlobWin 0 [expr round(670 * $fac1)] [expr round(670 * $fac1)]"
	(procedure "ViewMol" line 25)
	invoked from within
    "ViewMol ."
	invoked from within
    "if { [llength $argv] > 2 } {
	parseComLinArg [lrange $argv 2 end]
    } else {
	ViewMol .
    }"
	(file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 633)

Solution

Go to /usr/share/xcrysden/Tcl/custom-definitions
Search for the line "#set toglOpt(accum) false"
Change to "set toglOpt(accum) false"

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