From chen_liangd at 163.com Fri Nov 1 10:48:20 2013 From: chen_liangd at 163.com (chen_liangd) Date: Fri, 1 Nov 2013 17:48:20 +0800 (CST) Subject: [xcrysden] =?gbk?b?wLTX1GNoZW5fbGlhbmdktcTTyrz+?= Message-ID: <2b1f6694.ecf3.14213103d5b.Coremail.chen_liangd@163.com> hello? I am a newer of xcrysden and want to install this software under the cygwin bash shell.After installing, when I perform the command xcrysden,errors come.The error information is the +----------------------------------------------------------------+ |****************************************************************| |* *| |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*--------------------------------------------------------------*| |* *| |* Anton Kokalj (Tone.Kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2004 by Anton Kokalj *| |* *| |****************************************************************| +----------------------------------------------------------------+ Version: 1.4.1 XCRYSDEN reference: A. Kokalj: J. Mol. Graphics Modelling, 1999, Vol. 17, 176--179. A. Kokalj: Comput. Mater. Science, 2003, Vol. 28, 155--168. A. Kokalj and M. Causa: Proceedings of High Performance Graphics Systems and Applications European Workshop, Bologna, Italy, 2000, 51--54. Please report bugs to: Tone.Kokalj at 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. Graphics Modelling, 1999, Vol. 17, 176--179. Code available from http://www.xcrysden.org/. Error in startup script: conflicting versions provided for package "Tk": 8.5.11, then 8.5 while executing "package provide Tk $tk_version" (file "/home/dell/xcrysden/Tcl/xcInit.tcl" line 400) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131101/afb2d72e/attachment.htm From alhazikara at gmail.com Tue Nov 5 03:54:27 2013 From: alhazikara at gmail.com (Alhassan Shuaibu) Date: Tue, 5 Nov 2013 10:54:27 +0800 Subject: [xcrysden] Generating atomic coordinate Message-ID: <4741033767766053042@unknownmsgid> Hi please is there any way of generating atomic coordinate for Bi2Te3 hexagonal -trigonal structure? Sent from my Windows Phone -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131105/8289faa6/attachment.htm From dstrubbe at civet.berkeley.edu Sat Nov 9 20:09:52 2013 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Sat, 9 Nov 2013 14:09:52 -0500 Subject: [xcrysden] xcrysden mesa/tc/tk on MacOS In-Reply-To: <1359049781.19990.25.camel@catalyst.ijs.si> References: <1358268174.4537.13.camel@catalyst.ijs.si> <1358528690.3779.57.camel@catalyst.ijs.si> <1359049781.19990.25.camel@catalyst.ijs.si> Message-ID: Hi all, I would like to follow up on this report and give some good news. I found there is a very simple solution to get tcl/tk 8.5.13 and 8.6.1 to work from MacPorts in XCrySDen: just make sure tk installed with variant +x11 rather than the default +quartz, since XCrySDen is using X11. The only problem with the newer tk versions in MacPorts was that +quartz became the default. All variants for tcl were fine for compilation and runnning, using "-DUSE_INTERP_RESULT" in CFLAGS as Tone recommended. David On Thu, Jan 24, 2013 at 12:49 PM, Tone Kokalj wrote: > On Fri, 2013-01-18 at 12:59 -0500, David Strubbe wrote: > > > As I mentioned originally, the program compiles and runs fine for me > > with Tcl and Tk 8.5.12. Also, I checked that the same is true if I use > > the cflag -DUSE_INTERP_RESULT. Is this what you are asking? > > More or less. This indicates that other fixes besides > -DUSE_INTERP_RESULT are needed. I guess that due to backward > incompatibility of Tcl/Tk8.6 with the 8.5 and older versions some code > adjustment will probably be necessary. > > Regards, > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131109/6190efa9/attachment.htm From jxzhu at lanl.gov Sat Nov 9 21:49:05 2013 From: jxzhu at lanl.gov (Zhu, Jianxin) Date: Sat, 9 Nov 2013 20:49:05 +0000 Subject: [xcrysden] xcrysden mesa/tc/tk on MacOS In-Reply-To: Message-ID: David, How do we set in MacPorts to install tk with variant +x11? Thanks, Jianxin From: David Strubbe > Reply-To: XCrySDen mailing list > Date: Saturday, November 9, 2013 12:09 PM To: "tone. kokalj" >, XCrySDen mailing list > Subject: Re: [xcrysden] xcrysden mesa/tc/tk on MacOS Hi all, I would like to follow up on this report and give some good news. I found there is a very simple solution to get tcl/tk 8.5.13 and 8.6.1 to work from MacPorts in XCrySDen: just make sure tk installed with variant +x11 rather than the default +quartz, since XCrySDen is using X11. The only problem with the newer tk versions in MacPorts was that +quartz became the default. All variants for tcl were fine for compilation and runnning, using "-DUSE_INTERP_RESULT" in CFLAGS as Tone recommended. David On Thu, Jan 24, 2013 at 12:49 PM, Tone Kokalj > wrote: On Fri, 2013-01-18 at 12:59 -0500, David Strubbe wrote: > As I mentioned originally, the program compiles and runs fine for me > with Tcl and Tk 8.5.12. Also, I checked that the same is true if I use > the cflag -DUSE_INTERP_RESULT. Is this what you are asking? More or less. This indicates that other fixes besides -DUSE_INTERP_RESULT are needed. I guess that due to backward incompatibility of Tcl/Tk8.6 with the 8.5 and older versions some code adjustment will probably be necessary. Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131109/1a343355/attachment.htm From dstrubbe at civet.berkeley.edu Sat Nov 9 23:36:29 2013 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Sat, 9 Nov 2013 17:36:29 -0500 Subject: [xcrysden] xcrysden mesa/tc/tk on MacOS In-Reply-To: References: Message-ID: Like this: "sudo port install tk +x11" David On Sat, Nov 9, 2013 at 3:49 PM, Zhu, Jianxin wrote: > David, > > > How do we set in MacPorts to install tk with variant +x11? > > Thanks, > > Jianxin > > From: David Strubbe > Reply-To: XCrySDen mailing list > Date: Saturday, November 9, 2013 12:09 PM > To: "tone. kokalj" , XCrySDen mailing list < > xcrysden at democritos.it> > Subject: Re: [xcrysden] xcrysden mesa/tc/tk on MacOS > > Hi all, > > I would like to follow up on this report and give some good news. I > found there is a very simple solution to get tcl/tk 8.5.13 and 8.6.1 to > work from MacPorts in XCrySDen: just make sure tk installed with variant > +x11 rather than the default +quartz, since XCrySDen is using X11. The only > problem with the newer tk versions in MacPorts was that +quartz became the > default. All variants for tcl were fine for compilation and runnning, using > "-DUSE_INTERP_RESULT" in CFLAGS as Tone recommended. > > David > > > On Thu, Jan 24, 2013 at 12:49 PM, Tone Kokalj wrote: > >> On Fri, 2013-01-18 at 12:59 -0500, David Strubbe wrote: >> >> > As I mentioned originally, the program compiles and runs fine for me >> > with Tcl and Tk 8.5.12. Also, I checked that the same is true if I use >> > the cflag -DUSE_INTERP_RESULT. Is this what you are asking? >> >> More or less. This indicates that other fixes besides >> -DUSE_INTERP_RESULT are needed. I guess that due to backward >> incompatibility of Tcl/Tk8.6 with the 8.5 and older versions some code >> adjustment will probably be necessary. >> >> Regards, >> >> -- >> Anton Kokalj >> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia >> (tel: +386-1-477-3523 // fax:+386-1-477-3822) >> >> Please, if possible, avoid sending me Word or PowerPoint attachments. >> See: http://www.gnu.org/philosophy/no-word-attachments.html >> >> _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden >> > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131109/c6ceb173/attachment.htm From dstrubbe at civet.berkeley.edu Mon Nov 11 02:27:04 2013 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Sun, 10 Nov 2013 20:27:04 -0500 Subject: [xcrysden] meschach Message-ID: Dear Tone, What is the function of the Meschach library in XCrysDen? It seems that we can link it or not and the code still builds and runs. David Strubbe MIT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131110/5c9b7752/attachment.htm From tone.kokalj at ijs.si Mon Nov 11 13:56:34 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 11 Nov 2013 13:56:34 +0100 Subject: [xcrysden] myParam ignored in minor script In-Reply-To: <3FD5B49C-C21B-4C9D-81A9-3DD1511A8BF8@epfl.ch> References: <3FD5B49C-C21B-4C9D-81A9-3DD1511A8BF8@epfl.ch> Message-ID: <1384174594.4355.28.camel@catalyst.ijs.si> On Thu, 2013-10-31 at 17:46 +0100, Gabriele Sclauzero wrote: > > > > I have tried your script. Now I encounter an additional problem, not > > related to the previous. > > On my platform the code crashes if the thermometer is enabled with > > -cpl_thermometer 1 Perhaps the advice of Martin Kroeker can help here. He suggests to "export XLIB_SKIP_ARGB_VISUALS=1" before starting xcrysden. > > Anyway, after removing the option I could run the script, but the > > background does not change to red (see attached picture). That's really strange, and I do not understand what is the reason, because this works for me. Anyway, if I understood correctly, you experience this only for multi-script and not for a normal script. Hence you can consider to embed a normal xcrysden script into a shell script instead and make a loop on the shell-script level. See the example: ./examples/Scripting/plot_all_MO.sh (there is some info inside as the script is documented) The important thing is to replace all $ characters in xcrysden script with \$ to prevent shell substitution ... Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Mon Nov 11 13:58:40 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 11 Nov 2013 13:58:40 +0100 Subject: [xcrysden] =?utf-8?b?5p2l6IeqY2hlbl9saWFuZ2TnmoTpgq7ku7Y=?= In-Reply-To: <2b1f6694.ecf3.14213103d5b.Coremail.chen_liangd@163.com> References: <2b1f6694.ecf3.14213103d5b.Coremail.chen_liangd@163.com> Message-ID: <1384174720.4355.30.camel@catalyst.ijs.si> On Fri, 2013-11-01 at 17:48 +0800, chen_liangd wrote: > hello? > I am a newer of xcrysden and want to install this software under > the cygwin bash shell.After installing, when I perform the command > xcrysden,errors come.The error information is the > +----------------------------------------------------------------+ > |****************************************************************| > |* *| > |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| > |* = === = === *| > |*--------------------------------------------------------------*| > |* *| > |* Anton Kokalj (Tone.Kokalj at ijs.si) *| > |* Jozef Stefan Institute, Ljubljana, Slovenia *| > |* *| > |* Copyright (c) 1996--2004 by Anton Kokalj *| > |* *| > |****************************************************************| > +----------------------------------------------------------------+ > > Version: 1.4.1 Consider to use newer version, i.e.: http://www.xcrysden.org/download/xcrysden-1.5.53-cygwin.tar.gz and let me know if the problem persists. Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Mon Nov 11 14:04:00 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 11 Nov 2013 14:04:00 +0100 Subject: [xcrysden] Generating atomic coordinate In-Reply-To: <4741033767766053042@unknownmsgid> References: <4741033767766053042@unknownmsgid> Message-ID: <1384175040.4355.34.camel@catalyst.ijs.si> On Tue, 2013-11-05 at 10:54 +0800, Alhassan Shuaibu wrote: > > Hi please is there any way of generating atomic coordinate for Bi2Te3 > hexagonal -trigonal structure? I don't really know what you mean and what is the problem. Anyway, I would first google to find the crystal structure data, and that's it more or less. http://rruff.geo.arizona.edu/AMS/minerals/Tellurobismuthite -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Mon Nov 11 14:12:13 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 11 Nov 2013 14:12:13 +0100 Subject: [xcrysden] meschach In-Reply-To: References: Message-ID: <1384175533.4355.41.camel@catalyst.ijs.si> On Sun, 2013-11-10 at 20:27 -0500, David Strubbe wrote: > Dear Tone, > > > What is the function of the Meschach library in XCrysDen? None and you should ignore it. It was used for some testing of some new features. Meschach is a linear algebra library written in C. > It seems that we can link it or not and the code still builds and > runs. Precisely, because it is not used. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From ora at georgetown.edu Mon Nov 11 17:37:18 2013 From: ora at georgetown.edu (Oliver Albertini) Date: Mon, 11 Nov 2013 08:37:18 -0800 Subject: [xcrysden] problem running on OS X 10.9 Message-ID: Hello, I am trying to install xcrysden on Mavericks. Using the following Make.sys, and tcl/tk etc installed from macports, I was able to get everything compiled. However, at runtime, I get a seg fault with tk +xquartz. Thanks to David Strubbe, I installed +x11 version, but then the following error. MAKE = /opt/local/bin/gmake CC = /opt/local/bin/gcc-mp-4.8 CFLAGS = -O2 -m64 -L/opt/local/lib -DUSE_INTERP_RESULT -funroll-loops -fPIC -DTOGL_USE_FONTS -DHAVE_NO_GETLINE MATH = -lm FC = /opt/local/bin/gfortran-mp-4.8 FFLAGS = -O2 -m64 -L/opt/local/lib X_LIB = -L/opt/local/lib -lXmu -lX11 -lXext X_INCDIR = -I/opt/local/include COMPILE_TCLTK = no COMPILE_MESA = no TK_LIB = -L/opt/local/lib -ltk8.6 TCL_LIB = -L/opt/local/lib -ltcl8.6 GLU_LIB = -L/opt/local/lib -lGLU GL_LIB = -L/opt/local/lib -lGL MESCHACH_LIB = -L/opt/local/lib -lmeschach FFTW3_LIB = -L/opt/local/lib -lfftw3 LDLIB = -L/opt/local/lib # Include Directories TCL_INCDIR = TK_INCDIR = GL_INCDIR = MESCHACH_INCDIR = -I/opt/local/include/meschach FFTW3_INCDIR = -I/opt/local/include Error: Running on platform : unix Operating system : Darwin Package ImageMagick's convert: /usr/local/bin/convert Package Ppmtompeg: /opt/local/bin/ppmtompeg Package Xwd: /opt/X11/bin/xwd Executing: /Users/oliverralbertini/xcrysden/xcrysden-1.5.53/bin/ftnunit X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 3 (X_GetWindowAttributes) Resource id in failed request: 0xffffffff Serial number of failed request: 560 Current serial number in output stream: 561 Thanks, Oliver Albertini -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131111/9da65e88/attachment.htm From ora at georgetown.edu Thu Nov 14 01:08:41 2013 From: ora at georgetown.edu (Oliver Albertini) Date: Wed, 13 Nov 2013 16:08:41 -0800 Subject: [xcrysden] problem running on OS X 10.9 Message-ID: I got this to work by using fink to install mesa 7.0.2. It seemed easier than installing mesa 7.0.2 from source, and my attempt to install mesa 7.0.2 from macports was unsuccessful; 4 libraries were found to be broken during the check. Perhaps this has to do with my current level of tcl, which is 8.6. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131113/7b69e61f/attachment.htm From dstrubbe at civet.berkeley.edu Thu Nov 14 03:09:05 2013 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Wed, 13 Nov 2013 21:09:05 -0500 Subject: [xcrysden] problem running on OS X 10.9 In-Reply-To: References: Message-ID: mesa 7.0.2 is not in MacPorts, so I'm not sure what you mean you tried. Anyway, I am working on getting a port of xcrysden accepted into MacPorts, using a new port for mesa 7.0.2. I confirmed today that this worked on Mavericks. I suspect from the error you report that you are not linked as you think you are. I suggest make clean and make again, and then check with "otool -L bin/xcrys" that you have linked the libraries you wanted. David On Wed, Nov 13, 2013 at 7:08 PM, Oliver Albertini wrote: > I got this to work by using fink to install mesa 7.0.2. > > It seemed easier than installing mesa 7.0.2 from source, and my attempt to > install mesa 7.0.2 from macports was unsuccessful; 4 libraries were found > to be broken during the check. Perhaps this has to do with my current level > of tcl, which is 8.6. > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131113/42522f09/attachment.htm From ora at georgetown.edu Thu Nov 14 18:46:10 2013 From: ora at georgetown.edu (Oliver Albertini) Date: Thu, 14 Nov 2013 09:46:10 -0800 Subject: [xcrysden] problem running on OS X 10.9 Message-ID: To try and get a macports version of mesa 7.0.2, I used the following Portfile, the only change I made was tclsh8.5 -> tclsh8.6: https://gist.github.com/danmichaelo/1658983 and the following 'technique' to have macports install it: http://guide.macports.org/#development.local-repositories I got this info from this post to the xcrysden list: http://www.democritos.it/pipermail/xcrysden/2012-January/001068.html It seemed to be going well, all the way through to the binary check at the end, when it found the four broken binaries. With the fink mesa 7.0.2, xcrysden is also working for me on Mavericks, and I did have to use 'otool -L bin/xcrys' to ensure that the libraries libGLU.1.dylib and libGL.1.dylib from /sw/lib/mesa were linked. A working port of this would be great, so thank you. Oliver -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131114/3abe56a5/attachment.htm From dstrubbe at civet.berkeley.edu Thu Nov 14 21:34:57 2013 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Thu, 14 Nov 2013 15:34:57 -0500 Subject: [xcrysden] problem running on OS X 10.9 In-Reply-To: References: Message-ID: Try these Portfiles and patches: https://trac.macports.org/ticket/41319(mesa702) and https://trac.macports.org/ticket/41320 (xcrysden). mesa702 as from the github link unfortunately will give incorrect install names for the dylib's; I had to patch this incorrect behavior. That is why if you use otool I am confident you will find the xcrys binary that gave you the error in the original message was not linked correctly. David On Thu, Nov 14, 2013 at 12:46 PM, Oliver Albertini wrote: > To try and get a macports version of mesa 7.0.2, I used the following > Portfile, the only change I made was tclsh8.5 -> tclsh8.6: > > https://gist.github.com/danmichaelo/1658983 > > and the following 'technique' to have macports install it: > > http://guide.macports.org/#development.local-repositories > > I got this info from this post to the xcrysden list: > > http://www.democritos.it/pipermail/xcrysden/2012-January/001068.html > > It seemed to be going well, all the way through to the binary check at the > end, when it found the four broken binaries. > > With the fink mesa 7.0.2, xcrysden is also working for me on Mavericks, > and I did have to use 'otool -L bin/xcrys' to ensure that the libraries > libGLU.1.dylib and libGL.1.dylib from /sw/lib/mesa were linked. > > A working port of this would be great, so thank you. > > Oliver > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131114/b5272940/attachment.htm From ora at georgetown.edu Fri Nov 15 22:03:05 2013 From: ora at georgetown.edu (Oliver Albertini) Date: Fri, 15 Nov 2013 13:03:05 -0800 Subject: [xcrysden] problem running on OS X 10.9 Message-ID: Many thanks to David Strubbe, using his recommended Portfiles and patches, the installation of xcrysden can now be done with MacPorts alone. The fink-built mesa-7.0.2 or fink-built xcrysden is no longer necessary. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131115/9681118b/attachment.htm From mails2asa at gmail.com Sun Nov 17 10:20:42 2013 From: mails2asa at gmail.com (Asa Aravindh) Date: Sun, 17 Nov 2013 12:20:42 +0300 Subject: [xcrysden] displaying molecular surface in xcrysden Message-ID: Dear Xcrysden community, Greetings.. Is it possible to display the molecular surface for selective atoms in xcrysden?? When I click on the display; it shows for the entire geometry.. thanks in advance, Assa Assa Aravindh.S,PhD Post Doctoral Fellow Division of Physical Sciences and Engineering KAUST, Kingdom of Saudi Arabia Email: Assa.Sasikaladevi at kaust.edu.sa -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131117/f10dcc82/attachment.htm From tone.kokalj at ijs.si Tue Nov 19 15:32:21 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 19 Nov 2013 15:32:21 +0100 Subject: [xcrysden] problem running on OS X 10.9 In-Reply-To: References: Message-ID: <1384871541.19260.9.camel@catalyst.ijs.si> David and Oliver, Note that you can also use a newer version of Mesa for xcrysden. The sole reason the old 7.x versions are used by xcrysden is that I find them much easier to compile than the newer Mesa versions. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Tue Nov 19 15:34:24 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 19 Nov 2013 15:34:24 +0100 Subject: [xcrysden] displaying molecular surface in xcrysden In-Reply-To: References: Message-ID: <1384871664.19260.10.camel@catalyst.ijs.si> On Sun, 2013-11-17 at 12:20 +0300, Asa Aravindh wrote: > Dear Xcrysden community, > > > Greetings.. > > Is it possible to display the molecular surface for selective atoms > in xcrysden?? No, this is not possible. Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From dstrubbe at civet.berkeley.edu Tue Nov 19 15:54:38 2013 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Tue, 19 Nov 2013 09:54:38 -0500 Subject: [xcrysden] problem running on OS X 10.9 In-Reply-To: <1384871541.19260.9.camel@catalyst.ijs.si> References: <1384871541.19260.9.camel@catalyst.ijs.si> Message-ID: Unfortunately this is not true on MacOS, as we have discussed on this list before. 7.0.2 works; 7.8.2, 7.11.2, and 8.0.4 (at least from macports) do not work with xcrysden. The initialization of the window fails immediately with something like X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 3 (X_GetWindowAttributes) Resource id in failed request: 0xffffffff Serial number of failed request: 566 Current serial number in output stream: 567 On Tue, Nov 19, 2013 at 9:32 AM, Tone Kokalj wrote: > David and Oliver, > > Note that you can also use a newer version of Mesa for xcrysden. > The sole reason the old 7.x versions are used by xcrysden is that I find > them much easier to compile than the newer Mesa versions. > > Regards, Tone > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131119/552d67fb/attachment.htm From member at linkedin.com Sat Nov 23 10:49:05 2013 From: member at linkedin.com (baaouague khaled via LinkedIn) Date: Sat, 23 Nov 2013 09:49:05 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Fa=C3=A7a_parte_da_minha_rede_no_LinkedIn=2E?= Message-ID: <1721882799.25227414.1385200145559.JavaMail.app@ela4-app0098.prod> LinkedIn ------------ baaouague khaled solicitou sua adi??o como uma conex?o no LinkedIn: ------------------------------------------ Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn. Aceitar convite de baaouague khaled http://www.linkedin.com/e/-fe5rcs-hocoegrd-4k/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I504414912_125/e39SrCAJoS5vrCAJoyRJtCVFnSRJrScJr6RBfnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dj8NnP8NejgNd3gMdkALjkB2ciR3iQcLdzsNc3wRcPASdj4LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=3poFWrkvtdhC01 Visualizar perfil de baaouague khaled http://www.linkedin.com/e/-fe5rcs-hocoegrd-4k/rso/197724472/oED1/name/128644874_I504414912_125/?hs=false&tok=0PIncVPsFdhC01 ------------------------------------------ Voc? est? recebendo e-mails de convites. Este e-mail era para Andr? Pereira XCrysden. Saiba por que isto est? inclu?do: http://www.linkedin.com/e/-fe5rcs-hocoegrd-4k/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=3n52l6Dd1dhC01 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043 - EUA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20131123/acb95932/attachment-0001.htm From lorenzo.paulatto at impmc.upmc.fr Mon Nov 25 10:16:38 2013 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 25 Nov 2013 10:16:38 +0100 Subject: [xcrysden] compiling on tcl 8.6 Message-ID: <52931576.4090500@impmc.upmc.fr> Dear XCD users, in case you are trying to compile XCrysDen with TCL 8.6 and you're getting this error: Tcl_Interp? has no member named ?result? you have to add "-DUSE_INTERP_RESULT" (no quotes) to the CFLAGS in Make.sys. The code will then build with tcl8.6 (to be honest, I only did bindist-shared). This should solve the problem, I don't know if the feature is planned for removal eventually but give the frequency of TCL releases I think there's no immediate need to worry. -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 phone:+33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 5 From tone.kokalj at ijs.si Mon Nov 25 18:23:16 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 25 Nov 2013 18:23:16 +0100 Subject: [xcrysden] compiling on tcl 8.6 In-Reply-To: <52931576.4090500@impmc.upmc.fr> References: <52931576.4090500@impmc.upmc.fr> Message-ID: <1385400196.21028.8.camel@catalyst.ijs.si> On Mon, 2013-11-25 at 10:16 +0100, Lorenzo Paulatto wrote: > Dear XCD users, > in case you are trying to compile XCrysDen with TCL 8.6 and you're > getting this error: > Tcl_Interp? has no member named ?result? > > you have to add "-DUSE_INTERP_RESULT" (no quotes) to the CFLAGS in > Make.sys. The code will then build with tcl8.6 (to be honest, I only did > bindist-shared). > > This should solve the problem, I don't know if the feature is planned > for removal eventually but give the frequency of TCL releases I think > there's no immediate need to worry. Lorenzo, Thanks for the info! I agree that there is no immediate need to worry about this issue, but eventually the code will need to be adopted and this backward incompatibility fixed, moreover because the fix is not difficult. Regards. -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From likhonnaser at hotmail.com Sat Nov 30 16:12:42 2013 From: likhonnaser at hotmail.com (Abu Naser) Date: Sat, 30 Nov 2013 15:12:42 +0000 Subject: [xcrysden] Compilation problem Message-ID: Hi All, I am trying to compile with all external packages and getting the following error message. Could you please help me solve the problem? -o xcrys /root/XCrySDen-1.4.1s-all/external/lib/libtk8.4.so /root/XCrySDen-1.4.1s-all/external/lib/libtcl8.4.so /root/XCrySDen-1.4.1s-all/external/lib/libGLU.so /root/XCrySDen-1.4.1s-all/external/lib/libGL.so -L/usr/X11R6/lib -lXmu -lX11 -lXext -lm /root/XCrySDen-1.4.1s-all/external/lib/libGLU.so: undefined reference to `operator new[](unsigned int)' /root/XCrySDen-1.4.1s-all/external/lib/libGLU.so: undefined reference to `operator delete[](void*)' /root/XCrySDen-1.4.1s-all/external/lib/libGLU.so: undefined reference to `operator delete(void*)' /root/XCrySDen-1.4.1s-all/external/lib/libGLU.so: undefined reference to `__cxa_pure_virtual' /root/XCrySDen-1.4.1s-all/external/lib/libGLU.so: undefined reference to `__gxx_personality_v0' /root/XCrySDen-1.4.1s-all/external/lib/libGLU.so: undefined reference to `vtable for __cxxabiv1::__vmi_class_type_info' /root/XCrySDen-1.4.1s-all/external/lib/libGLU.so: undefined reference to `vtable for __cxxabiv1::__class_type_info' /root/XCrySDen-1.4.1s-all/external/lib/libGLU.so: undefined reference to `operator new(unsigned int)' /root/XCrySDen-1.4.1s-all/external/lib/libGLU.so: undefined reference to `vtable for __cxxabiv1::__si_class_type_info' collect2: ld returned 1 exit status make[2]: *** [xcrys] Error 1 make[2]: Leaving directory `/root/XCrySDen-1.4.1s-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/root/XCrySDen-1.4.1s-all/C' make: *** [src-C] Error 2 -------------- next part -------------- An HTML attachment was scrubbed... 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