From goy11002 at gmail.com Thu Mar 5 01:33:55 2015 From: goy11002 at gmail.com (Michael Smith) Date: Wed, 4 Mar 2015 17:33:55 -0700 Subject: [xcrysden] Trouble installing Message-ID: <3F965CD3-65EC-4903-A045-3D9AB061130C@gmail.com> Hello, I am trying to install Xcrysden 1.6 on a Unix OS I'm having running into this error listed below. What I have been doing is copying the Make.sys static file and then using the command: "make all" which will then gives me this error. Please help In file included from togl.h:48, from togl.c:16: /home/mgoytia/xcrysden-1.5.53/external/src/tcl8.5.11/generic/tcl.h:400: warning: ISO C90 does not support ?long long? /home/mgoytia/xcrysden-1.5.53/external/src/tcl8.5.11/generic/tcl.h:401: warning: ISO C90 does not support ?long long? togl.c:40:76: error: X11/Xmu/StdCmap.h: No such file or directory togl.c: In function ?get_rgb_colormap?: togl.c:614: warning: implicit declaration of function ?XmuLookupStandardColormap? togl.c: In function ?Togl_CreateCommand?: togl.c:1023: warning: ISO C forbids conversion of function pointer to object pointer type togl.c: In function ?Togl_Widget?: togl.c:1388: warning: ISO C forbids conversion of object pointer to function pointer type In file included from togl.c:4079: togl_ppm.c: In function ?Togl_DumpToPpmFile?: togl_ppm.c:43: warning: unused variable ?dpy? make[2]: *** [togl.o] Error 1 make[2]: Leaving directory `/home/mgoytia/xcrysden-1.5.53/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home/mgoytia/xcrysden-1.5.53/C' make: *** [src-C] Error 2 Michael Goytia Undergraduate Research Assistant Brigham Young University-Idaho goy11002 at byui.edu From gsabo at crimson.ua.edu Thu Mar 5 04:17:11 2015 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Wed, 04 Mar 2015 20:17:11 -0700 Subject: [xcrysden] Trouble installing In-Reply-To: <3F965CD3-65EC-4903-A045-3D9AB061130C@gmail.com> References: <3F965CD3-65EC-4903-A045-3D9AB061130C@gmail.com> Message-ID: <54F7CAB7.7020701@crimson.ua.edu> The post at the following link might help you: http://www.democritos.it/pipermail/xcrysden/2009-February/000570.html On 3/4/2015 5:33 PM, Michael Smith wrote: > Hello, > > I am trying to install Xcrysden 1.6 on a Unix OS > > I'm having running into this error listed below. > What I have been doing is copying the Make.sys static > file and then using the command: "make all" which will then gives > me this error. Please help > > In file included from togl.h:48, > from togl.c:16: > /home/mgoytia/xcrysden-1.5.53/external/src/tcl8.5.11/generic/tcl.h:400: warning: ISO C90 does not support ?long long? > /home/mgoytia/xcrysden-1.5.53/external/src/tcl8.5.11/generic/tcl.h:401: warning: ISO C90 does not support ?long long? > togl.c:40:76: error: X11/Xmu/StdCmap.h: No such file or directory > togl.c: In function ?get_rgb_colormap?: > togl.c:614: warning: implicit declaration of function ?XmuLookupStandardColormap? > togl.c: In function ?Togl_CreateCommand?: > togl.c:1023: warning: ISO C forbids conversion of function pointer to object pointer type > togl.c: In function ?Togl_Widget?: > togl.c:1388: warning: ISO C forbids conversion of object pointer to function pointer type > In file included from togl.c:4079: > togl_ppm.c: In function ?Togl_DumpToPpmFile?: > togl_ppm.c:43: warning: unused variable ?dpy? > make[2]: *** [togl.o] Error 1 > make[2]: Leaving directory `/home/mgoytia/xcrysden-1.5.53/C' > make[1]: *** [compile] Error 2 > make[1]: Leaving directory `/home/mgoytia/xcrysden-1.5.53/C' > make: *** [src-C] Error 2 > > Michael Goytia > Undergraduate Research Assistant > Brigham Young University-Idaho > goy11002 at byui.edu From mulwawinfred at gmail.com Tue Mar 10 11:31:15 2015 From: mulwawinfred at gmail.com (Winfred Mulwa) Date: Tue, 10 Mar 2015 12:31:15 +0200 Subject: [xcrysden] converting from pgm to jpeg Message-ID: Dear all, I saved my xcrysden image in the pgm format. Is there a way i can convert it to jpeg? Please assist. Regards Mulwa Winfred. D Phil Student, Computational Material Science Group, University of the Free State - QwaQwa, South Africa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150310/6784238c/attachment.htm From martin at ruby.chemie.uni-freiburg.de Tue Mar 10 12:27:39 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Tue, 10 Mar 2015 12:27:39 +0100 (CET) Subject: [xcrysden] converting from pgm to jpeg In-Reply-To: Message-ID: <20150310112739.E668E801B3@ruby.chemie.uni-freiburg.de> > I saved my xcrysden image in the pgm format. Is there a > way i can convert it to jpeg? "convert" from the ImageMagick or GraphicsMagick package should do this (on the commandline), or use "display" from the same package and then "save as" a jpeg from its menu. -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From goy11002 at gmail.com Wed Mar 11 05:35:24 2015 From: goy11002 at gmail.com (Michael Smith) Date: Tue, 10 Mar 2015 22:35:24 -0600 Subject: [xcrysden] Trouble installing, running Message-ID: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> When I type: ./xcrysden I get "/home/michael/xc/xcrysden-1.5.60-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.5.so: cannot open shared object file: No such file or directory" Michael Goytia Undergraduate Research Assistant Brigham Young University-Idaho goy11002 at byui.edu From gsabo at crimson.ua.edu Wed Mar 11 06:42:20 2015 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Tue, 10 Mar 2015 23:42:20 -0600 Subject: [xcrysden] Trouble installing, running In-Reply-To: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> References: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> Message-ID: <54FFD5BC.9020609@crimson.ua.edu> It looks like you need to install libtk8.5.so. For example, for Ubuntu, you can see that libtk8.5.so is part of the tk8.5 development package [ http://packages.ubuntu.com/lucid/amd64/tk8.5-dev/filelist ] and would be installed with "sudo apt-get install tk8.5-dev". Since we do not know what unix you are using, you will have to consult your operating system documentation. Or you might have to look at the Tk documentation [ http://www.tcl.tk/software/tcltk/8.5.html ] depending on how you need to install for your system. On 3/10/2015 10:35 PM, Michael Smith wrote: > When I type: ./xcrysden > I get > > "/home/michael/xc/xcrysden-1.5.60-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.5.so: cannot open shared object file: No such file or directory" > > Michael Goytia > Undergraduate Research Assistant > Brigham Young University-Idaho > goy11002 at byui.edu From goy11002 at gmail.com Wed Mar 11 08:01:19 2015 From: goy11002 at gmail.com (Michael Smith) Date: Wed, 11 Mar 2015 01:01:19 -0600 Subject: [xcrysden] Trouble installing, running In-Reply-To: <54FFD5BC.9020609@crimson.ua.edu> References: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> <54FFD5BC.9020609@crimson.ua.edu> Message-ID: <32E195A6-797F-45B8-AD93-5B370E0ABCD2@gmail.com> I'm using a fedora. Michael Goytia Undergraduate Research Assistant Brigham Young University-Idaho goy11002 at byui.edu > On Mar 10, 2015, at 11:42 PM, Gavin Abo wrote: > > It looks like you need to install libtk8.5.so. > > For example, for Ubuntu, you can see that libtk8.5.so is part of the > tk8.5 development package [ > http://packages.ubuntu.com/lucid/amd64/tk8.5-dev/filelist ] and would be > installed with "sudo apt-get install tk8.5-dev". > > Since we do not know what unix you are using, you will have to consult > your operating system documentation. Or you might have to look at the Tk > documentation [ http://www.tcl.tk/software/tcltk/8.5.html ] depending on > how you need to install for your system. > >> On 3/10/2015 10:35 PM, Michael Smith wrote: >> When I type: ./xcrysden >> I get >> >> "/home/michael/xc/xcrysden-1.5.60-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.5.so: cannot open shared object file: No such file or directory" >> >> Michael Goytia >> Undergraduate Research Assistant >> Brigham Young University-Idaho >> goy11002 at byui.edu > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden From goy11002 at gmail.com Wed Mar 11 08:23:10 2015 From: goy11002 at gmail.com (Michael Smith) Date: Wed, 11 Mar 2015 01:23:10 -0600 Subject: [xcrysden] Trouble installing, running In-Reply-To: <54FFD5BC.9020609@crimson.ua.edu> References: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> <54FFD5BC.9020609@crimson.ua.edu> Message-ID: <3CE5E643-E24D-4BD6-8CE2-A83BFA642BDA@gmail.com> I am also extremely new to linux. Michael Goytia Undergraduate Research Assistant Brigham Young University-Idaho goy11002 at byui.edu > On Mar 10, 2015, at 11:42 PM, Gavin Abo wrote: > > It looks like you need to install libtk8.5.so. > > For example, for Ubuntu, you can see that libtk8.5.so is part of the > tk8.5 development package [ > http://packages.ubuntu.com/lucid/amd64/tk8.5-dev/filelist ] and would be > installed with "sudo apt-get install tk8.5-dev". > > Since we do not know what unix you are using, you will have to consult > your operating system documentation. Or you might have to look at the Tk > documentation [ http://www.tcl.tk/software/tcltk/8.5.html ] depending on > how you need to install for your system. > >> On 3/10/2015 10:35 PM, Michael Smith wrote: >> When I type: ./xcrysden >> I get >> >> "/home/michael/xc/xcrysden-1.5.60-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.5.so: cannot open shared object file: No such file or directory" >> >> Michael Goytia >> Undergraduate Research Assistant >> Brigham Young University-Idaho >> goy11002 at byui.edu > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden From gsabo at crimson.ua.edu Wed Mar 11 10:19:47 2015 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Wed, 11 Mar 2015 03:19:47 -0600 Subject: [xcrysden] Trouble installing, running In-Reply-To: <32E195A6-797F-45B8-AD93-5B370E0ABCD2@gmail.com> References: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> <54FFD5BC.9020609@crimson.ua.edu> <32E195A6-797F-45B8-AD93-5B370E0ABCD2@gmail.com> Message-ID: <550008B3.3060305@crimson.ua.edu> You can try [ http://forums.fedoraforum.org/showthread.php?t=203254 ]: yum install tk-devel However, the version of tk that it installs might change depending on what version of Fedora you have. So if it installs a version other than 8.5, the fedora forum is likely the best place to search or ask on how to install the 8.5 version. An alternative to using 8.5 would be to try to compile xcrysden for the tk version that it installs, and the information at the following links might be helpful: http://www.democritos.it/pipermail/xcrysden/2013-February/001331.html http://www.linuxquestions.org/questions/linux-software-2/installing-xcrysden-4175449852/ On 3/11/2015 1:01 AM, Michael Smith wrote: > I'm using a fedora. > > Michael Goytia > Undergraduate Research Assistant > Brigham Young University-Idaho > goy11002 at byui.edu > > > >> On Mar 10, 2015, at 11:42 PM, Gavin Abo wrote: >> >> It looks like you need to install libtk8.5.so. >> >> For example, for Ubuntu, you can see that libtk8.5.so is part of the >> tk8.5 development package [ >> http://packages.ubuntu.com/lucid/amd64/tk8.5-dev/filelist ] and would be >> installed with "sudo apt-get install tk8.5-dev". >> >> Since we do not know what unix you are using, you will have to consult >> your operating system documentation. Or you might have to look at the Tk >> documentation [ http://www.tcl.tk/software/tcltk/8.5.html ] depending on >> how you need to install for your system. >> >>> On 3/10/2015 10:35 PM, Michael Smith wrote: >>> When I type: ./xcrysden >>> I get >>> >>> "/home/michael/xc/xcrysden-1.5.60-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.5.so: cannot open shared object file: No such file or directory" >>> >>> Michael Goytia >>> Undergraduate Research Assistant >>> Brigham Young University-Idaho >>> goy11002 at byui.edu From goy11002 at gmail.com Wed Mar 11 16:19:29 2015 From: goy11002 at gmail.com (Michael Goytia) Date: Wed, 11 Mar 2015 09:19:29 -0600 Subject: [xcrysden] Trouble installing, running In-Reply-To: <550008B3.3060305@crimson.ua.edu> References: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> <54FFD5BC.9020609@crimson.ua.edu> <32E195A6-797F-45B8-AD93-5B370E0ABCD2@gmail.com> <550008B3.3060305@crimson.ua.edu> Message-ID: Gavin, All I can seem to do is install 1:8.6 using the command: "sudo yum install tk tk-devel tcl tcl-devel" I tried to search for 8.5 using "sudo yum search tk8.5" but that doesn't work or leads me to downloading 8.6. Does xcrysden only support 8.5? I have tried the source code route in which I have to go through and debug header files that lead me to a dead end as well On Wed, Mar 11, 2015 at 3:19 AM, Gavin Abo wrote: > You can try [ http://forums.fedoraforum.org/showthread.php?t=203254 ]: > > yum install tk-devel > > However, the version of tk that it installs might change depending on > what version of Fedora you have. So if it installs a version other than > 8.5, the fedora forum is likely the best place to search or ask on how > to install the 8.5 version. An alternative to using 8.5 would be to try > to compile xcrysden for the tk version that it installs, and the > information at the following links might be helpful: > > http://www.democritos.it/pipermail/xcrysden/2013-February/001331.html > > http://www.linuxquestions.org/questions/linux-software-2/installing-xcrysden-4175449852/ > > On 3/11/2015 1:01 AM, Michael Smith wrote: > > I'm using a fedora. > > > > Michael Goytia > > Undergraduate Research Assistant > > Brigham Young University-Idaho > > goy11002 at byui.edu > > > > > > > >> On Mar 10, 2015, at 11:42 PM, Gavin Abo wrote: > >> > >> It looks like you need to install libtk8.5.so. > >> > >> For example, for Ubuntu, you can see that libtk8.5.so is part of the > >> tk8.5 development package [ > >> http://packages.ubuntu.com/lucid/amd64/tk8.5-dev/filelist ] and would > be > >> installed with "sudo apt-get install tk8.5-dev". > >> > >> Since we do not know what unix you are using, you will have to consult > >> your operating system documentation. Or you might have to look at the Tk > >> documentation [ http://www.tcl.tk/software/tcltk/8.5.html ] depending > on > >> how you need to install for your system. > >> > >>> On 3/10/2015 10:35 PM, Michael Smith wrote: > >>> When I type: ./xcrysden > >>> I get > >>> > >>> "/home/michael/xc/xcrysden-1.5.60-bin-shared/bin/xcrys: error while > loading shared libraries: libtk8.5.so: cannot open shared object file: No > such file or directory" > >>> > >>> Michael Goytia > >>> Undergraduate Research Assistant > >>> Brigham Young University-Idaho > >>> goy11002 at byui.edu > _______________________________________________ > 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/20150311/b939cb81/attachment.htm From gsabo at crimson.ua.edu Wed Mar 11 16:50:48 2015 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Wed, 11 Mar 2015 09:50:48 -0600 Subject: [xcrysden] Trouble installing, running In-Reply-To: References: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> <54FFD5BC.9020609@crimson.ua.edu> <32E195A6-797F-45B8-AD93-5B370E0ABCD2@gmail.com> <550008B3.3060305@crimson.ua.edu> Message-ID: <55006458.4060300@crimson.ua.edu> Yes, the recent binary packages on the xcrysden website were compiled against 8.5, such that they only support 8.5. Have you tried the Semishared binary (xcrysden-1.5.60-linux_x86_64-semishared.tar.gz if your Fedora is 64 bit or xc-1.5.24-linux_x86-semishared.tar.gz if your Fedora is 32 bit) [ http://www.xcrysden.org/Download.html ]? The semishared package is statically linked and includes the tk8.5 library files; so you shouldn't need to install tk8.5 unlike the shared package that it looks like you were trying to use. On 3/11/2015 9:19 AM, Michael Goytia wrote: > Gavin, > > All I can seem to do is install 1:8.6 using the command: > > "sudo yum install tk tk-devel tcl tcl-devel" > > I tried to search for 8.5 using > > "sudo yum search tk8.5" > > but that doesn't work or leads me to downloading 8.6. Does xcrysden > only support 8.5? > > > > I have tried the source code route in which I have to go through and > debug header files that lead me to a dead end as well > > On Wed, Mar 11, 2015 at 3:19 AM, Gavin Abo > wrote: > > You can try [ http://forums.fedoraforum.org/showthread.php?t=203254 ]: > > yum install tk-devel > > However, the version of tk that it installs might change depending on > what version of Fedora you have. So if it installs a version > other than > 8.5, the fedora forum is likely the best place to search or ask on how > to install the 8.5 version. An alternative to using 8.5 would be > to try > to compile xcrysden for the tk version that it installs, and the > information at the following links might be helpful: > > http://www.democritos.it/pipermail/xcrysden/2013-February/001331.html > http://www.linuxquestions.org/questions/linux-software-2/installing-xcrysden-4175449852/ > > On 3/11/2015 1:01 AM, Michael Smith wrote: > > I'm using a fedora. > > > > Michael Goytia > > Undergraduate Research Assistant > > Brigham Young University-Idaho > > goy11002 at byui.edu > > > > > > > >> On Mar 10, 2015, at 11:42 PM, Gavin Abo > wrote: > >> > >> It looks like you need to install libtk8.5.so . > >> > >> For example, for Ubuntu, you can see that libtk8.5.so > is part of the > >> tk8.5 development package [ > >> http://packages.ubuntu.com/lucid/amd64/tk8.5-dev/filelist ] and > would be > >> installed with "sudo apt-get install tk8.5-dev". > >> > >> Since we do not know what unix you are using, you will have to > consult > >> your operating system documentation. Or you might have to look > at the Tk > >> documentation [ http://www.tcl.tk/software/tcltk/8.5.html ] > depending on > >> how you need to install for your system. > >> > >>> On 3/10/2015 10:35 PM, Michael Smith wrote: > >>> When I type: ./xcrysden > >>> I get > >>> > >>> "/home/michael/xc/xcrysden-1.5.60-bin-shared/bin/xcrys: error > while loading shared libraries: libtk8.5.so : > cannot open shared object file: No such file or directory" > >>> > >>> Michael Goytia > >>> Undergraduate Research Assistant > >>> Brigham Young University-Idaho > >>> goy11002 at byui.edu > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150311/e6108909/attachment-0001.htm From goy11002 at gmail.com Wed Mar 11 20:54:59 2015 From: goy11002 at gmail.com (Michael Smith) Date: Wed, 11 Mar 2015 13:54:59 -0600 Subject: [xcrysden] Trouble installing, running In-Reply-To: <55006458.4060300@crimson.ua.edu> References: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> <54FFD5BC.9020609@crimson.ua.edu> <32E195A6-797F-45B8-AD93-5B370E0ABCD2@gmail.com> <550008B3.3060305@crimson.ua.edu> <55006458.4060300@crimson.ua.edu> Message-ID: <9548236A-1006-4793-995F-A2B2652F2AB3@gmail.com> Gavin, I appreciate all your help so far. Seem like your suggestions aren't working for fedora. I can however instal a virtual machine using fedora boxes. What OS would you suggest to install Xcrysden on with less errors? Michael Goytia Undergraduate Research Assistant Brigham Young University-Idaho goy11002 at byui.edu > On Mar 11, 2015, at 9:50 AM, Gavin Abo wrote: > > Yes, the recent binary packages on the xcrysden website were compiled against 8.5, such that they only support 8.5. > > Have you tried the Semishared binary (xcrysden-1.5.60-linux_x86_64-semishared.tar.gz if your Fedora is 64 bit or xc-1.5.24-linux_x86-semishared.tar.gz if your Fedora is 32 bit) [ http://www.xcrysden.org/Download.html ]? The semishared package is statically linked and includes the tk8.5 library files; so you shouldn't need to install tk8.5 unlike the shared package that it looks like you were trying to use. > >> On 3/11/2015 9:19 AM, Michael Goytia wrote: >> Gavin, >> >> All I can seem to do is install 1:8.6 using the command: >> >> "sudo yum install tk tk-devel tcl tcl-devel" >> >> I tried to search for 8.5 using >> >> "sudo yum search tk8.5" >> >> but that doesn't work or leads me to downloading 8.6. Does xcrysden only support 8.5? >> >> >> >> I have tried the source code route in which I have to go through and debug header files that lead me to a dead end as well >> >>> On Wed, Mar 11, 2015 at 3:19 AM, Gavin Abo wrote: >>> You can try [ http://forums.fedoraforum.org/showthread.php?t=203254 ]: >>> >>> yum install tk-devel >>> >>> However, the version of tk that it installs might change depending on >>> what version of Fedora you have. So if it installs a version other than >>> 8.5, the fedora forum is likely the best place to search or ask on how >>> to install the 8.5 version. An alternative to using 8.5 would be to try >>> to compile xcrysden for the tk version that it installs, and the >>> information at the following links might be helpful: >>> >>> http://www.democritos.it/pipermail/xcrysden/2013-February/001331.html >>> http://www.linuxquestions.org/questions/linux-software-2/installing-xcrysden-4175449852/ >>> >>> On 3/11/2015 1:01 AM, Michael Smith wrote: >>> > I'm using a fedora. >>> > >>> > Michael Goytia >>> > Undergraduate Research Assistant >>> > Brigham Young University-Idaho >>> > goy11002 at byui.edu >>> > >>> > >>> > >>> >> On Mar 10, 2015, at 11:42 PM, Gavin Abo wrote: >>> >> >>> >> It looks like you need to install libtk8.5.so. >>> >> >>> >> For example, for Ubuntu, you can see that libtk8.5.so is part of the >>> >> tk8.5 development package [ >>> >> http://packages.ubuntu.com/lucid/amd64/tk8.5-dev/filelist ] and would be >>> >> installed with "sudo apt-get install tk8.5-dev". >>> >> >>> >> Since we do not know what unix you are using, you will have to consult >>> >> your operating system documentation. Or you might have to look at the Tk >>> >> documentation [ http://www.tcl.tk/software/tcltk/8.5.html ] depending on >>> >> how you need to install for your system. >>> >> >>> >>> On 3/10/2015 10:35 PM, Michael Smith wrote: >>> >>> When I type: ./xcrysden >>> >>> I get >>> >>> >>> >>> "/home/michael/xc/xcrysden-1.5.60-bin-shared/bin/xcrys: error while loading shared libraries: libtk8.5.so: cannot open shared object file: No such file or directory" >>> >>> >>> >>> Michael Goytia >>> >>> Undergraduate Research Assistant >>> >>> Brigham Young University-Idaho >>> >>> goy11002 at byui.edu > _______________________________________________ > 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/20150311/2b298bef/attachment.htm From gsabo at crimson.ua.edu Thu Mar 12 10:30:16 2015 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Thu, 12 Mar 2015 03:30:16 -0600 Subject: [xcrysden] Trouble installing, running In-Reply-To: <9548236A-1006-4793-995F-A2B2652F2AB3@gmail.com> References: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> <54FFD5BC.9020609@crimson.ua.edu> <32E195A6-797F-45B8-AD93-5B370E0ABCD2@gmail.com> <550008B3.3060305@crimson.ua.edu> <55006458.4060300@crimson.ua.edu> <9548236A-1006-4793-995F-A2B2652F2AB3@gmail.com> Message-ID: <55015CA8.2000003@crimson.ua.edu> I tried the xcrysden semishared binary package on Fedora 12 installed on a USB stick, and it worked fine for me. If it helps, below are my notes: 1. Go to: https://getfedora.org/en/workstation/download/ 2. Download: Fedora-Live-Workstation-x86_64-21-5.iso 3. Go to: http://linuxliveusb.com/ 4. Download: LinuxLive USB Creator 2.9.2.exe 5. Run: LinuxLive USB Creator 2.9.2.exe a. Click OK b. Click Next c. Click Install d. Click Next e. "Run LinuxLive USB Creator" should be checked, then click Finish 6. In LinuxLive USB Creator: a. For Choose Your Key, select the USB stick b. For Choose a Source, select ISO/IMG/ZIP, and select Fedora-Live-Workstation-x86_64-21-5.iso c. For Persistence, select 2000 MB d. Click the lightning icon to start the creation of the bootable USB stick 7. Boot from the USB stick a. Select persistence mode b. Select Try Fedora 8. Open a terminal and perform the following: [liveuser at localhost ~]$ wget http://www.xcrysden.org/download/xcrysden-1.5.60-linux_x86_64-semishared.tar.gz [liveuser at localhost ~]$ tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz [liveuser at localhost ~]$ cd xcrysden-1.5.60-bin-semishared/scripts/ [liveuser at localhost scripts]$ ./xcConfigure.sh ... Used defaults Do you have a CRYSTAL package ([y]es/[n]o): n Is this correct ([y]es/[n]o): y Would you like to add xcrysden icon to the desktop ([y]es/[n]o): y ... [liveuser at localhost scripts]$ source ~/.bashrc [liveuser at localhost xcrysden-1.5.60-bin-semishared]$ xcrysden ... /home/liveuser/xcrysden-1.5.60-bin-semishared/bin/xcrys: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory ... [liveuser at localhost scripts]$ sudo yum install libXScrnSaver ... Is this ok [y/d/N]: y ... Reference: http://forums.fedoraforum.org/showthread.php?t=296176 [liveuser at localhost xcrysden-1.5.60-bin-semishared]$ xcrysden ... error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory ... liveuser at localhost scripts]$ sudo yum install libquadmath Is this ok [y/d/N]: y [liveuser at localhost scripts]$ xcrysden On 3/11/2015 1:54 PM, Michael Smith wrote: > Gavin, > > I appreciate all your help so far. Seem like your suggestions aren't > working for fedora. I can however instal a virtual machine using > fedora boxes. What OS would you suggest to install Xcrysden on with > less errors? > > Michael Goytia > Undergraduate Research Assistant > Brigham Young University-Idaho > goy11002 at byui.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150312/2a9bb7ab/attachment.htm From mulwawinfred at gmail.com Thu Mar 12 14:47:00 2015 From: mulwawinfred at gmail.com (Winfred Mulwa) Date: Thu, 12 Mar 2015 15:47:00 +0200 Subject: [xcrysden] How to label atoms in a cell Message-ID: Dear all, I am trying to label Cu2+ atom in a supercell. When i press S it labels Cu instead of Cu2+. How do i include the 2+ ? Pls assist. Regards Mulwa Winfred. D Phil Student, Computational Material Science Group, University of the Free State - QwaQwa, South Africa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150312/5dee7b08/attachment.htm From gsabo at crimson.ua.edu Thu Mar 12 21:28:21 2015 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Thu, 12 Mar 2015 14:28:21 -0600 Subject: [xcrysden] How to label atoms in a cell In-Reply-To: References: Message-ID: <5501F6E5.4080002@crimson.ua.edu> You can use the Edit Custom Atom-Labels and Fonts page [ http://www.xcrysden.org/doc/modify.html#__toc__1 ]. On 3/12/2015 7:47 AM, Winfred Mulwa wrote: > Dear all, > I am trying to label Cu2+ atom in a supercell. > When i press S it labels Cu instead of Cu2+. > How do i include the 2+ ? Pls assist. > Regards > Mulwa Winfred. > D Phil Student, Computational Material Science Group, > University of the Free State - QwaQwa, > South Africa. From goy11002 at gmail.com Thu Mar 12 22:11:21 2015 From: goy11002 at gmail.com (Michael Smith) Date: Thu, 12 Mar 2015 15:11:21 -0600 Subject: [xcrysden] Trouble installing, running In-Reply-To: <55015CA8.2000003@crimson.ua.edu> References: <572B3ED5-DA2A-4460-A4BB-FDAAFF636413@gmail.com> <54FFD5BC.9020609@crimson.ua.edu> <32E195A6-797F-45B8-AD93-5B370E0ABCD2@gmail.com> <550008B3.3060305@crimson.ua.edu> <55006458.4060300@crimson.ua.edu> <9548236A-1006-4793-995F-A2B2652F2AB3@gmail.com> <55015CA8.2000003@crimson.ua.edu> Message-ID: <12A92156-D937-400F-85F5-F26822E3BC23@gmail.com> Gavin, Thanks this really helps! I'll Let you if it works ! Michael Goytia Undergraduate Research Assistant Brigham Young University-Idaho goy11002 at byui.edu > On Mar 12, 2015, at 3:30 AM, Gavin Abo wrote: > > I tried the xcrysden semishared binary package on Fedora 12 installed on a USB stick, and it worked fine for me. > > If it helps, below are my notes: > > 1. Go to: https://getfedora.org/en/workstation/download/ > 2. Download: Fedora-Live-Workstation-x86_64-21-5.iso > 3. Go to: http://linuxliveusb.com/ > 4. Download: LinuxLive USB Creator 2.9.2.exe > 5. Run: LinuxLive USB Creator 2.9.2.exe > a. Click OK > b. Click Next > c. Click Install > d. Click Next > e. "Run LinuxLive USB Creator" should be checked, then click Finish > 6. In LinuxLive USB Creator: > a. For Choose Your Key, select the USB stick > b. For Choose a Source, select ISO/IMG/ZIP, and select Fedora-Live-Workstation-x86_64-21-5.iso > c. For Persistence, select 2000 MB > d. Click the lightning icon to start the creation of the bootable USB stick > 7. Boot from the USB stick > a. Select persistence mode > b. Select Try Fedora > 8. Open a terminal and perform the following: > > [liveuser at localhost ~]$ wget http://www.xcrysden.org/download/xcrysden-1.5.60-linux_x86_64-semishared.tar.gz > [liveuser at localhost ~]$ tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz > [liveuser at localhost ~]$ cd xcrysden-1.5.60-bin-semishared/scripts/ > [liveuser at localhost scripts]$ ./xcConfigure.sh > ... > Used defaults > Do you have a CRYSTAL package ([y]es/[n]o): n > Is this correct ([y]es/[n]o): y > Would you like to add xcrysden icon to the desktop ([y]es/[n]o): y > ... > [liveuser at localhost scripts]$ source ~/.bashrc > [liveuser at localhost xcrysden-1.5.60-bin-semishared]$ xcrysden > ... > /home/liveuser/xcrysden-1.5.60-bin-semishared/bin/xcrys: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory > ... > > [liveuser at localhost scripts]$ sudo yum install libXScrnSaver > ... > Is this ok [y/d/N]: y > ... > > Reference: http://forums.fedoraforum.org/showthread.php?t=296176 > > [liveuser at localhost xcrysden-1.5.60-bin-semishared]$ xcrysden > ... > error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory > ... > > liveuser at localhost scripts]$ sudo yum install libquadmath > > Is this ok [y/d/N]: y > > [liveuser at localhost scripts]$ xcrysden > >> On 3/11/2015 1:54 PM, Michael Smith wrote: >> Gavin, >> >> I appreciate all your help so far. Seem like your suggestions aren't working for fedora. I can however instal a virtual machine using fedora boxes. What OS would you suggest to install Xcrysden on with less errors? >> >> Michael Goytia >> Undergraduate Research Assistant >> Brigham Young University-Idaho >> goy11002 at byui.edu > _______________________________________________ > 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/20150312/25625287/attachment.htm From yikim2008 at gmail.com Thu Mar 12 23:32:17 2015 From: yikim2008 at gmail.com (YONG-IL KIM) Date: Thu, 12 Mar 2015 22:32:17 +0000 Subject: [xcrysden] Error:Periodic Table of Elements Message-ID: Dear all, I installed XCrysDen (ver1.5.60) on my MacBook Air with OS x( 10.10.2) There was a problem about the menu, "Periodic Table of Elements". 1) From the menu, (File and Utilies...) when clicking on "Periodic Table of Elements" ========================================= Application Error Error: cannot geometry manager grid inside .a0. f which already has slaves managed by pack cannot geometry manager grid inside .a0. f which already has slaves managed by pack while executing "grid $b" (procedure "ptable" line 108) Invoked from within "ptable ." Invoked from within ". Menu.vmfile.menu.util invoke active"." ("uplevel" body line 1) Invoked from within ""uplevel #0 [list $w invoke active]" (procedure "tk : : MenuInvoke" line 50) Invoked from within "tk : : MenuInvoke .menu.vmfile.menu.util 1" (command bound to event) ========================================= 2) From Atom Coordinates, when clicking on "Periodic Table", Application Error Error: cannot geometry manager grid inside .a0. f which already has slaves managed by pack cannot geometry manager grid inside .a0. f which already has slaves managed by pack while executing "grid $b" (procedure "ptable" line 108) Invoked from within "ptable .atom command ptableSelectionAtomicNumber -variable inp(NAT,1)" Invoked from within ". Atom. f. can.f.fri.frm2_1.b invoke" ("uplevel" body line 1) Invoked from within "uplevel #0 [list $w invoke]" (procedure "tk : : ButtonUp" line 22) Invoked from within "tk : : buttonUp .atom.f.cav.f.fri.frm2_1.b" (command bound to event) ========================================= Please let me know how to fix the problem, Thank you for your attention, Regards, Yong-Il Kim. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150312/2ef7d362/attachment.htm From member at linkedin.com Sun Mar 15 16:30:48 2015 From: member at linkedin.com (Acharya Kandala L N) Date: Sun, 15 Mar 2015 15:30:48 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Andr=C3=A9_Pereira=2C_voc=C3=AA_poderia_me_a?= =?utf-8?q?dicionar_=C3=A0_sua_rede_do_LinkedIn=3F?= Message-ID: <1080773457.1202022.1426433448967.JavaMail.app@lva1-app4669.prod> Ol?, Andr? Pereira. Fa?a parte da minha rede no LinkedIn. Acharya Kandala L N PhD student at Universidad Aut?noma de Madrid Aceitar: http://www.linkedin.com/blink?simpleRedirect=0Sdj8QczwTcPAOdPgRejwOe3ARfkh9rCZFt65QqnpKqioMc3lvcP4PdPANcj8OdzwQdjAUczwVdkAZh4BJpnhF9DdecjtDujBVfnBBiShBsC5EsOoUcBZOpm9JpmRvpnhFtCVFfmJB9ClQqnpKqntBryRQs6lzoS4JoyRJtCVFnSRJrScJr6RBfmtKqmJzon9Q9DtCllAQtmkQk79Ji551fmVBqSZkp6BJ9ClQqnpKinhMpmdzgmZBr3Rx9zwRbmYScSVIojtFbn4MoCMQczRBfP9SbSkLrmZzbCVFp6lHrCBIbDtTtOYLeDdMt7hE&msgID=I5982895486221197313_500&markAsRead= Visualizar o perfil de Acharya Kandala L N: http://www.linkedin.com/blink?simpleRedirect=3oScjgNcP8Sfkh9sClyrmlJ9Btoq54ZrClHrRhEt7lx9ClJomUZpn1Vl6xQtm4Cc30RnPcNcPsVcj4OczoUd3kVe38Uejl9nPgTe3gQdzwOcjRQs6lzoQ5KrSBQonhFtCVF9zwOnT9BoCRBrlZBt6BSrCAZqSkCpnhFtCVFtSlKbmlJomUJoyRJtCVFnSRJrScJr6RBfmtKqmJzon9Q9DtCllAQtmkQk79Ji551fmVBqSZkp6BJ9DpMrzRQ9zwRbmYScSVIojtFbn4MoCMQczRBfP9SbSkLrmZzbCVFp6lHrCBIbDtTtOYLeDdMt7hE&msgID=I5982895486221197313_500&markAsRead= Voc? est? recebendo e-mails sobre Convite. Cancele a inscri??o clicando aqui: http://www.linkedin.com/blink?simpleRedirect=0UdiRLdzdKr64TqiRNc69Id38Zp6BB9Dt2sPtpblgMcR56lQVvrSpMpmB2dk5GjntklDFLpkBJozlicSFUcT5Ap7ppt4Z7qOR8qkESozlBq4RIsTpUh6lTlk51gl5zuD1GdTFkdmMJi551fmhFrSMCe39vsClyrmlJnSlQqnpKqjRHpipBt6BSrCBTpmUJoDlPrDkJpyRJtCVFnSRJrScJr6RBfmtKqmJzon9Q9DtCllAQtmkQk79Ji551fmVBqSZkp6BJ9CVRr3RQ9zwRbmYScSVIojtFbn4MoCMQczRBfP9SbSkLrmZzbCVFp6lHrCBIbDtTtOYLeDdMt7hE&msgID=I5982895486221197313_500&markAsRead=. Este e-mail foi enviado para Andr? Pereira XCrysden (Estudante na Universidade Estadual Paulista 'J?lio de Mesquita Filho'). Saiba por que inclu?mos isso neste link: http://www.linkedin.com/blink?simpleRedirect=0Ue3sQfmh9pmNzqnhOoioUcBZOpm9JpmRvpnhFtCVFfmJB9DtCllAQtmkQk79Ji551fmVBqSZkp6BJ9CNOlmlzqnpOpldOpmRLt7dRoPRx9zwRbmYScSVIojtFbn4MoCMQczRBfP9SbSkLrmZzbCVFp6lHrCBIbDtTtOYLeDdMt7hE&msgID=I5982895486221197313_500&markAsRead= © 2015 LinkedIn Ireland Limited. LinkedIn, a logomarca do LinkedIn e InMail s?o marcas registradas da LinkedIn Corporation nos Estados Unidos e/ou em outros pa?ses. Todos os direitos reservados. LinkedIn ? um nome comercial registrado da LinkedIn Ireland Limited. Registrada na Irlanda como uma empresa Privada e Ltda. Registro n?mero 477441. Registrada em: 70 Sir John Roberson?s Quay, Dublin 2 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150315/5674de39/attachment-0001.htm From member at linkedin.com Tue Mar 17 11:02:36 2015 From: member at linkedin.com (Mourad Boujnah) Date: Tue, 17 Mar 2015 10:02:36 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Andr=C3=A9_Pereira=2C_voc=C3=AA_poderia_me_a?= =?utf-8?q?dicionar_=C3=A0_sua_rede_do_LinkedIn=3F?= Message-ID: <998977964.617132.1426586556557.JavaMail.app@lva1-app5704.prod> Ol?, Andr? Pereira. Fa?a parte da minha rede no LinkedIn. Mourad Boujnah ?tudiant(e) (Universit? Mohammed V) Aceitar: http://www.linkedin.com/blink?simpleRedirect=0Ud3oVdP4Rc3kNczoTcPkPe3ARfkh9rCZFt65QqnpKqioMc3lvd30PczwQcz4Nd3gSdPcRcPwVdkAZh4BJpnhF9Ax4kP5PrQdIfnBBiShBsC5EsOoUcBZOpm9JpmRvpnhFtCVFfmJB9ClQqnpKqntBryRQs6lzoS4JoyRJtCVFnSRJrScJr6RBfmtKqmJzon9Q9DtCllAQtmkQk79Ji551fmVBqSZkp6BJ9ClQqnpKinhMpmdzgmZBr3Rx9D8QbnBNr7cQp3tFbn4MoCMQczRBfP9SbSkLrmZzbCVFp6lHrCBIbDtTtOYLeDdMt7hE&msgID=I5983537644112482304_500&markAsRead= Visualizar o perfil de Mourad Boujnah: http://www.linkedin.com/blink?simpleRedirect=djwRejwPc34Qfkh9sClyrmlJ9DoVhQ4ZrClHrRhEt7lx9ClJomUZpn1Vl6xQtm4Cc30RnPgMcP8Ud38NcjgQdzsPdjcUejl9nPgTe3gQdzwOcjRQs6lzoQ5KrSBQonhFtCVF9zwOnT9BoCRBrlZBt6BSrCAZqSkCpnhFtCVFtSlKbmlJomUJoyRJtCVFnSRJrScJr6RBfmtKqmJzon9Q9DtCllAQtmkQk79Ji551fmVBqSZkp6BJ9DpMrzRQ9D8QbnBNr7cQp3tFbn4MoCMQczRBfP9SbSkLrmZzbCVFp6lHrCBIbDtTtOYLeDdMt7hE&msgID=I5983537644112482304_500&markAsRead= Voc? est? recebendo e-mails sobre Convite. Cancele a inscri??o clicando aqui: http://www.linkedin.com/blink?simpleRedirect=1Od2RVsmNPd6gTqiRNc69Id38Zp6BB9DtkoShiplB9j3BPoldDhk8MtntGkkpDumxRlCBPmj9JcC5MgmVHkCpygktIt5FqpQdyhkN6ujBxdmJAumwNj6VTlk51gl5LinsTklt5lkoSi551fmhFrSMCe39vsClyrmlJnSlQqnpKqjRHpipBt6BSrCBTpmUJoDlPrDkJpyRJtCVFnSRJrScJr6RBfmtKqmJzon9Q9DtCllAQtmkQk79Ji551fmVBqSZkp6BJ9CVRr3RQ9D8QbnBNr7cQp3tFbn4MoCMQczRBfP9SbSkLrmZzbCVFp6lHrCBIbDtTtOYLeDdMt7hE&msgID=I5983537644112482304_500&markAsRead=. Este e-mail foi enviado para Andr? Pereira XCrysden (Estudante na Universidade Estadual Paulista 'J?lio de Mesquita Filho'). Saiba por que inclu?mos isso neste link: http://www.linkedin.com/blink?simpleRedirect=0Ue3sQfmh9pmNzqnhOoioUcBZOpm9JpmRvpnhFtCVFfmJB9DtCllAQtmkQk79Ji551fmVBqSZkp6BJ9CNOlmlzqnpOpldOpmRLt7dRoPRx9D8QbnBNr7cQp3tFbn4MoCMQczRBfP9SbSkLrmZzbCVFp6lHrCBIbDtTtOYLeDdMt7hE&msgID=I5983537644112482304_500&markAsRead= © 2015 LinkedIn Ireland Limited. LinkedIn, a logomarca do LinkedIn e InMail s?o marcas registradas da LinkedIn Corporation nos Estados Unidos e/ou em outros pa?ses. Todos os direitos reservados. LinkedIn ? um nome comercial registrado da LinkedIn Ireland Limited. Registrada na Irlanda como uma empresa Privada e Ltda. Registro n?mero 477441. Registrada em: 70 Sir John Roberson?s Quay, Dublin 2 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150317/57dc4ce3/attachment-0001.htm From charles.goehry at gmail.com Fri Mar 20 13:56:17 2015 From: charles.goehry at gmail.com (Goehry charles) Date: Fri, 20 Mar 2015 12:56:17 +0000 Subject: [xcrysden] xcrysden custom-definitions Message-ID: dear xcrysden users, I'd like to change some defaults in xcrysden, with the use of the custom-definitions file. I could change atom color, default bond lengths, etc, but I was however unsuccessful when trying to show e.g. 2 unit cells in the x-direction. I tried: *set nxdir 2* but it makes no difference. Also, I'd like to display "translational asymmetric unit" by default, as well as "orient to the XZ plane" Thank you in advance for your help. Best regards, Charles -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150320/a844bb0e/attachment.htm From gsabo at crimson.ua.edu Fri Mar 20 19:03:12 2015 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Fri, 20 Mar 2015 12:03:12 -0600 Subject: [xcrysden] xcrysden custom-definitions In-Reply-To: References: Message-ID: <550C60E0.6010702@crimson.ua.edu> Currently, I think it is not possible to adjust nxdir with the custom-definitions file. You could see if changing "set nxdir 1" to "set nxdir 2" in xcInit.tcl in the Tcl directory of xcrysden would work instead for what you want to do or not. On 3/20/2015 6:56 AM, Goehry charles wrote: > dear xcrysden users, > > I'd like to change some defaults in xcrysden, with the use of the > custom-definitions file. > > I could change atom color, default bond lengths, etc, but I was > however unsuccessful when trying to show e.g. 2 unit cells in the > x-direction. I tried: > *set nxdir 2* > but it makes no difference. > > Also, I'd like to display "translational asymmetric unit" by default, > as well as "orient to the XZ plane" > > Thank you in advance for your help. > > Best regards, > > Charles -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150320/593a3afb/attachment.htm