From s.abouelhasab at gmail.com Sun Aug 5 18:02:21 2018 From: s.abouelhasab at gmail.com (Sarah Gamal) Date: Sun, 5 Aug 2018 18:02:21 +0200 Subject: [xcrysden] error: reading file/tmp/xc_struc.3200 Message-ID: Dear all; I got this error "error: reading file/tmp/xc_struc.3200", and in the details:- can't read "sInfo(ldatagrid2D)": no such variable Any help please? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20180805/81590765/attachment.htm From gsabo at crimson.ua.edu Tue Aug 7 03:34:04 2018 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Mon, 6 Aug 2018 19:34:04 -0600 Subject: [xcrysden] error: reading file/tmp/xc_struc.3200 In-Reply-To: References: Message-ID: <30a2dd7a-fec3-b74a-bac1-ccba6f3e2c94@crimson.ua.edu> Can you send the XCrySDen input file(s) and steps for reproducing the error? What XCrySDen version is giving you that error? Is the account you are logged into have file permissions to write and read to the /tmp directory?? If you don't have file permission to write to /tmp, maybe try changing XCRYSDEN_SCRATCH variable in your .bashrc from "/tmp" to your home directory "/home/username/xcrys_tmp" (where username is replaced by your user name). If the program worked before but it just started happening recently, maybe try using xc_cleanscratch.? As it says on the XCrySDen website: "From time to time clean the scratch directory" [ http://web.mit.edu/xcrysden_v1.5.60/www/XCRYSDEN/doc/install.html ]. Are you using English (en_US.UTF-8) as the locale [ https://docs.fedoraproject.org/en-US/Fedora/24/html/System_Administrators_Guide/ch-System_Locale_and_Keyboard_Configuration.html ]?? It might be that XCrySDen fails to work right for some scripts if non-English locale is used on computer. Are you using "xcrysden --pwi pw.in"? If so, instead of for example: ~/xcrysden-1.5.60-bin-semishared/xcrysden --pwi pw.in What happens if you do it in two different steps instead using pwi2xsf.sh and the xcrysden --xsf option: ~/xcrysden-1.5.60-bin-semishared/scripts/pwi2xsf.sh pw.in ~/xcrysden-1.5.60-bin-semishared/xcrysden --xsf pwi2xsf.xsf_out It doesn't seem to cause me any problems, but maybe it causes problems for others.? In the pwi2xsf.sh file of XCrySDen 1.5.60, you might also try opening this file in a text editor (like gedit) and remove the "\00" seen on line 205 to see if that causes the error to disappear or not. On 8/5/2018 10:02 AM, Sarah Gamal wrote: > Dear all; > I got this error "error: reading file/tmp/xc_struc.3200", and in the > details:- > can't read "sInfo(ldatagrid2D)": no such variable > > Any help please? From vruwink at illinois.edu Tue Aug 21 23:34:08 2018 From: vruwink at illinois.edu (Vruwink, Timothy Roger) Date: Tue, 21 Aug 2018 21:34:08 +0000 Subject: [xcrysden] Xcrysen 1.5.60 Mac GLX issues Message-ID: <30A80A7B-AB8E-4D72-8E81-492415FAA9CA@illinois.edu> Hi - I built Xcrysden 1.5.60 successfully, but am having problems running it. If I ssh over to the server I have it loaded, with X forwarding enabled and type xcrysden & I see XQuartz start to load, but then get the following error: Package ImageMagick's convert: /usr/bin/convert Package ImageMagick's import: /usr/bin/import Package Xwd: /usr/bin/xwd Executing: /software/xcrysden-1.5.60/lib/xcrysden-1.5.60/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: 791 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: 793 Error in startup script: Togl: couldn't get visual while executing "togl .mesa -width 400 -height 400 -ident .mesa -rgba true -redsize 1 -greensize 1 -blu..." (procedure "PlaceGlobWin" line 105) invoked from within "PlaceGlobWin 0 [expr round(650 * $fac1)] [expr round(650 * $fac1)]" (procedure "ViewMol" line 25) invoked from within "ViewMol ." invoked from within "if { [llength $argv] > 2 } { parseComLinArg [lrange $argv 2 end] } else { ViewMol . }" (file "/software/xcrysden-1.5.60/share/xcrysden-1.5.60/Tcl/xcInit.tcl" line 609) X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 12 ResourceID in failed request: 0xffffffff Serial number of failed request: 796 Both GLXinfo and GLXgears work as expected. If I try the same from a Windows machine - with X forwarding , xcrysden works as expected. Any ideas what?s going on? Thanks Tim From gsabo at crimson.ua.edu Wed Aug 22 02:33:52 2018 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Tue, 21 Aug 2018 18:33:52 -0600 Subject: [xcrysden] Xcrysen 1.5.60 Mac GLX issues In-Reply-To: <30A80A7B-AB8E-4D72-8E81-492415FAA9CA@illinois.edu> References: <30A80A7B-AB8E-4D72-8E81-492415FAA9CA@illinois.edu> Message-ID: <8435b637-6228-5f00-e2f4-9b19099515d1@crimson.ua.edu> Have you tried adjusting the Togl options like what is mentioned in the following two posts: http://www.democritos.it/pipermail/xcrysden/2016-October/001851.html http://www.democritos.it/pipermail/xcrysden/2016-October/001852.html On 8/21/2018 3:34 PM, Vruwink, Timothy Roger wrote: > Hi - > > I built Xcrysden 1.5.60 successfully, but am having problems running it. > If I ssh over to the server I have it loaded, with X forwarding enabled and type xcrysden & > I see XQuartz start to load, but then get the following error: > > Package ImageMagick's convert: /usr/bin/convert > Package ImageMagick's import: /usr/bin/import > Package Xwd: /usr/bin/xwd > Executing: /software/xcrysden-1.5.60/lib/xcrysden-1.5.60/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: 791 > 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: 793 > Error in startup script: Togl: couldn't get visual > while executing > "togl .mesa -width 400 -height 400 -ident .mesa -rgba true -redsize 1 -greensize 1 -blu..." > (procedure "PlaceGlobWin" line 105) > invoked from within > "PlaceGlobWin 0 [expr round(650 * $fac1)] [expr round(650 * $fac1)]" > (procedure "ViewMol" line 25) > invoked from within > "ViewMol ." > invoked from within > "if { [llength $argv] > 2 } { > parseComLinArg [lrange $argv 2 end] > } else { > ViewMol . > }" > (file "/software/xcrysden-1.5.60/share/xcrysden-1.5.60/Tcl/xcInit.tcl" line 609) > X Error of failed request: BadWindow (invalid Window parameter) > Major opcode of failed request: 12 > ResourceID in failed request: 0xffffffff > Serial number of failed request: 796 > > Both GLXinfo and GLXgears work as expected. > > If I try the same from a Windows machine - with X forwarding , xcrysden works as expected. > > Any ideas what?s going on? > > Thanks > > Tim From matic.poberznik at gmail.com Wed Aug 22 09:23:50 2018 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Wed, 22 Aug 2018 09:23:50 +0200 Subject: [xcrysden] Xcrysen 1.5.60 Mac GLX issues In-Reply-To: <30A80A7B-AB8E-4D72-8E81-492415FAA9CA@illinois.edu> References: <30A80A7B-AB8E-4D72-8E81-492415FAA9CA@illinois.edu> Message-ID: <9073de08-ce11-d62c-122e-01e52d66cdfa@gmail.com> Dear Tim, a google search yielded this workaround: https://superuser.com/questions/203587/remotely-connecting-to-ubuntu-server-from-a-macbook-cant-run-pymol Have you tried this already? I would however suggest to run xcrysden locally on a mac (it works much faster that way) and I seem to recall that installation via macports is pretty straightforward, though I can't try it at the momemnt. Best Regards, Matic -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia From gsabo at crimson.ua.edu Wed Aug 22 14:17:04 2018 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Wed, 22 Aug 2018 06:17:04 -0600 Subject: [xcrysden] Xcrysen 1.5.60 Mac GLX issues In-Reply-To: <9073de08-ce11-d62c-122e-01e52d66cdfa@gmail.com> References: <30A80A7B-AB8E-4D72-8E81-492415FAA9CA@illinois.edu> <9073de08-ce11-d62c-122e-01e52d66cdfa@gmail.com> Message-ID: FYI, the following post might be helpful for the local macports install: http://www.democritos.it/pipermail/xcrysden/2015-October/001752.html On 8/22/2018 1:23 AM, Matic Poberznik wrote: > Dear Tim, > > a google search yielded this workaround: > > https://superuser.com/questions/203587/remotely-connecting-to-ubuntu-server-from-a-macbook-cant-run-pymol > > Have you tried this already? > > I would however suggest to run xcrysden locally on a mac (it works much > faster that way) and I seem to recall that installation via macports is > pretty straightforward, though I can't try it at the momemnt. > > Best Regards, > > Matic > -------------- next part -------------- An HTML attachment was scrubbed... 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