Hi folks, several people that I know of need Swiss Protein Viewer on their boxes. I've tried everything I know, but I run into problems getting it working. http://forums.gentoo.org/viewtopic-t-151152-highlight-spdbv.html http://forums.gentoo.org/viewtopic-t-241165-highlight-spdbv.html I've tried installing via the spdbv install script, but when I try to run it I get: jeff@speedy jeff $ ./SPDBV/bin/spdbv.Linux ./SPDBV/bin/spdbv.Linux: error while loading shared libraries: libXm.so.3: canno t open shared object file: No such file or directory and this may also be useful: jeff@speedy jeff $ ldd ./SPDBV/bin/spdbv.Linux linux-gate.so.1 => (0xffffe000) libX11.so.6 => /emul/linux/x86/usr/lib/libX11.so.6 (0x55583000) libXm.so.3 => not found libXp.so.6 => /emul/linux/x86/usr/lib/libXp.so.6 (0x5564e000) libXt.so.6 => /emul/linux/x86/usr/lib/libXt.so.6 (0x55656000) libXext.so.6 => /emul/linux/x86/usr/lib/libXext.so.6 (0x556aa000) libXi.so.6 => /emul/linux/x86/usr/lib/libXi.so.6 (0x556ba000) libXmu.so.6 => /emul/linux/x86/usr/lib/libXmu.so.6 (0x556c2000) libGL.so.1 => /usr/lib32/opengl/nvidia/lib/libGL.so.1 (0x556d8000) libGLU.so.1 => /emul/linux/x86/usr/lib/libGLU.so.1 (0x55750000) libpthread.so.0 => /lib32/libpthread.so.0 (0x557cd000) libz.so.1 => /emul/linux/x86/lib/libz.so.1 (0x557e0000) libm.so.6 => /lib32/libm.so.6 (0x557f1000) libc.so.6 => /lib32/libc.so.6 (0x55815000) libdl.so.2 => /lib32/libdl.so.2 (0x5592c000) libSM.so.6 => /emul/linux/x86/usr/lib/libSM.so.6 (0x55930000) libICE.so.6 => /emul/linux/x86/usr/lib/libICE.so.6 (0x55939000) libGLcore.so.1 => /usr/lib32/opengl/nvidia/lib/libGLcore.so.1 (0x55950000) libnvidia-tls.so.1 => /usr/lib32/opengl/nvidia/lib/tls/libnvidia-tls.so.1 (0x560a2000) libstdc++.so.6 => /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/32/libstdc++.so.6 (0x560a4000) libgcc_s.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.3/32/libgcc_s.so.1 (0x56172000) /lib/ld-linux.so.2 (0x55555000) The URL for spdbv (a HUGE biosci app) is here: http://www.expasy.org/spdbv/ If anyone can help...thanks!
jeff@speedy jeff $ locate libXm.so.3 /usr/lib/libXm.so.3 /usr/lib/libXm.so.3.0.2 jeff@speedy jeff $ ls -l /usr/lib/libXm.* -rw-r--r-- 1 root root 4214976 Mar 8 21:51 /usr/lib/libXm.a -rwxr-xr-x 1 root root 812 Mar 8 21:51 /usr/lib/libXm.la lrwxrwxrwx 1 root root 14 Mar 8 21:51 /usr/lib/libXm.so -> libXm.so.3.0.2 lrwxrwxrwx 1 root root 14 Mar 8 21:51 /usr/lib/libXm.so.3 -> libXm.so.3.0.2 -rwxr-xr-x 1 root root 2529552 Mar 8 21:51 /usr/lib/libXm.so.3.0.2
Created attachment 82083 [details] a quick mock-up for the 3.7sp5 version So, there is an interest after all? Although having spent some 20 min getting this thing to install in proper places I can see why nobody rushed to prepare an ebuild for it :). Please NOTE!! This is just a quick something! I just wanted to try this viewer since rasmol's handling of large pics seemed suboptimal. I did not pay much attention to getting all the modular X deps correctly (although I added openmotif, as requested on the package install page). I did not care if it install stuff in a "proper" way yet, just that it goes where it makes sense and works.. Oh, and I completely ignored the license issue for now! If somebody wants to pick this up, these 2.5 issues (LICENSE, correct deps on modular X and possibly some cleaning up) have to be get right first. The package works though, I redid the wrapper script and it starts, but tends to not do all directory operations and sometimes crawl at weird places (I guess this is what you get using a precompiled binary prepared against almost ice-age old libs) and not accept some pdb files (what do you know!). Otherwise it performs its primary function of viewing pdb well, but, as usual, ymmv.. George
I might try to fix this up later, but as far as I can tell there are MUCH better applications to do the same thing. SPDBV's glory days are over...(if it ever had any)
(In reply to comment #2) > This is just a quick something! I just wanted to try this viewer since rasmol's > handling of large pics seemed suboptimal. You might want to check out vmd and pymol.
Deep View devs don't seem interested in supporting the Linux platform. With the availability of vmd and pymol, I don't think we'll ever see a decent Linux package for SPDBV in gentoo. Closing.
