Bug 90105 – swiss-pdbviewer requested

• Product: Gentoo Linux
• Status: RESOLVED WONTFIX

[Description Jeffrey Gardner (RETIRED) 2005-04-23 02:00:36 UTC]

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!

[Comment 1 Jeffrey Gardner (RETIRED) 2005-04-23 02:08:21 UTC]

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

[Comment 2 George Shapovalov (RETIRED) 2006-03-14 02:29:00 UTC]

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

[Comment 3 Jeffrey Gardner (RETIRED) 2006-03-14 04:31:57 UTC]

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)

[Comment 4 Donnie Berkholz (RETIRED) 2006-03-14 13:47:46 UTC]

(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.

[Comment 5 Jeffrey Gardner (RETIRED) 2006-10-16 21:41:51 UTC]

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.