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#1 2010-02-18 18:19:32

rent0n
Member
From: Italy
Registered: 2009-10-29
Posts: 457
Website

Help me with Cn3D!

Hi there,

I'm a biologist and I would need to install Cn3D, a program to visualize protein structures, on my i686 Arch Linux laptop I use in the lab.
Basically there are both a UNIX version and a Windows version but I can't use any of them.

Regarding the UNIX version it is just an executable, so there's nothing to install. However it returns me an error because it searches for libgtk1, and can't find it. It also probably uses very old libjpg, libpng and libtiff. It is possible to run this on Arch in some way?

The Windows version is a .msi file, so I tried to open it with msiexec Cn3d but I get a lot of errors also in this case. I'll post the exact errors in this post as soon as I am back to the lab.

In the meanwhile, has someone got any hints? I really need that program! sad
[Also, if someone would like to make a PKGBUILD and put it in the AUR, that would be much appreciated!]

Thanks! smile


rent0n@deviantART | rent0n@bitbucket | rent0n@identi.ca | LRU #337812
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#2 2010-02-18 19:17:00

test1000
Member
Registered: 2005-04-03
Posts: 834

Re: Help me with Cn3D!

unless running the windows version through wine isn't an option then you could probably get the linux version to run by installing this: "Requires system-installed shared libraries of GTK 1.2.7 - 1.2.10, and standard image libraries (libpng, libz, libjpeg, libtiff)."

in your home directory for example. If you are lucky it will just be a question of downloading the correct version of the libraries(the one the apps complains it needs...), passing the right dir to the ./configure script and make install in the right dir... then you would have to load the program or webbrowser or whatever like this: export LD_PRELOAD=lib1:lib2:... PROGRAMNAME

(im not sure about the way to seperate entries with LD_PRELOAD... you could also have many export LD_PRELOAD lines ofc)

you could also try to email the people who make the app and request a recompile/fix of their app.. i imagine gtk1 is pretty old and unsupported now..


KISS = "It can scarcely be denied that the supreme goal of all theory is to make the irreducible basic elements as simple and as few as possible without having to surrender the adequate representation of a single datum of experience." - Albert Einstein

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#3 2010-02-19 14:36:12

rent0n
Member
From: Italy
Registered: 2009-10-29
Posts: 457
Website

Re: Help me with Cn3D!

It seems very complicated...however the program has no installation, the file itself is an executable. Where can I find these old libraries for arch?

Here are the errors I was talking about:

UNIX version:

./Cn3D 
./Cn3D: error while loading shared libraries: libgtk-1.2.so.0: cannot open shared object file: No such file or directory

Windows version:

msiexec Cn3D.msi
wine: Unhandled privileged instruction at address 0x651e1a (thread 0017), starting debugger...
Unhandled exception: privileged instruction in 32-bit code (0x00651e1a).
Register dump:
 CS:0073 SS:007b DS:007b ES:007b FS:0033 GS:003b
 EIP:00651e1a ESP:0064e728 EBP:00651e1a EFLAGS:00010206(  R- --  I   - -P- )
 EAX:00000000 EBX:b76360fc ECX:00131128 EDX:0064e9a0
 ESI:7efff774 EDI:b76365a0
Stack dump:
0x0064e728:  006de662 0064e738 00000246 7efff774
0x0064e738:  0064e9c8 b7634dad b76365a0 0064e9a0
0x0064e748:  001311b0 0064e9ac 00131068 0064e9a8
0x0064e758:  00000040 00000000 00000000 00000000
0x0064e768:  0000004c 7ffd0000 b7587018 00000002
0x0064e778:  0064e820 00131068 00000000 0064e9a0
Backtrace:
=>0 0x00651e1a in hardlock.sys (+0x1e1a) (0x00651e1a)
0x00651e1a: movl    %cr4,%esi
Modules:
Module    Address            Debug info    Name (29 modules)
PE      650000-  6f7400    Export          hardlock.sys
ELF    7bf00000-7bf03000    Deferred        <wine-loader>
ELF    7ea5e000-7ea74000    Deferred        hal<elf>
  \-PE    7ea60000-7ea74000    \               hal
ELF    7ea74000-7ea87000    Deferred        comm.drv16.so
PE    7ea80000-7ea87000    Deferred        comm.drv16
ELF    7ea87000-7ea9a000    Deferred        system.drv16.so
PE    7ea90000-7ea9a000    Deferred        system.drv16
ELF    7ea9a000-7eb36000    Deferred        krnl386.exe16.so
PE    7eab0000-7eb36000    Deferred        krnl386.exe16
ELF    7eb36000-7eb71000    Deferred        ntoskrnl<elf>
  \-PE    7eb40000-7eb71000    \               ntoskrnl
ELF    7eb71000-7ebdf000    Deferred        rpcrt4<elf>
  \-PE    7eb80000-7ebdf000    \               rpcrt4
ELF    7ebdf000-7ec35000    Deferred        advapi32<elf>
  \-PE    7ebf0000-7ec35000    \               advapi32
ELF    7ec35000-7ec41000    Deferred        libnss_files.so.2
ELF    7edf2000-7ef28000    Deferred        kernel32<elf>
  \-PE    7ee00000-7ef28000    \               kernel32
ELF    7ef28000-7ef4e000    Deferred        libm.so.6
ELF    7ef4e000-7f000000    Deferred        ntdll<elf>
  \-PE    7ef60000-7f000000    \               ntdll
ELF    b74bd000-b74c1000    Deferred        libdl.so.2
ELF    b74c1000-b7608000    Deferred        libc.so.6
ELF    b7608000-b7621000    Deferred        libpthread.so.0
ELF    b7623000-b7637000    Deferred        winedevice<elf>
  \-PE    b7630000-b7637000    \               winedevice
ELF    b7637000-b7772000    Deferred        libwine.so.1
ELF    b7773000-b7791000    Deferred        ld-linux.so.2
Threads:
process  tid      prio (all id:s are in hex)
00000008 ntdll.dll
    00000009    0
0000000a wineboot.exe
    0000000b    0
0000000c winemenubuilder.exe
    0000000d    0
0000000e services.exe
    00000016    0
    00000015    0
    00000014    0
    00000010    0
    0000000f    0
00000011 (D) C:\windows\system32\winedevice.exe
    00000017    0 <==
    00000013    0
    00000012    0
Backtrace:
=>0 0x00651e1a in hardlock.sys (+0x1e1a) (0x00651e1a)
Usage:
  Install a product:
    msiexec {package|productcode} [property]
    msiexec /i {package|productcode} [property]
    msiexec /package {package|productcode} [property]
    msiexec /a package [property]
  Repair an installation:
    msiexec /f[p|o|e|d|c|a|u|m|s|v] {package|productcode}
  Uninstall a product:
    msiexec /x {package|productcode} [property]
  Advertise a product:
    msiexec /j[u|m] package [/t transform] [/g languageid]
    msiexec {u|m} package [/t transform] [/g languageid]
  Apply a patch:
    msiexec /p patchpackage [property]
    msiexec /p patchpackage /a package [property]
  Modifiers for above operations:
    msiexec /l[*][i|w|e|a|r|u|c|m|o|p|v|][+|!] logfile
    msiexec /q{|n|b|r|f|n+|b+|b-}
  Register a module:
    msiexec /y module
  Unregister a module:
    msiexec /z module
  Display usage and copyright:
    msiexec {/h|/?}
NOTE: Product code on commandline unimplemented as of yet

Copyright 2004 Vincent Béron

Any hints for the windows version?

Thanks! smile


rent0n@deviantART | rent0n@bitbucket | rent0n@identi.ca | LRU #337812
aspire: Acer Aspire 5920 Arch Linux x86_64 | beetle: Gericom Beetle G733 Arch Linux i686

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#4 2010-02-19 14:43:12

test1000
Member
Registered: 2005-04-03
Posts: 834

Re: Help me with Cn3D!

have you tried:

wine Cn3D.msi

?


KISS = "It can scarcely be denied that the supreme goal of all theory is to make the irreducible basic elements as simple and as few as possible without having to surrender the adequate representation of a single datum of experience." - Albert Einstein

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#5 2010-02-19 14:43:29

Allan
Pacman
From: Brisbane, AU
Registered: 2007-06-09
Posts: 11,365
Website

Re: Help me with Cn3D!

rent0n wrote:
./Cn3D 
./Cn3D: error while loading shared libraries: libgtk-1.2.so.0: cannot open shared object file: No such file or directory
pacman -S gtk

Do a "readelf -d <binary>" to see what other libraries you need.  libjpeg is probably libjpeg6 from the AUR.

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#6 2010-02-19 15:52:11

rent0n
Member
From: Italy
Registered: 2009-10-29
Posts: 457
Website

Re: Help me with Cn3D!

@test1000: that command gives me th same output as msiexec...

Allan wrote:
rent0n wrote:
./Cn3D 
./Cn3D: error while loading shared libraries: libgtk-1.2.so.0: cannot open shared object file: No such file or directory
pacman -S gtk

Do a "readelf -d <binary>" to see what other libraries you need.  libjpeg is probably libjpeg6 from the AUR.

The gtk issue is solved installing gtk. Now it complains about libpng.so.2: I tried installing libpng12 from AUR but doesn't help. Symlinking libpng.so to libpng.so.2 makes the program start but it exits with "Illegal Instruction".

This is the output of readelf -d Cn3D:

Dynamic section at offset 0xeef438 contains 37 entries:
  Tag        Type                         Name/Value
 0x00000001 (NEEDED)                     Shared library: [libgtk-1.2.so.0]
 0x00000001 (NEEDED)                     Shared library: [libgdk-1.2.so.0]
 0x00000001 (NEEDED)                     Shared library: [libgmodule-1.2.so.0]
 0x00000001 (NEEDED)                     Shared library: [libglib-1.2.so.0]
 0x00000001 (NEEDED)                     Shared library: [libdl.so.2]
 0x00000001 (NEEDED)                     Shared library: [libXi.so.6]
 0x00000001 (NEEDED)                     Shared library: [libXext.so.6]
 0x00000001 (NEEDED)                     Shared library: [libX11.so.6]
 0x00000001 (NEEDED)                     Shared library: [libm.so.6]
 0x00000001 (NEEDED)                     Shared library: [libpng.so.2]
 0x00000001 (NEEDED)                     Shared library: [libjpeg.so.62]
 0x00000001 (NEEDED)                     Shared library: [libtiff.so.3]
 0x00000001 (NEEDED)                     Shared library: [libz.so.1]
 0x00000001 (NEEDED)                     Shared library: [libpthread.so.0]
 0x00000001 (NEEDED)                     Shared library: [libc.so.6]
 0x0000000f (RPATH)                      Library rpath: [/home/paul/Programs/c++/GCC-Release/lib]
 0x0000000c (INIT)                       0x837b63c
 0x0000000d (FINI)                       0x8bd5d40
 0x00000004 (HASH)                       0x8048128
 0x00000005 (STRTAB)                     0x81223fc
 0x00000006 (SYMTAB)                     0x808d4fc
 0x0000000a (STRSZ)                      2379288 (bytes)
 0x0000000b (SYMENT)                     16 (bytes)
 0x00000015 (DEBUG)                      0x0
 0x00000003 (PLTGOT)                     0x8f38b28
 0x00000002 (PLTRELSZ)                   5872 (bytes)
 0x00000014 (PLTREL)                     REL
 0x00000017 (JMPREL)                     0x8379f4c
 0x00000011 (REL)                        0x8379cec
 0x00000012 (RELSZ)                      608 (bytes)
 0x00000013 (RELENT)                     8 (bytes)
 0x6ffffffc (VERDEF)                     0x8379bf4
 0x6ffffffd (VERDEFNUM)                  2
 0x6ffffffe (VERNEED)                    0x8379c2c
 0x6fffffff (VERNEEDNUM)                 3
 0x6ffffff0 (VERSYM)                     0x8367214
 0x00000000 (NULL)                       0x0

Any hints?


rent0n@deviantART | rent0n@bitbucket | rent0n@identi.ca | LRU #337812
aspire: Acer Aspire 5920 Arch Linux x86_64 | beetle: Gericom Beetle G733 Arch Linux i686

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#7 2010-02-19 17:31:52

Runiq
Member
From: Germany
Registered: 2008-10-29
Posts: 1,053

Re: Help me with Cn3D!

I haven't used this program before, but from what I've seen it looks similar to PyMOL. If that looks useful to you, you can find it in the AUR.

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#8 2010-02-21 20:56:45

rent0n
Member
From: Italy
Registered: 2009-10-29
Posts: 457
Website

Re: Help me with Cn3D!

Thanks but Cn3D is a bit different from other protein visualization softwares because it is mainly aimed at biologists and not at chemists...
I also use Rasmol, which is very similar to Pymol, but I really would need to use Cn3D for its peculiar features...

Ubuntu has a ncbi-x11-tools package that works out of the box... How can I have a working Cn3D on Arch?

Help please smile


rent0n@deviantART | rent0n@bitbucket | rent0n@identi.ca | LRU #337812
aspire: Acer Aspire 5920 Arch Linux x86_64 | beetle: Gericom Beetle G733 Arch Linux i686

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#9 2010-02-21 21:07:46

graysky
Wiki Maintainer
From: :wq
Registered: 2008-12-01
Posts: 10,595
Website

Re: Help me with Cn3D!

Might wanna post a request to the AUR package requests forum.  Someone might make you a PKGBUILD.


CPU-optimized Linux-ck packages @ Repo-ck  • AUR packagesZsh and other configs

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#10 2010-02-21 21:46:03

rent0n
Member
From: Italy
Registered: 2009-10-29
Posts: 457
Website

Re: Help me with Cn3D!


rent0n@deviantART | rent0n@bitbucket | rent0n@identi.ca | LRU #337812
aspire: Acer Aspire 5920 Arch Linux x86_64 | beetle: Gericom Beetle G733 Arch Linux i686

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#11 2010-02-22 04:17:50

leepesjee
Member
Registered: 2008-11-06
Posts: 57

Re: Help me with Cn3D!

I might want to have a go at this. I've just been making an update to the rasmol PKGBUILD, so i'am into molecular visualisation anyway.
Don't know if it will come out handy in a PKGBUILD, as it seems you need to create a build environment with ncbi C and C++ toolkits first. I'll just try to build something that works first.

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#12 2010-02-22 10:54:00

rent0n
Member
From: Italy
Registered: 2009-10-29
Posts: 457
Website

Re: Help me with Cn3D!

That would be great!
I'm sorry I don't have the skills (nor the time actually) to do this kind of work, but I can help in testing the package.

Thank you, also for the work on Rasmol (I left a comment on the AUR page, because there seem to be some dependencies problems).


rent0n@deviantART | rent0n@bitbucket | rent0n@identi.ca | LRU #337812
aspire: Acer Aspire 5920 Arch Linux x86_64 | beetle: Gericom Beetle G733 Arch Linux i686

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