[Request] Cn3D

Corex · 2010-03-01 22:27:04

I'll try it tomorrow once i fix the damn vmware to work as i wan't to ^^

rent0n · 2010-03-02 18:33:23

Ok, I have to admit, I'm impressed, guys.

It took me all the morning to compile the whole thing on my Pentium 4 (never compiled for so long in its life, I think), but the program works flawlessy!
And what can I say about the GTK interfcae? Awesome.
It runs a bit slower compared to Rasmol for example but this has probably nothing to do with the packaging.

I just have one question: how it is possible that version number is 4.2 when the latest downloadable binary on the NCBI page is 4.1?

Thank you very much leepesjee and Corex, the Arch Linux community is great.

EDIT: tcsh is installed via pacman as a dependency but it is not required after installing since it shows up with pacman -Qdt, right?

Last edited by rent0n (2010-03-02 18:39:11)

leepesjee · 2010-03-02 20:48:15

Hi rentOn,

Glad that it works!

Yeah, the build time is way too long. We'll see wat we can do about that.
Apparently 4.2 is the latest stable. I don't know why they distribute an older binary.
Indeed tcsh is only a makedepend: needed to make the packagae and not needed afterwards.

Do you still have the source tree around, or used the -L flag with makepkg?
In that case, would you be so kind to report the output of (in the src dir)

grep CFLAGS -A 16 out.confcpp.txt

or (in the start dir)

grep CFLAGS -A 16 cn3d*build.log

Another question: I have copied the full content of the data directory. I know the program wants bstdt.val. Don't know about the rest. I put them there just to be sure. Do you have any idea about these files?

Exactly what do you mean with slow (graphics, pure computing speed ...).
Please feel free to report back any other issues.

@Corex
I found out that the C++ toolkit configure test for the C toolkit does not work well on my x86_64 system (it checks for lib64 on a wrong location). Besides that, it also uses the wrong *mcbi.mk, also because of a wrong test. That did not prevent building a working program. I really begin to wonder if we need the C toolkit at all.

rent0n · 2010-03-03 10:50:57

I'm afraid I don't have the src directory anymore, but I have a very small / (7.5 Gb) and it was almost full after compiling so I removed everything.

I don't know about data, though I think it just contains examples or something like that. I would keep that, you never know.

I mean that moving and rotating the protein is a bit slower and seems more difficult than in Rasmol, where movements are more "natural". However, I think this is related to the program itself.

Again, thank you!

Corex · 2010-03-03 14:56:35

I've haven't worked much because my server needed attention, after i'm done with it i'm back to ncbi ^^

Gonna try to improve the makeflags and shrink the sources since it's rly rly way to big

leepesjee · 2010-03-06 12:48:38

I'm definte now it doesn't need to compile the C-toolbox. We only need the data dir, which does not need compiling. That simplifies things. No tcsh makedepend for instance. Experimented a bit with "--without-..." flags to reduce the memory usage and build time. Still takes quite some time.
Updated the package in aur.

Last edited by leepesjee (2010-03-06 12:50:54)

rent0n · 2010-05-12 08:41:55

leepesjee, despite the fact Cn3D works perfectly, I encountered a problem while trying to install bibus, a reference manager. Basically it has wxgtk as a dependency and this conflicts with wxwidgets-ncbi, so I can't install bibus:

┌─[enrico@beetle][~]
└─[$] aurget -S bibus
resolving dependencies...

warning: the following (3) packages will be installed by pacman: python-pysqlite unixodbc wxpython

searching AUR...

Targets (1): bibus-1.5.1-1 

Proceed with installation? [Y/n] 
:: Retrieving source tarball from AUR...
--2010-05-12 10:33:25--  http://aur.archlinux.org/packages/bibus/bibus.tar.gz
Resolving aur.archlinux.org... 208.92.232.29
Connecting to aur.archlinux.org|208.92.232.29|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 983 [application/x-tgz]
Saving to: `/home/enrico/.aur/bibus.tar.gz'

100%[==============>] 983         --.-K/s   in 0s      

2010-05-12 10:33:30 (76.2 MB/s) - `/home/enrico/.aur/bibus.tar.gz' saved [983/983]

:: Extracting source tarball...
:: Building package...
==> Making package: bibus 1.5.1-1 i686 (Wed May 12 10:33:30 CEST 2010)
==> Checking Runtime Dependencies...
==> Installing missing dependencies...
resolving dependencies...
looking for inter-conflicts...
:: wxgtk conflicts with wxwidgets-ncbi. Remove wxwidgets-ncbi? [Y/n] 
error: failed to prepare transaction (could not satisfy dependencies)
:: cn3d: requires wxwidgets-ncbi
==> ERROR: Pacman failed to install missing dependencies.
error: bibus failed while building, remove source files from /home/enrico/.aur/bibus? [Y/n]

Do you think it is possible to find a reasonable solution to this problem?

Cheers,

leepesjee · 2010-05-12 20:09:33

Hi rentOn,
I also encountered problems like this. In fact, I'm struggling with wxpython as well (which i think is your problem). I tried using provides=('wxgtk') in the wxwidgets-ncbi PKBUILD. This satisfies the wxgtk dependency of wxpython, but I get error messages when try to import wx in python. I think it's some option in the configuration of wxwidgets-ncbi that's missing.
You can try to install wxpython with pacman -d. After this, you will probably be able to install bibus, but i doubt if you can run it. Good thing to do nonetheless, as the error message you get might give a clue about what's missing in the wxwidgets-ncbi build.

rent0n · 2010-05-13 08:20:29

Yes, perfect prediction:
I installed wxpython with the -d option and then bibus.
When I start bibus I get this error:

┌─[enrico@beetle][~]
└─[$] bibus 
Traceback (most recent call last):
  File "/usr/share/bibus/bibus.py", line 43, in <module>
    import wx
  File "/usr/lib/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/__init__.py", line 45, in <module>
    from wx._core import *
  File "/usr/lib/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 4, in <module>
    import _core_
ImportError: libwx_gtk2u_adv-2.8.so.0: cannot open shared object file: No such file or directory

Any ideas?

leepesjee · 2010-05-13 10:48:25

OK, this is as expected.
There seem to be conflicting compile options. The --enable-unicode option is one, but there may be others.
I doubt if it's possible to compile wx, so that it satifies both cn3d and wxpython. Instead of figuring this out this, I made a few changes to the wxwidgets-ncbi package, so that it now installs in /opt/ncbi and doesn't conflict with system-wide installed wx-version anymore, so you can have both wxwidgets-ncbi and wxgtk on your system. Please try the updated version (remove the existing one with pacman -Rd).

After that, you have to make sure that cn3d uses wxwidgets-ncbi in /opt. This can be done the hard way or the easy way. The hard way is to recompile cn3d with options pointing wxwidgets to the right location. Allready tested this and it works. I will update cn3d (which needs some maintainance anyway) on AUR today. The easy way is to make a little change to the cn3d startup script. You have to add a line to /usr/bin/cn3d so that it looks like:

#!/bin/bash
export LD_LIBRARY_PATH=/opt/ncbi/wxwidgets-ncbi/lib
cd /opt/ncbi/bin
./cn3d

You need super-user privileges for that.

rent0n · 2010-05-13 13:50:31

To avoid errors I removed everything related to bibus and cn3d with -Rns.
cn3d now fails to build, I guess because of a syntax error in the PKGBUILD related to dependencies (but I might be wrong):

┌─[enrico@beetle][~]
└─[$] aurget -S cn3d
resolving dependencies...
searching AUR...

Targets (1): cn3d-4.2-4 

Proceed with installation? [Y/n] 
:: Retrieving source tarball from AUR...
--2010-05-13 15:46:55--  http://aur.archlinux.org/packages/cn3d/cn3d.tar.gz
Resolving aur.archlinux.org... 208.92.232.29
Connecting to aur.archlinux.org|208.92.232.29|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2713 (2.6K) [application/x-tgz]
Saving to: `/home/enrico/.aur/cn3d.tar.gz'

100%[==============>] 2,713       --.-K/s   in 0s      

2010-05-13 15:47:00 (77.3 MB/s) - `/home/enrico/.aur/cn3d.tar.gz' saved [2713/2713]

:: Extracting source tarball...
:: Building package...
==> Making package: cn3d 4.2-4 i686 (Thu May 13 15:47:00 CEST 2010)
==> Checking Runtime Dependencies...
==> Installing missing dependencies...
wxwidgets-ncbi>=2.8.10-2 package not found, searching for group...
error: 'wxwidgets-ncbi>=2.8.10-2': not found in sync db
==> ERROR: Pacman failed to install missing dependencies.
error: cn3d failed while building, remove source files from /home/enrico/.aur/cn3d? [Y/n]

leepesjee · 2010-05-13 14:27:44

You choose to go the hard way, I see
It looks you didn't update the wxwidgets-ncbi. You have to do that before starting the cn3d build.
If I wasn't clear: you don't have to recompile. You can also edit the /usr/bin/cn3d script, as I mentioned, with the existing cn3d in place.

rent0n · 2010-05-14 08:47:37

Uhm, I don't get it.
When I try to install wxwidgets-ncbi I get a 404 error:

┌─[enrico@beetle][~]
└─[$] aurget -S wxwidgets-ncbi
resolving dependencies...
searching AUR...

Targets (1): wxwidgets-ncbi-2.8.10-2 

Proceed with installation? [Y/n] 
:: Retrieving source tarball from AUR...
--2010-05-14 10:43:17--  http://aur.archlinux.org/packages/wxwidgets-ncbi/wxwidgets-ncbi.tar.gz
Resolving aur.archlinux.org... 208.92.232.29
Connecting to aur.archlinux.org|208.92.232.29|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 588 [application/x-tgz]
Saving to: `/home/enrico/.aur/wxwidgets-ncbi.tar.gz'

100%[==============>] 588         --.-K/s   in 0s      

2010-05-14 10:43:22 (40.2 MB/s) - `/home/enrico/.aur/wxwidgets-ncbi.tar.gz' saved [588/588]

:: Extracting source tarball...
:: Building package...
==> Making package: wxwidgets-ncbi 2.8.10-2 i686 (Fri May 14 10:43:23 CEST 2010)
==> Checking Runtime Dependencies...
==> Checking Buildtime Dependencies...
==> Retrieving Sources...
  -> Downloading wxWidgets-2.8.10.tar.gz...
--2010-05-14 10:43:23--  http://sourceforge.net/project/wxwindows/wxAll/2.8.10/wxWidgets-2.8.10.tar.gz
Resolving sourceforge.net... 216.34.181.60
Connecting to sourceforge.net|216.34.181.60|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2010-05-14 10:43:28 ERROR 404: Not Found.

==> ERROR: Failure while downloading wxWidgets-2.8.10.tar.gz
    Aborting...
error: wxwidgets-ncbi failed while building, remove source files from /home/enrico/.aur/wxwidgets-ncbi? [Y/n]

EDIT: I get the same error when I try to build it manually but sourceforge.net is up.

Last edited by rent0n (2010-05-14 08:54:14)

leepesjee · 2010-05-14 10:46:53

Ah, I'm sorry. I messed up the download location. It should be ('downloads' was missing):
http://downloads.sourceforge.net/projec … .10.tar.gz
You can change it in the source line in PKGBUILD.
I will update it an AUR also.

leepesjee · 2010-08-21 12:30:54

RentOn,

Did you manage to make it work?
BTW, I just found out that the cn3d build doesn't work properly when called from an internet-browser.
The startup scripts needs a little tweak for that. I updated it in AUR. There's no need to reinstall, just edit the startup script (with su privilages). It should look like:

$ cat /usr/bin/cn3d
#!/bin/bash
cd /opt/ncbi/bin
./cn3d $@

So, the only difference is the addition of $@ to the ./cn3d line.

Arch Linux

#51 2010-03-01 22:27:04

Re: [Request] Cn3D

#52 2010-03-02 18:33:23

Re: [Request] Cn3D

#53 2010-03-02 20:48:15

Re: [Request] Cn3D

#54 2010-03-03 10:50:57

Re: [Request] Cn3D

#55 2010-03-03 14:56:35

Re: [Request] Cn3D

#56 2010-03-06 12:48:38

Re: [Request] Cn3D

#57 2010-05-12 08:41:55

Re: [Request] Cn3D

#58 2010-05-12 20:09:33

Re: [Request] Cn3D

#59 2010-05-13 08:20:29

Re: [Request] Cn3D

#60 2010-05-13 10:48:25

Re: [Request] Cn3D

#61 2010-05-13 13:50:31

Re: [Request] Cn3D

#62 2010-05-13 14:27:44

Re: [Request] Cn3D

#63 2010-05-14 08:47:37

Re: [Request] Cn3D

#64 2010-05-14 10:46:53

Re: [Request] Cn3D

#65 2010-08-21 12:30:54

Re: [Request] Cn3D

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