BioBlender now released!

An open space where people who use Blender in an academic environment can share progress and the typical problems and needs of academic environments.

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MonZop
Posts: 25
Joined: Wed Dec 16, 2009 9:51 am
Location: Pisa

BioBlender now released!

Postby MonZop » Mon Oct 04, 2010 3:55 pm

We have built a version of Blender for biologists, and we wish to have people using and telling us what they think, if it works, what else can be useful etc.
With Bioblender people can move proteins (using the game engine) and show them in a photorealistic way, with their physical properties mapped to the surface.

You are welcome to download from here and let us know.

Xalt
Posts: 8
Joined: Fri Dec 18, 2009 1:11 pm
Location: The Netherlands

Postby Xalt » Fri Oct 15, 2010 5:02 pm

Hi Monica,

Great, I'm definately gonna try it out soon! I saw you are also speaking about this at the conference. Unfortunately I won't be attending the conference this time :( I hope they're putting the talks on internet again so I can watch afterwards. Anyways I wish you good luck with your talk and work!

Leonard

pep
Posts: 32
Joined: Wed Dec 16, 2009 7:58 pm
Location: Costa Rica

Postby pep » Fri Oct 15, 2010 8:30 pm

When i saw "BioBlender released" i wanted to try it immediately, then i realized it was a Windows version and that there will be an exposition on BioBlender at the conference. So i postponed my test.

Today, reading the new post, i noticed you welcomed feedback.
So even if i run on Linux, i downloaded BioBlender to have a peek, but... :( it doesn't run on my machine.

OpenSuse 11.2 64bit and WIne 1.3.2 seems to dislike it.

I had a look at the scripts directory with the idea that if "BioBlender is simply a regular Blender 2.53 Beta binary release with a few custom scripts and data files" i could manage to move scripts and data to a working version of Blender 2.53, but in

BioBlender02/Bin/2.53/scripts/ui/BioBlender/bin/

i find apbs.exe and scivis.exe that are obviously windows applications.

So before i start a long struggle (i am a perpetual newbie in computing) what do you think:

better waiting conference and/or Linux version
or
try to make my Frankenstein version of BioBlender and ask for help in the journey?

ciao
Pep

TiZeta
Posts: 20
Joined: Tue Nov 29, 2005 2:53 pm
Location: Italy

Postby TiZeta » Mon Oct 18, 2010 1:23 pm

Hi Pep!
I can only tell you that in Ubuntu Lucid it works 100% under Wine.
But, for example, it doesn't work in Jaunty, the older one.
Wine must be at least 1.2, and this is you case, 1.3... so I think I need more information.

If you run it from console (open console -> go to the folder containg Bioblender - and type

Code: Select all

wine blender.exe

)
what's the error message that you get?
:)

pep
Posts: 32
Joined: Wed Dec 16, 2009 7:58 pm
Location: Costa Rica

Postby pep » Mon Oct 18, 2010 4:21 pm

Hi TiZeta
this is the console output in the attempt of running wine+bioblender

pep@linux-sf6t:~/Download/BioBlender02/Bin> wine ./blender.exe
fixme:actctx:parse_depend_manifests Could not find dependent assembly L"Microsoft.VC90.CRT" ( 9.0.21022.8 )
fixme:system:SetProcessDPIAware stub!
found bundled python: Z:\home\pep\Download\BIOB~3UI\Bin\2.53\python
wine: Unhandled page fault on read access to 0x00000000 at address 0x7cbb087d (thread 0009), starting debugger...

then blender open his windows and wine put out a error message.
Mysterious enough to me; any suggestion ?
thanks for your help
pep

TiZeta
Posts: 20
Joined: Tue Nov 29, 2005 2:53 pm
Location: Italy

Postby TiZeta » Mon Oct 18, 2010 5:52 pm

Try the solution here:
http://ubuntuforums.org/showthread.php?t=847535
It is basically winetricks, a script that downloads and installs some wine stuff.
Among all, it contains a windows runtime library that seems to be the solution to this problem, vcrun2008.
Let us know if it works!
:)

pep
Posts: 32
Joined: Wed Dec 16, 2009 7:58 pm
Location: Costa Rica

Postby pep » Mon Oct 18, 2010 6:17 pm

ok, i downloaded winetricks and run it but what i get is

pep@linux-sf6t:~/bin/BioBlender02> su
Password:
linux-sf6t:/home/pep/bin/BioBlender02 # ./winetricks
bash: ./winetricks: Permission denied
linux-sf6t:/home/pep/bin/BioBlender02 # ./winetricks
wine: created the configuration directory '/root/.wine'
wine: configuration in '/root/.wine' has been updated.
zenity: symbol lookup error: zenity: undefined symbol: g_malloc_n
linux-sf6t:/home/pep/bin/BioBlender02 #

and... stuck again :roll:

sure there is no way to just move the scripts?

thanks TiZeta
ciao
Pep

TiZeta
Posts: 20
Joined: Tue Nov 29, 2005 2:53 pm
Location: Italy

Postby TiZeta » Mon Oct 18, 2010 7:27 pm

i think you have to do something like

Code: Select all

./winetricks vcrun2008

the zenity error should be related to the dialog box that pops out if you don't give command line arguments. So if you avoid the dialog maybe it will work.

Copying the scripts directly will let you with a very slow and functionally limited BioBlender. In fact, the exe itself has been patched for speed (so it's not exactly the standard blender25) and in addition some of the modules that the program calls, only work in windows :( ....
:)

pep
Posts: 32
Joined: Wed Dec 16, 2009 7:58 pm
Location: Costa Rica

Postby pep » Mon Oct 18, 2010 8:05 pm

As you say, writing

./winetricks vcrun2008

worked, so let's forget zenity for now.
Machine started downloading, windows installer installed and i can't say for sure that everything went well because in the console there was a lot of text.

I started wine ./blender.exe and i get the same error

fixme:actctx:parse_depend_manifests Could not find dependent assembly L"Microsoft.VC90.CRT" ( 9.0.21022.8 )
fixme:system:SetProcessDPIAware stub!

i tried fixing up in wine+windows the archive, then disinstalled and reinstalled, but the error stay there and Bioblender don't want to start. :(

The only new thing is that when i close the frozen window i find in the console a long report of the error.

It starts with

wine: Unhandled page fault on read access to 0x00000000 at address 0x7cb9c87d (thread 0009), starting debugger...
Unhandled exception: page fault on read access to 0x00000000 in 32-bit code (0x7cb9c87d).

(...) and finish with
Backtrace:
=>0 0x7cb9c87d _wgetenv+0x3d() in msvcrt (0x01adf94c)
err:seh:raise_exception Unhandled exception code c0000005 flags 0 addr 0xf7545306
wine client error:9: write: Bad file descriptor

If you are interested in the whole report, maybe 150 lines, as it seems to be reproducible, i can post it.

... But why it keeps complaining

Could not find dependent assembly L"Microsoft.VC90.CRT"

if i just installed it?

Mysterious :roll:

ciao
Pep

TiZeta
Posts: 20
Joined: Tue Nov 29, 2005 2:53 pm
Location: Italy

Postby TiZeta » Tue Oct 19, 2010 3:59 pm

Uhm, i'm out of ideas by now...
Something you could try:
You use Wine 1.3, the developement version. Do you need it for some specific reason? It's surely more up-to-date than 1.2 but as a developement version, it could be buggy or unstable. One solution could be to use stable version of Wine, 1.2.

As very last thing, you could try a live CD containing wine by default. Linspire and Knoppix should have it. In this case, however, videocard driver could be a problem, for 3D acceletation. As far as I rememember, Knoppix had a way to overcome this problem. This would let you try a different Wine version without touching your current installation at all.
:)

TiZeta
Posts: 20
Joined: Tue Nov 29, 2005 2:53 pm
Location: Italy

Postby TiZeta » Tue Oct 19, 2010 5:16 pm

Stop!
Maybe we've found the solution.
Even in Lucid Lynx, if installed "out of the box" it gives the same error as yours.
We have solved in this way:
Downloaded and installed the windows 32 bit version * (to see if that worked), then ran the installer with wine. This starts the installation of stable Blender on you Wine installation, but it's non what we are interested in.
The installer will bring you to a microsoft webpage: from there, download vcredist_x86.exe and run it with wine: this solved the problem with Bioblender too.
In my case, vcredist_x86.exe was probably already installed for some reason.

* this one:
http://www.blender.org/dl/http://downlo ... indows.exe
:)

pep
Posts: 32
Joined: Wed Dec 16, 2009 7:58 pm
Location: Costa Rica

Postby pep » Thu Oct 21, 2010 5:20 am

... so i downloaded 32bit windows version of Blender and, as you said, it installed vcredist_x86.exe. It complained also for a python absence but i didn't care (blender works even with the internal subset, isn't it ?) and then i could start blender 49b that seems to run flawless - i didn't test too much just see if menus were there and the cube rotate etc. -

What i wanted to test is bioblender so i fired the version i had installed before and it dosn't work :( it comes out with the same Microsoft.VC90.CRT error.

Looking for downgrading wine to 1.2 give an interesting result: there is no easy way to do it in SUSE 11.2.

So right now my point is: blender 2.49b and wine works fine
bioblender and wine don't.

I can update to SUSE 11.3, can switch to Ubuntu or even look for a windows machine :shock: but if you have any spare idea i'll appreciate it.

Thanks for your patience TiZeta

TiZeta
Posts: 20
Joined: Tue Nov 29, 2005 2:53 pm
Location: Italy

workaround for Mac and Linux

Postby TiZeta » Tue Feb 22, 2011 11:28 am

we must thank Eric for this:

workaround for Mac and Linux


1. install wine (tutorial here for mac users: davidbaumgold.com/tutorials/wine-mac/)
2. go to blender.org and download the 2.49 windows release
3. run blender 2.49 installer in wine (again, see tutorial above for mac). choose to put application data in installation directory.
4. it will prompt for dll installation, go to the website and download the .exe from Microsoft.
5. run the downloaded exe in wine again, and there should be no problem installing the dll.
6. after this you can delete the blender2.49
7. you can now run bioblender in Mac OSX or Linux.

Yeah!! :D
:)

Guavajelly
Posts: 1
Joined: Wed Jun 15, 2011 11:20 pm

Postby Guavajelly » Wed Jun 15, 2011 11:47 pm

Hi I am trying to run Bioblender on a machine running Windows 7 (32-bit). I have installed all required parts (Numpy, Pymol, Python 2.5, and Visual C++ Runtime library) but when I go and run the .exe file it begins to start up and then crashes. The first couple time the Command line window had a few lines of text, but now it doesnt even get far enough to have anything.

Im not normally a windows user and i have little (ok basically none) experience with coding but getting Bioblender running at my office is a must.

If someone could give me some advice it would be much appreciated. I know i have given very little info so ask me Ill find what your looking for.

ralucutza
Posts: 3
Joined: Wed Jan 20, 2010 2:34 pm
Location: Pisa, Italy

Postby ralucutza » Thu Jul 14, 2011 12:58 pm

Guavajelly wrote:Hi I am trying to run Bioblender on a machine running Windows 7 (32-bit). I have installed all required parts (Numpy, Pymol, Python 2.5, and Visual C++ Runtime library) but when I go and run the .exe file it begins to start up and then crashes. The first couple time the Command line window had a few lines of text, but now it doesnt even get far enough to have anything.

Im not normally a windows user and i have little (ok basically none) experience with coding but getting Bioblender running at my office is a must.

If someone could give me some advice it would be much appreciated. I know i have given very little info so ask me Ill find what your looking for.



Please try the new version of BioBlender (BioBlender v0.5.2). Let us know if it works.

Raluca


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