PyRx 0.8 for linux?

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PyRx 0.8 for linux?

Postby Rifampin » Sat Jan 16, 2016 5:26 pm

Hello I'm a med student just started to learn molecular docking a while ago. I'm using linux and I've been searching around looking for old PyRx (below 0.9 which is free) and I only found version 0.7 for linux. Is there no version 0.8 for linux? or it just hidden somewhere deep in the web?

Is there any (or a lot) difference between PyRx 0.7 and 0.8?

Thanks ^^
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Re: PyRx 0.8 for linux?

Postby sargis » Sun Jan 17, 2016 2:50 am

Hello and thanks for the message. I might have accidentally deleted PyRx-0.8-Linux-x86-Install. I've uploaded it again and it's now available at https://sourceforge.net/projects/pyrx/f ... l/download

The list of changes between PyRx 0.7 and 0.8 is at http://pyrx.sourceforge.net/blog/97-pyr ... nouncement

I recommend getting latest version of PyRx since that's the only version supported currently. It will pay for itself in no time considering how much CPU hours cost in the cloud.
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Re: PyRx 0.8 for linux?

Postby Rifampin » Sun Jan 17, 2016 5:22 pm

Thank you!
I'll consider buying the latest version when I'm done with my college tuition (hehe)
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Re: PyRx 0.8 for linux?

Postby sargis » Sun Jan 17, 2016 6:07 pm

Rifampin wrote:Thank you!
I'll consider buying the latest version when I'm done with my college tuition (hehe)

You are very welcome. Thank you too!
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64-bit version for PyRx below 0.9

Postby Rifampin » Mon Jan 18, 2016 5:35 am

Sorry I ran into problem when I tried to install PyRx 0.8 on my 64-bit linux (precisely debian jessie). I ran into this error :

Code: Select all
invalid command name "bind"
    while executing
"::unknown bind Text <Tab>"
    ("uplevel" body line 1)
    invoked from within
"uplevel 1 $next $args"
    (procedure "::obj::Unknown" line 3)
    invoked from within
"bind Text <Tab>"
    (procedure "::InstallJammer::InitializeGui" line 19)
    invoked from within
"::InstallJammer::InitializeGui "
    (procedure "::InstallJammer::InitInstall" line 63)
    invoked from within
"::InstallJammer::InitInstall"
    (file "/installkitvfs/main.tcl" line 38295)

Is this error came from my side or PyRx (<0.9) just not supposed to run on 64-bit machine?
p.s. I have already installed all 32-bit libraries for 64-bit linux

Thanks in advance
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Re: 64-bit version for PyRx below 0.9

Postby sargis » Mon Jan 18, 2016 4:20 pm

Rifampin wrote:Sorry I ran into problem when I tried to install PyRx 0.8 on my 64-bit linux (precisely debian jessie). I ran into this error :

Code: Select all
invalid command name "bind"
    while executing
"::unknown bind Text <Tab>"
    ("uplevel" body line 1)
    invoked from within
"uplevel 1 $next $args"
    (procedure "::obj::Unknown" line 3)
    invoked from within
"bind Text <Tab>"
    (procedure "::InstallJammer::InitializeGui" line 19)
    invoked from within
"::InstallJammer::InitializeGui "
    (procedure "::InstallJammer::InitInstall" line 63)
    invoked from within
"::InstallJammer::InitInstall"
    (file "/installkitvfs/main.tcl" line 38295)

Is this error came from my side or PyRx (<0.9) just not supposed to run on 64-bit machine?
p.s. I have already installed all 32-bit libraries for 64-bit linux

Thanks in advance

This might be because of incomplete download. Make sure the final size of the file in your disk is the same as your browser indicates it should at the beginning of download. I'v seen similar problem before with sourceforge downloads, but none with fastspring (>=0.9) downloads.
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SOLUTION: Installing the 32 bit version in 64-bit OS

Postby Rifampin » Sat Feb 27, 2016 5:19 pm

Hi sarge, it's been a while since I ask the question above but I found a way to make the 32 bit installer work in 64. The error doesn't have anything to do with incomplete download. It's because 32-bit library dependencies. (FYI, i'm using ubuntu 14.04.3 LTS now)

If you look around on the internet most likely you will find answers that instruct you to install 32 bit libraries like this
Code: Select all
sudo dpkg --add-architecture i386
sudo apt-get update
sudo apt-get install lib32z1 lib32ncurses5 lib32bz2-1.0 lib32stdc++6 libgtk2.0-0:i386 libpangox-1.0-0:i386 libpangoxft-1.0-0:i386 libidn11:i386 libglu1-mesa:i386

However, those library won't satisfy the installer to work. I dig deeper and found that you must install these libraries too
Code: Select all
sudo apt-get install libjpeg62:i386 libsdl1.2debian:i386 libcanberra-gtk-module:i386 libpng12-0 libxss1:i386 libxss1

also on the PyRx download page it says you have to install libsdl. If you do sudo apt-get install libsdl you won't find any package. You have to install libsdl1.2debian:i386 instead. I also installed libsdl1.2-dev because I wasn't sure --for this one I use synaptic package manager because I cant download it via terminal somehow.
Code: Select all
sudo apt-get install libsdl1.2debian:i386

I can install the program perfectly afterwards :D However (sigh) when I run the program, it only appear for split seconds (I can see the splash screen and the PyRx window) and then closes automatically with this output
Code: Select all
(python:16343): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -5 and height 21

(python:16343): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -5 and height 21

(python:16343): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -5 and height 21

Segmentation fault (core dumped)

I suppose it's something that can only be fixed by the program creator. Any leads?

EDIT : 14/03/2016 Segmentation fault crashing issue can be fixed by installing Nvidia driver
If you still can't run the program after installing all the dependencies above, try to trace the problem using this command
Code: Select all
strace ./PyRx-0.8-Linux-x86-Install

You will see A LOT of lines before the initial error message appear. There will be some shared object missing (.so) that you need to install. Cheers! :D
Last edited by Rifampin on Mon Mar 14, 2016 5:59 am, edited 2 times in total.
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Re: PyRx 0.8 for linux?

Postby sargis » Sun Feb 28, 2016 3:16 am

Thanks for the update. Glad you manged to install these libraries and posted how to do that. I think the segmentation fault can be fixed by installing graphics card drivers. What kind of hardware are you running this on?
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Re: PyRx 0.8 for linux?

Postby Rifampin » Tue Mar 01, 2016 10:32 am

CPU : Intel(R) Core(TM) i3-3110M CPU @ 2.40GHz
RAM : 4,00 GB
Display : Intel HD Graphic 4000 & Nvidia GeForce 610M

The nvidia driver im using in ubuntu is noveau (x.org x server --or something). Should I install nvidia binary driver? (I did that once and ended up with black screen after booting)
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Re: PyRx 0.8 for linux?

Postby sargis » Tue Mar 01, 2016 3:52 pm

Rifampin wrote:CPU : Intel(R) Core(TM) i3-3110M CPU @ 2.40GHz
RAM : 4,00 GB
Display : Intel HD Graphic 4000 & Nvidia GeForce 610M

The nvidia driver im using in ubuntu is noveau (x.org x server --or something). Should I install nvidia binary driver? (I did that once and ended up with black screen after booting)

Yes, you can try nvidia driver. I have instructions for CentOS 6, but don't know much of that would apply to ubuntu http://pyrx.sourceforge.net/blog/103-in ... n-centos-6

I've tested PyRx 9.x on Ubuntu 10.04 running on VirtualBox and it worked fine.
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