Changeset [89] and Changeset [104] are compatible with... ?

[RaduT]

Hello ,

This topic is actually some sort of continuation of my previous topic [104] Implemented hydrogen bond visualization: http://mgl.scripps.edu/forum/viewtopic.php?f=25&t=1585.
Well, as far as I understood the changeset 104 is not compatible with PyRx 0.8 (see Problem with Changeset 89: http://mgl.scripps.edu/forum/viewtopic.php?f=25&t=1538&p=3808), so I uninstalled PyRx 0.8.

I installed PyRx 0.7 (in a custom folder: "C:\Program Files(x86)\PyRx07") and I applied the following changesets: 86 (successfully), 87 (successfully) and 88 (half-successfully: PyRx 0.7 is running with no errors / but I still can't see the update tab in menu...).

I tried to apply the changeset 89 but I received an error:

Code: Select all

Traceback (most recent call last):
  File "C:\Program Files (x86)\PyRx07\runPyRx.py", line 92, in <module>
    startPyRx()
  File "C:\Program Files (x86)\PyRx07\runPyRx.py", line 39, in startPyRx
    frame = MainFrame(None, -1, size=(width, height-200))
  File "C:\Program Files (x86)\PyRx07\lib\site-packages\PyRx\wxMainFrame.py", line 132, in __init__
    self.molNav = MolNavigator(self) #Navigator -> Molecules tab
  File "C:\Program Files (x86)\PyRx07\lib\site-packages\PyRx\molNavigator.py", line 26, in __init__
    CT.CustomTreeCtrl.__init__(self, frame.navigator, id=-1, agwStyle=style)
TypeError: __init__() got an unexpected keyword argument 'agwStyle'

Problem starting PyRx. Please visit PyRx forum for a possible solution: http://mgl.scripps.edu/forum

So, I rolled-back the changeset 89 and PyRx 0.7 started properly.

2nd test: I tried to apply the changeset 104 but I received an error (almost the same, but with "bonus"):

Code: Select all

Traceback (most recent call last):
  File "C:\Program Files (x86)\PyRx07\runPyRx.py", line 92, in <module>
    startPyRx()
  File "C:\Program Files (x86)\PyRx07\runPyRx.py", line 39, in startPyRx
    frame = MainFrame(None, -1, size=(width, height-200))
  File "C:\Program Files (x86)\PyRx07\lib\site-packages\PyRx\wxMainFrame.py", line 134, in __init__
    self.molNav = MolNavigator(self) #Navigator -> Molecules tab
  File "C:\Program Files (x86)\PyRx07\lib\site-packages\PyRx\molNavigator.py", line 24, in __init__
    CT.CustomTreeCtrl.__init__(self, frame.navigator, id=-1, agwStyle=style)
TypeError: __init__() got an unexpected keyword argument 'agwStyle'

Problem starting PyRx. Please visit PyRx forum for a possible solution: http://mgl.scripps.edu/forum

3rd test: I tried to apply the changesets 89 and 104 but I received the following errors:

Code: Select all

Traceback (most recent call last):
  File "C:\Program Files (x86)\PyRx07\runPyRx.py", line 92, in <module>
    startPyRx()
  File "C:\Program Files (x86)\PyRx07\runPyRx.py", line 39, in startPyRx
    frame = MainFrame(None, -1, size=(width, height-200))
  File "C:\Program Files (x86)\PyRx07\lib\site-packages\PyRx\wxMainFrame.py", line 134, in __init__
    self.molNav = MolNavigator(self) #Navigator -> Molecules tab
  File "C:\Program Files (x86)\PyRx07\lib\site-packages\PyRx\molNavigator.py", line 24, in __init__
    CT.CustomTreeCtrl.__init__(self, frame.navigator, id=-1, agwStyle=style)
TypeError: __init__() got an unexpected keyword argument 'agwStyle'

Problem starting PyRx. Please visit PyRx forum for a possible solution: http://mgl.scripps.edu/forum

So... I rolled-back changesets 89 and 104 and PyRx 0.7 started properly (changesets 86, 87 and 88 are still applied).

I really need to use the features of changesets 89 and 104! Whit what version of PyRx are those two compatible and what modifications (changesets) are prerequired before applying them?

PS: I installed PyRx 0.6 (in a custom folder: "C:\Program Files(x86)\PyRx06") and it is not running - PyRx 0.7 is still running without changesets 89 and 104.

Thanks to anybody who read my short novel !

[sargis]

Thank you for the message. The easiest way to get this working is to install the latest 0.9 version of PyRx. You can install VirtualBox or VMware on Windows and then install Ubuntu or other Linux distribution. To implement hydrogen bond visualization, we use ePMV package that is included with 0.9 version and which is not available in any of the previous versions 0.6, 0.7 or 0.8.

Also, I would recommend using PyRx to run virtual screening and use other packages for visualization. Since I don't have resources that other molecular visualization packages have, I won't be able to implement many of the visualization options available elsewhere.

[RaduT]

The easiest way to get this working is to install the latest 0.9 version of PyRx. You can install VirtualBox or VMware on Windows and then install Ubuntu or other Linux distribution.

Hello Sargis and thank you!

I experienced with VirtualBox, but this software can manage only one CPU (core) with Fedora and Ubuntu, so I abandoned this idea.

With the help of a good friend and colleague I managed to install and run PyRx 0.9 under a Linux OS on another HDD (my first contact with Linux OSes)!

Just as "field-experience" I have to say that:
- First, we installed Fedora 16 Desktop Edition - The GNOME-based default Fedora Desktop, 32-bit (http://download.fedoraproject.org/pub/fedora/linux/releases/16/Live/i686/Fedora-16-i686-Live-Desktop.iso), but we couldn't install PyRx 0.9 on it!
- Second, we tried to install PyRx 0.9 under Ubuntu 10.11, 32-bit (http://d2ce223loljjr2.cloudfront.net/ubuntu-11.10-desktop-i386.iso) - some problem, we couldn't install PyRx 0.9 on this OS! Personal observation: Ubuntu is moving like an old and respectable lady comparative with Fedora!!!
- Third attempt: we successfully installed PyRx 0.9 under Fedora 16 KDE Spin - KDE-based Fedora desktop, 32-bit (http://download.fedoraproject.org/pub/fedora/linux/releases/16/Live/i686/Fedora-16-i686-Live-KDE.iso)!!! Another personal observation: Print-Screen button is not working under this OS (if matters, I'm using a wirelesses kit: KB + mouse), but I didn't updated the OS.

Referring only at PyRx 0.9 I can say that:
- PyRx 0.9 (installed as it is, without any update or other modification) is running smooth and fast under Fedora 16 KDE Spin - KDE-based Fedora desktop, 32-bit
- I can see ribbons
- I can see the H-bonds buttons, but it seems that it is not functioning... why? Or please be more explicit when you are saying (open-source only):

I would recommend using PyRx to run virtual screening and use other packages for visualization.

As always, my best regards!

[sargis]

Hello Sargis and thank you!

Hello Radu. You are very welcome! I'm glad you could install PyRx 0.9 under Fedora 16 KDE Spin - KDE-based Fedora desktop, 32-bit (third time's a charm).

- I can see the H-bonds buttons, but it seems that it is not functioning... why? Or please be more explicit when you are saying (open-source only):

For the H-bonds to function the molecule needs to have Hydrogen atoms. You can convert your molecule to pdbqt or open a molecule that has Hydrogens in it.

Regarding the open-source molecular viewer, PyMOL is the most used one:

http://www.pymolwiki.org/index.php/Disp ... r_Contacts

See also: http://depth-first.com/articles/2011/11 ... n-windows/