PyRx installation problem in Ubuntu 12.04

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PyRx installation problem in Ubuntu 12.04

Postby bpadmanabhan » Thu May 24, 2012 12:27 pm

Hi All,

I am trying to use PyRx (0.7 / 0.9 version) on the Linux system (Ubuntu 12.04 version; 32 bit).

1. PyRx 0.7 version (dowloded the file, PyRx-0.7-Linux-x86-RHEL5-Install)

Installation was complete with the errors as below:

$ ./PyRx-0.7-Linux-x86-RHEL5-Install
$
(python2.5:3383): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -4 and height 17

(python2.5:3383): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -4 and height 17

(python2.5:3383): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -5 and height 17

(python2.5:3383): LIBDBUSMENU-GLIB-WARNING **: Trying to remove a child that doesn't believe we're it's parent.

(python2.5:3383): LIBDBUSMENU-GLIB-WARNING **: Trying to remove a child that doesn't believe we're it's parent.

(python2.5:3383): LIBDBUSMENU-GLIB-WARNING **: Trying to remove a child that doesn't believe we're it's parent.

(python2.5:3383): LIBDBUSMENU-GLIB-WARNING **: Trying to remove a child that doesn't believe we're it's parent.

Can be envoked PyRx GUI , and could run Vina program. However, in the GUI window, a row ' File Edit View Help ' is completely missing, and hence could not able to set the parameters (Preferences) and access other options.

$ ./run.sh

(python2.5:3474): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -4 and height 17

(python2.5:3474): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -4 and height 17

(python2.5:3474): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -5 and height 17

2. PyRx-0.9 (PyRx_0.9new-Linux-86-Install)

I then tried the latest version 0.9. The installation is failed with the errors:

(python:2965): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -4 and height 17

(python:2965): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -4 and height 17

(python:2965): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -5 and height 17
Segmentation fault (core dumped)

The GUI crashes with the same 'core dumped' message whenver is envoked.

3. Tried to compile/install the source file

I downloaded the PyRx-0.5-Source.zip file but could not find the 'setup.py' file or the relevant header file for compilation. The link for PyRx-0.9 source file is redirected to the PyRx homepage.

Your inputs to resolve these issues are greatly appreciated.

Regards,
B. Padmanabhan.
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Re: PyRx installation problem in Ubuntu 12.04

Postby sargis » Thu May 24, 2012 9:54 pm

Thank you for the message. Please see below for possible solutions.
bpadmanabhan wrote:I am trying to use PyRx (0.7 / 0.9 version) on the Linux system (Ubuntu 12.04 version; 32 bit).

1. PyRx 0.7 version (dowloded the file, PyRx-0.7-Linux-x86-RHEL5-Install)

Installation was complete with the errors as below:

$ ./PyRx-0.7-Linux-x86-RHEL5-Install
$
(python2.5:3383): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -4 and height 17

(python2.5:3383): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -4 and height 17

(python2.5:3383): Gtk-WARNING **: gtk_widget_size_allocate(): attempt to allocate widget with width -5 and height 17

(python2.5:3383): LIBDBUSMENU-GLIB-WARNING **: Trying to remove a child that doesn't believe we're it's parent.

(python2.5:3383): LIBDBUSMENU-GLIB-WARNING **: Trying to remove a child that doesn't believe we're it's parent.

(python2.5:3383): LIBDBUSMENU-GLIB-WARNING **: Trying to remove a child that doesn't believe we're it's parent.

(python2.5:3383): LIBDBUSMENU-GLIB-WARNING **: Trying to remove a child that doesn't believe we're it's parent.

This WARNING messages are fine. I don't know where they are coming from, but they can be safely ignored.

bpadmanabhan wrote:Can be envoked PyRx GUI , and could run Vina program. However, in the GUI window, a row ' File Edit View Help ' is completely missing, and hence could not able to set the parameters (Preferences) and access other options.

Please remove ~/.mgltools/PyRx/.PyRx_Perspective* and try again.

bpadmanabhan wrote:
2. PyRx-0.9 (PyRx_0.9new-Linux-86-Install)

I then tried the latest version 0.9. The installation is failed with the errors:

The GUI crashes with the same 'core dumped' message whenver is envoked.

I don't have access to Ubuntu 12.04 and not sure why it crushes. You can install 10.x virtual machine and try it there, since PyRx is know to work on 10.x.

bpadmanabhan wrote:3. Tried to compile/install the source file

I downloaded the PyRx-0.5-Source.zip file but could not find the 'setup.py' file or the relevant header file for compilation. The link for PyRx-0.9 source file is redirected to the PyRx homepage.


I fixed PyRx-0.9-Source.zip link, thanks. I also downloaded and unzipped PyRx-0.5-Source.zip. This file contains PyRx source folder and a bunch for other files inducing setup.py. It should in the folder in the where you unzipped PyRx-0.5-Source.zip.

I won't recommend to compile/install PyRx from source though, unless you are familiar development tools.

HTH
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Re: PyRx installation problem in Ubuntu 12.04

Postby bpadmanabhan » Fri May 25, 2012 4:13 am

Thank you for your reply message.

> Please remove ~/.mgltools/PyRx/.PyRx_Perspective* and try again.

As suggested, I removed '.PyRx_Perspective' file and tried again. But getting the same error.

Regards,
B. Padmanabhan.
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Re: PyRx installation problem in Ubuntu 12.04

Postby sargis » Fri May 25, 2012 8:27 pm

bpadmanabhan wrote:Thank you for your reply message.

> Please remove ~/.mgltools/PyRx/.PyRx_Perspective* and try again.

As suggested, I removed '.PyRx_Perspective' file and tried again. But getting the same error.


By getting the same error do you mean "File Edit View Help" menus are still missing? .PyRx_Perspective store the info about various PyRx panel perspective. Removing .PyRx_Perspective is equivalent to resting the perspective.

HTH
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Re: PyRx installation problem in Ubuntu 12.04

Postby bpadmanabhan » Sat May 26, 2012 10:22 am

Dear Sargis,

> By getting the same error do you mean "File Edit View Help" menus are still missing? .PyRx_Perspective store the info about various PyRx panel > perspective. Removing .PyRx_Perspective is equivalent to resting the perspective.

Yes, this line is still missing.

When I checked the file '.PyRx_Perspective', the first line starts as
"layout2|name=Navigator;caption=Navigator;state=12601340;.......

Is there anything missing before the 'Navigator' panel definintion?

Regards,
Paddy.
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Re: PyRx installation problem in Ubuntu 12.04

Postby sargis » Sat May 26, 2012 5:09 pm

Dear Paddy,

bpadmanabhan wrote:> By getting the same error do you mean "File Edit View Help" menus are still missing? .PyRx_Perspective store the info about various PyRx panel > perspective. Removing .PyRx_Perspective is equivalent to resting the perspective.

Yes, this line is still missing.


Thanks. This is strange; I have no idea why "File Edit View Help" menus are missing then.

bpadmanabhan wrote:When I checked the file '.PyRx_Perspective', the first line starts as
"layout2|name=Navigator;caption=Navigator;state=12601340;.......

Is there anything missing before the 'Navigator' panel definintion?


This seems to be fine. When you remove .PyRx_Perspective, it's no longer used. We can compare our .PyRx_Perspective by attaching it here, but I'm not sure this would help us solve the problem of missing menus.

Bests,
Sargis
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Re: PyRx installation problem in Ubuntu 12.04

Postby bpadmanabhan » Sun May 27, 2012 2:29 pm

Dear Sargis,

Here is the PyRx_Perspective:

layout2|name=Navigator;caption=Navigator;state=12601340;dir=1;layer=0;row=2;pos=0;prop=100000;bestw=600;besth=700;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=105;floaty=176;floatw=608;floath=724|name=Graphics;caption=View;state=12584956;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=1200;besth=700;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=Controls;caption=Controls;state=12584956;dir=3;layer=0;row=0;pos=0;prop=100000;bestw=1200;besth=350;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=toolbar;caption=Toolbar;state=2108156;dir=1;layer=10;row=0;pos=0;prop=100000;bestw=182;besth=30;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|dock_size(1,10,0)=32|dock_size(5,0,0)=399|dock_size(3,0,0)=270|dock_size(1,0,2)=270|

Regards,
Paddy.
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Re: PyRx installation problem in Ubuntu 12.04

Postby sargis » Sun May 27, 2012 4:16 pm

Dear Paddy,

Thank you. I copied PyRx_Perspective from my Windows PC below:

layout2|name=Navigator;caption=Navigator;state=12584956;dir=4;layer=0;row=0;pos=0;prop=100000;bestw=596;besth=846;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=Graphics;caption=View;state=12584956;dir=5;layer=0;row=0;pos=0;prop=100000;bestw=1196;besth=846;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=Controls;caption=Controls;state=12601340;dir=3;layer=0;row=0;pos=0;prop=100000;bestw=1196;besth=421;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|name=toolbar;caption=Toolbar;state=2108156;dir=1;layer=10;row=0;pos=0;prop=100000;bestw=146;besth=23;minw=-1;minh=-1;maxw=-1;maxh=-1;floatx=-1;floaty=-1;floatw=-1;floath=-1|dock_size(4,0,0)=394|dock_size(5,0,0)=394|dock_size(3,0,0)=307|dock_size(1,10,0)=25|

After looking at this I can see that the geometries and the states of Toolbar, Controls, View (Graphic), and Navigator are defined here. So something else might be causing the missing menu bar.
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Re: PyRx installation problem in Ubuntu 12.04

Postby bpadmanabhan » Fri Jun 15, 2012 6:50 am

Dear Sargis,

Atlast, I found this ...

The 'menu bar' appears at the top row of PyRx Window. You will have to bring the cursor there and click, to display the menu bar. Please see the attached figure file. I came across this when I had similar in running 'Coot'. Different display format in Ubuntu ?!

Thanks.

Regards,
Paddy.
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Re: PyRx installation problem in Ubuntu 12.04

Postby bpadmanabhan » Fri Jun 15, 2012 6:59 am

Dear Sargis,

Atlast, I found this ...

The 'menu bar' appears at the top row of PyRx Window. You will have to bring the cursor there and click, to display the menu bar. Please see the attached figure file. I came across this when I had a similar problem in running 'Coot'. Different display format in Ubuntu ?!

Thanks.

Regards,
Paddy.
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