sreflex normal modes

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mpapiz
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sreflex normal modes

#1 Post by mpapiz » 2016.10.24 18:50

In sreflex output report files there are lines such as

uc01 2.72 6.50 5 n10s3xn12s-1_X_n9s-2xn16s-2

the last system corresponds to normal modes. I there a document explaining nomenclature of these modes as I cannot find anything in the sreflex paper. I am guessing that n10 and n9 means mode 9 and 10 but what does the rest mean

sasha
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Joined: 2014.03.05 17:56

Re: sreflex normal modes

#2 Post by sasha » 2016.10.25 18:04

mpapiz wrote:In sreflex output report files there are lines such as

uc01 2.72 6.50 5 n10s3xn12s-1_X_n9s-2xn16s-2

the last system corresponds to normal modes. I there a document explaining nomenclature of these modes as I cannot find anything in the sreflex paper. I am guessing that n10 and n9 means mode 9 and 10 but what does the rest mean
Hi mpapiz,

Thanks for your interest. You are right, that's the internal coding for the normal modes used to generate the model.
The string you wrote, n10s3xn12s-1_X_n9s-2xn16s-2, means:
n10s3: normal mode nr. 10, 3 steps in the positive direction (the larger the number of steps, the larger the movement following that normal mode)
x: the lower case x separates each normal mode based movement
n12s-1: normal mode nr. 12, 1 step in negative direction
the _X_ characters separate the restrained stage coding from the unrestrained stage (restrained _X_ unrestrained)
Importantly, the normal modes are recalculated for the restrained model before starting the unrestrained stage.
n9s-2: normal mode nr. 9, 2 steps in negative direction
n16s-2: nm 16, 2 steps in negative direction.

Best,

sasha

mpapiz
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Re: sreflex normal modes

#3 Post by mpapiz » 2016.10.26 19:11

many thanks sasha for the info the normal modes make sense now.
I am also trying to refine the model using Massha running on Ubuntu 16.04 under wine as it appears Massha is only runs in Windows at the moment. I am using the homodimer option and it seams to hang when "computing". How well does this run under wine or do you recommend I use a Wiindows system.
Miroslav

mpapiz
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Re: sreflex normal modes

#4 Post by mpapiz » 2016.10.26 19:52

Also is there anyway to obtain trajectories for these normal modes, graphical or numerical.
Miroslav

sasha
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Re: sreflex normal modes

#5 Post by sasha » 2016.10.31 15:59

Dear Miroslav,

thanks for your interest, I'll answer below.
mpapiz wrote:many thanks sasha for the info the normal modes make sense now.
I am also trying to refine the model using Massha running on Ubuntu 16.04 under wine as it appears Massha is only runs in Windows at the moment. I am using the homodimer option and it seams to hang when "computing". How well does this run under wine or do you recommend I use a Wiindows system.
Miroslav
yes, MASSHA on Wine has certain limitations as you mention. To get similar functionality on Linux (and other platforms as well), we have recently developed SASpy, which is a PyMOL plugin.
If you don't have PyMOL yet, you can install the open-source version for Ubuntu with "sudo apt-get install pymol".
You will be able to edit the model using the mouse (select "Editing mode" on PyMOL) and then use SASpy to calculate fits and refine them (use SASREF tab, with 'local' option) among other functions.

SASpy is part of ATSAS 2.7.2 (the plugin file is located at /usr/share/atsas/pymolplugin/saspy.py) and you can also find it on GitHub, a longer description is available in the applications note:
http://bioinformatics.oxfordjournals.or ... 32/13/2062
mpapiz wrote:Also is there anyway to obtain trajectories for these normal modes, graphical or numerical.
Miroslav
Currently this is not available, but I will add specific options to SREFLEX to provide normal modes and intermediate structures (~trajectories) for the next ATSAS release (2.8.0). If you are on a rush, I can forward you a testing version of SREFLEX with those options available. Please contact me through:
https://www.embl-hamburg.de/biosaxs/panjkovich.html

Best,

sasha

mpapiz
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Posts: 5
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Re: sreflex normal modes

#6 Post by mpapiz » 2016.11.01 15:16

Thanks for the SASpy plugin suggestion I installed the plugin in Pymol ver 1.7.2.1 but get the error below.
Am I running the right version of pymol or do you thing there is something missing in my python installation which seams to be ver 2.7.
Miroslav


Setting sasref mode to global
Just removed sasref_thread from the list, with index 0
Exception in thread sasref_thread:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/usr/lib/python2.7/threading.py", line 754, in run
self.__target(*self.__args, **self.__kwargs)
File "/home/miroslav/.pymol/startup/saspy.py", line 970, in sasref
systemCommand(["crysol"] + ["-p"] + [fid] + [pdbtmpfn])
File "/home/miroslav/.pymol/startup/saspy.py", line 578, in systemCommand
status = subprocess.call(command, **kwargs)
File "/usr/lib/python2.7/subprocess.py", line 523, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

ckerr
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Location: EMBL Hamburg

Re: sreflex normal modes

#7 Post by ckerr » 2016.11.02 10:00

mpapiz wrote: File "/home/miroslav/.pymol/startup/saspy.py", line 970, in sasref
systemCommand(["crysol"] + ["-p"] + [fid] + [pdbtmpfn])
File "/home/miroslav/.pymol/startup/saspy.py", line 578, in systemCommand
status = subprocess.call(command, **kwargs)
File "/usr/lib/python2.7/subprocess.py", line 523, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
I have seen this error before, it is normally because the PyMol program can't find your installation of ATSAS. Did you install ATSAS with a RMP/DEB package or with the .tgz tarball?

mpapiz
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Posts: 5
Joined: 2016.10.14 21:12

Re: sreflex normal modes

#8 Post by mpapiz » 2016.11.04 14:41

Hi I installed it using tarball and added to .bashrc
#setup Atsas suite
export ATSAS=$HOME/ATSAS/ATSAS-2.7.2-5
export PATH=${ATSAS}/bin:$PATH
export LD_LIBRARY_PATH=${ATSAS}/lib/x86_64-linux-gnu/atsas:$LD_LIBRARY_PATH

I can run programs from terminal command or by accessing the search you computer icon in top left corner however I get the error

Quick win error
Internal Error - unexpected error
file "qwgwnd.c" line 3084

However this does not stop me running the program
The full version of pymol, that does not run the plugin, I access from the task bar on the side.

I have found a work around with an educational pymol version which is installed to run from terminal i.e. $pymol
in that case the the plugin works. It may be something to do with the fact that when I go through the terminal the ATSAS software is linked to the terminal session so when i run pymol it sees the links. But I am not sure how to do this with the full version of pymol in the task bar.

sasha
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Posts: 46
Joined: 2014.03.05 17:56

Re: sreflex normal modes

#9 Post by sasha » 2016.11.08 17:01

Dear Miroslav,

Thanks for your message, I'll answer point by point below. You are using Ubuntu 16.04, right?
mpapiz wrote:Hi I installed it using tarball and added to .bashrc
#setup Atsas suite
export ATSAS=$HOME/ATSAS/ATSAS-2.7.2-5
export PATH=${ATSAS}/bin:$PATH
export LD_LIBRARY_PATH=${ATSAS}/lib/x86_64-linux-gnu/atsas:$LD_LIBRARY_PATH

I can run programs from terminal command or by accessing the search you computer icon in top left corner
These settings look fine.
mpapiz wrote: however I get the error

Quick win error
Internal Error - unexpected error
file "qwgwnd.c" line 3084
I am not familiar with this Quick win error, I am told that this may be related to WINE.
WINE is not needed by SASpy, do you get the same error if you execute "crysol" for example?
mpapiz wrote: However this does not stop me running the program
The full version of pymol, that does not run the plugin, I access from the task bar on the side.
Which program do you mean by "the program"? Given the quick win error, is that MASSHA?
There are many different ways to obtain PyMOL, which one are you referring to as the "full version of pymol"?
If you are on Ubuntu, the recommendation is to use the open source version of PyMOL that can be installed by using "sudo apt-get install pymol". You can also launch that version from the command line, for example on my machine (Ubuntu 14.04) the binary is at:
/usr/bin/pymol

If that version cannot run SASpy, please try again using the latest github SASpy version:
https://raw.githubusercontent.com/embls ... r/saspy.py
I added a check for the presence of the binaries which should make things easier.

In any case, I was not aware of this "task bar issue", but after reading your post I could reproduce the problem.
When called from the 'task bar', the Linux open-source version of PyMOL will NOT load the user defined PATH, it will only load system wide settings. There are different ways to solve this issue:

-Define the ATSAS PATH within PyMOL by typing into the PyMOL console:
os.environ["PATH"] += os.pathsep + "/xxx/yyy/ATSAS/bin:"
(where xxx/yyy is the path to your local ATSAS installation)

-launch PyMOL from the terminal (should be at /usr/bin/pymol or type 'which pymol' on a terminal to find it). I personally prefer to call 'pymol xxxx.pdb' than going to the task bar.

-If you have admin permissions, set the PATH to ATSAS for the whole system, in Ubuntu this can be set at /etc/environment
mpapiz wrote: I have found a work around with an educational pymol version which is installed to run from terminal i.e. $pymol
in that case the the plugin works. It may be something to do with the fact that when I go through the terminal the ATSAS software is linked to the terminal session so when i run pymol it sees the links. But I am not sure how to do this with the full version of pymol in the task bar.
Thanks for this hint, it helped me to understand the problem. I would try uninstalling the educational version and then locating the PyMOL binary or init script of the 'full' installation (I assume it is the open source version installed through get-apt). It should work well if you call it from the terminal.

I hope that helps. Thanks again for your detailed description of the problems and please let us know how it goes.

Best,

sasha

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