Troubleshooting

From FoldX plugin for YASARA

Jump to: navigation, search

Contents

Advance note

Whenever you run into a problem or you experience a crash, always check first if you have carefully followed the installation instructions and you are using the latest version of the plugin, the latest version of YASARA and the latest version of FoldX. Remember that your FoldX version expires every year in January, so then you have to download a new version. If the problem persists, check if the issue is listed here. If not, don't hesitate to contact us.

Analyze menu does not open

As explained in the first use section of this documentation website, the Analyze menu only becomes active when a structure is loaded. So open a structure with e.g.:

File > Load > PDB file

Now the Analyze menu is active and a FoldX submenu should be present.

FoldX menu does not show up

You are using an old YASARA version
The plugin only works from YASARA 10.11.22 and higher. Please upgrade to the latest version.
You forgot to download and install the plugin
It is not enough to install YASARA and FoldX to be able to run FoldX from YASARA. You need to download and unzip the plugin zip file from the homepage or HERE. Please consult the Installation and first use section for details on installing and unzipping the plugin in the correct location.
You are using Windows Vista or Windows 7
This workaround comes from the YASARA documentation:
YASARA does not have write permissions in its own directory. Especially Windows Vista/7 has a deep sitting problem dealing with permissions, i.e. even if you installed YASARA in the 'Program Files' folder, providing all the required authorization, Windows may still prevent it from running correctly. To fix this issue, right-click on the 'yasara' folder, then click Properties > Security, select group 'Users', click 'Edit', tick 'Full control - Allow', click 'Apply'. Verify that there is now really a hook in the 'Allow' column for 'Full control'. If you do not have the required administrator privileges to perform this operation, simply install YASARA in your home directory.
You forgot to install Python
Install Python from within YASARA with:
Help > Install program > Python

Error: Cannot read FoldX ... output

You are using Windows Vista or Windows 7
This workaround comes from the YASARA documentation:
YASARA does not have write permissions in its own directory. Especially Windows Vista/7 has a deep sitting problem dealing with permissions, i.e. even if you installed YASARA in the 'Program Files' folder, providing all the required authorization, Windows may still prevent it from running correctly. To fix this issue, right-click on the 'yasara' folder, then click Properties > Security, select group 'Users', click 'Edit', tick 'Full control - Allow', click 'Apply'. Verify that there is now really a hook in the 'Allow' column for 'Full control'. If you do not have the required administrator privileges to perform this operation, simply install YASARA in your home directory.
Your FoldX version has expired
In january of each year, your FoldX version expires and will not provide output anymore leading to this error. To see if this is really the problem, scroll a bit through the YASARA console output and if you see the line "Your time has expired.", you found the problem. Just download and install the new version from http://foldx.crg.es and configure the plugin again with:
Analyze > FoldX > Configure plugin
There are modified amino acids in your structure
Only a few modified amino acids are supported by FoldX as indicated in this list. Other modified amino acids such as methylated lysines (example 4DOM.pdb) are not recognised by FoldX and trying to mutate those or residues close to them will result in an immediate stop of FoldX calculations leading to this error. A workaround is to first use the YASARA Swap command to swap all modified residues to their original counterpart, so for methylated lysines you swap to lysine. After that, repair and mutate.
Your FoldX executable file does not have the executable permissions
If you're running Mac OSX or Linux, you may have to change the permissions of the FoldX executable file to set it as executable. Open a terminal window and navigate to the folder that contains the FoldX executable file you downloaded. If the filename is e.g. FoldX.Linux32, you then type in the terminal:
chmod +x FoldX.Linux32
Now the file can be executed.

Unchecking the Move neighbours option results in a crash

When Move neighbours is unchecked, FoldX does not generate a reference wild type structure, as the plugin expects. This will result in a plugin crash when interaction energy change was selected as output. This should be fixed in the next FoldX release. In the meantime, always leave the Move neighbours option checked. If you really don't want neighbouring residues to move, you can use the Fix residue option to freeze residues manually using:

Analyze > FoldX > Fix residue

Build homology model issues

Error - The given template sequence in the sequence file was not found in the template structure.

If you are sure that the alignment file contains the correct template sequence, check the structure for multiple residues with the same residue number (e.g. 1EJG residue 25). If multiple residues with the same residue number are present, these additional residues will make the structure-extracted template sequence longer and the plugin will raise an error because the structure contains more residues than the provided template sequence.

Solution 1: Run a FoldX RepairPDB first. You can do this manually from Analyze > FoldX > Repair object.
Alternatively you can check the Repair option in one of the selection menus from the Build homology model command. 
Repairing the structure will only keep the residue that occurs first in the PDB file and delete the next one(s).
Solution 2: Manually delete the additional residues so that each residue number occurs only once.

FoldX runs take a long time, how can I follow the progress?

Currently, there is no real-time FoldX output given to monitor the progression of e.g. a multiple mutation run. However, if you want to peek at the FoldX output while it runs, you can open the console by pressing the spacebar. Mind that once the console is open, FoldX output will not progress, it's like a progress snapshot. To see the next snapshot, close the console by clicking outside of it and reopen it.

Personal tools