Hi,
I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol to move the layer along the fibril axis to make the next layer, and then repeat this step to make other layers.
For example, to make a 4-layer fibril from the original fibril layer (chains D and J of PDB structure 2LMO), my commands are:
fetch 2lmo; hide all;
create layer1, chain D+J; translate [0.02, 0.25, 4.47], layer1, camera = 0;
create layer2, layer1; translate [0.02, 0.25, 4.47], layer2, camera = 0;
create layer3, layer2; translate [0.02, 0.25, 4.47], layer3, camera = 0;
create layer4, layer3; translate [0.02, 0.25, 4.47], layer4, camera = 0;
as cartoon, (chain D+J) + layer1 + layer2 + layer3
The result is shown in the attached PyMol session file.
From the Internet, I learned about the Iterate and Alter commands in PyMol, but they are intended for repeating an operation "on the atoms in a selection", not for repeating an operation "for multiple times". Therefore, I am wondering if there is a way to repeat the translation (or other operations in general) in PyMol by iteration or other methods. I need to construct a fibril structure of 10 - 20 layers and apply this method to different protein fibrils, so the automation of this process will help a lot.
Thank you for your help in advance!
Regards,
Gangtong
You can use the programming language python from within pymol, which allows you to do loops. Either you write a separate python script "script.py" which you invoke with "run script.py" (https://pymolwiki.org/index.php/Python_Integration) or you embed a python segment within an ordinary pml script, e.g. just to make a loop by bracketing your python commands between "python" and "python end" commands.
Note that to call pymol commands from within python code, you need to use the pymol api format, e.g.
"cmd.translate(list vector, string selection = "all", int state = 0, int camera = 1, string object = None)"
instead of "translate vector [,selection [,state [,camera [,object ]]]]"
So you can make a loop that runs over a given number of iterations:
python for i in range(1, 25): ...
python end
Annemarie Honegger
Hi Dr. Honegger,
Thank you for your help! I will try using Python scripts in PyMol to implement the iteration.
Regards,
Gangtong
Dear Gangtong Huang ,
I am also trying to prepare fibrils from PDB files, however keeping the information about the twist of the fibril. How can I include a rotational angle combined with the translation in order to create such a fibril.
In addition, I was thinking that one can identify an iteration element "i" that defines a fixed increment over "z" axis and one can use a single layer , say chain D+J, as a starting layer building all 20 layers.
Thanks in advance,
Riza
Instead of doing a simple translation, you need to get the transformation matrix relating the individual units to also include the rotational parameter. see https://sourceforge.net/p/pymol/mailman/message/24391007/ for an example on how to determine the transformation matrix, which you can then repeatedly apply to copies of your units using "transform_object" https://pymolwiki.org/index.php/Transform_object or transform_selection https://pymolwiki.org/index.php/Transform_selection
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