How to show two peptide structures side by side on Pymol. I have 100 PDB files. I want to show all the 3D image structures side side in a two-dimensional array form. How could I do the same in Pymol?
Annemarie Honegger Susanta Roy Thanks for answering! I have a doubt. I have aligned multiple .cif files. I want to show each aligned cluster separately in grid mode. Is that possible in pymol ?
Did you try it? Align your proteins, orient and centre on the page, then type
"set grid_mode,1" into the command line, and it will show them side by side as shown in the examples on page https://pymolwiki.org/index.php/Grid_mode
However, this separates out each individual object onto a separate grid point.
If you talk about an "aligned cluster" in each grid point, you have a problem, as I suppose each of these cluster consists of multiple objects, which will go to different grid points.
Therefore, you have to first merge the objects you want to stay together into a single object. Use the "create" https://pymolwiki.org/index.php/Create or "join_states" https://pymolwiki.org/index.php/Join_states to merge the entities into a single state or a multistage object. If you create a single state object, you may have to alter chain labels to avoid having multiple residues with identical chain and residue label within the same object. With a multistage object, this is not a problem, but you need to specify "set all_states, on" to display everything.
Annemarie Honegger Thanks for you response. In the symbol
, I am able to use set grid_mode but I couldn't label each image in each grid to identify each of the structures. How could I label each one of the images in Pymol?
You would have to attach the labels to a component of the different objects, e.g. define a pseudoatom in a suitable position, and then label this pseudo atom. https://pymolwiki.org/index.php/Label.
When creating static images, e.g. figures for publications, I prefer to export the molecular images as high-resolution ray-traced png files, and then do most labelling in a generic graphics program.
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