[PyMOL] Moving a duplicated object a given distance from the original object

Hello everyone, I have a linear molecule (obj1) which I have duplicated (obj2). I want to move obj2 (which is currently 100% overlapped with obj1) with respect to obj1 along the x axis by 10 nm. Can I achieve this by translate [10,0,0] , obj2 I don't know what the distance units are in the vect

[PyMOL] The default tunnel calculation settings for CAVER 2.1.2

Hello everyone, Two years ago I used CAVER 2.1.2 for calculation of intra-molecular tunnels. I know that the current version of CAVER allows us to view and change the configuration file (for default tunnel calculation settings). I couldn't find such a configuration file for CAVER 2.1.2. Does anybo

[PyMOL] Iterating through states of a topology object (trajectories) and writing out a distance

Hi all, I have loaded a topology file by the name of "topo" into pymol and loaded the trajectory file on top of it. Now pymol says "amn1136_xd1.trj" appended into object "topo". CmdLoadTraj: 250 total states in the object. I want go through these states and write the distance between two atoms t

[PyMOL] Any option to make tunnels lines wider in PyMol CAVER?

Hi all, Is there any option/command in CAVER to make the tunnels when represented as lines, look wider (increase the width of the tunnel lines)? I have created a movie with the tunnels represented as lines. I would like to have the lines representing the tunnels wider. Thank you very much Sajeew

[PyMOL] Can CAVER be run iteratively through a python script?

Hi all, I have a few hundred pdb snapshots of a protein in which I have to check a tunnel with the same starting point. Without opening them one by one and running CAVER separately for each snapshot, is there any way to run CAVER iteratively using a Python script? If there is, it would save me loa

[PyMOL] x,y,z coordinates of the pseudo-atoms that make a tunnel

Hi all, I want to place copies of CO2 along a tunnel created by PyMol CAVER. Is there any way I can get the xyz coordinates of the pseudo-atoms that comprise the tunnel, when I select the pseudo-atoms I want? Thank you Sajeewa Dewage --

[PyMOL] Aligning Pymol session files corresponding to different molecular dynamics snapshots

Hello, I have three intramolecular tunnels in three pymol session (.pse) files. Two .pse files are corresponding to the same snapshot in molecular dynamics. The third .pse file is for a different snapshot. I want to merge these .pse files using commands like load first.pse load second.pse,partial

[PyMOL] Finding distances along molecular tunnels

Hello everyone, I have 2 molecular tunnels inside one protein corresponding to two starting points, created by the CAVER plugin. The two tunnels join to form one common tunnel. I want to measure 1) The distance between the two starting points of the tunnels 2) The distance from each starting po

[PyMOL] problem in running pymol in batch mode

Hi everyone, I am trying to run pymol in the batch mode from the command line using pymol -cqr script.py But I get the following errors. Could you please advice me how to prevent these errors? Traceback (most recent call last): File "", line 1, in ImportError: No module named pymol PyMOL-ERRO

[PyMOL] execute a set of pml files on a set of pse files iteratively and saving without opening the Pymol GUI

Hi everyone, I have a set of (240 files) of pse files like 1.pse 2.pse . . . 240.pse I also have a set of(240 files) pml files like 1.pml 2.pml . . . 240.pml I want execute the pml files iteratively on the corresponding pse files and save the new pse files as 1new.pse,2new.pse, so on. from the

[PyMOL] superimposing pse files

Hello everyone, I have created molecular tunnels for two starting points using CAVER and saved them as two different pse(Pymol session) files. Is there any way I can superimpose the two tunnels? Can I superimpose the two pse files (I tried and it doesn't happen. One pse overrides the other). I wan