[PyMOL] pymol crashes when try opening a file created by gromacs

Hi! I am running a simulation using Gromacs. I was able to visualise the .pdb file using pymol. But when I tried to visuals the files created by Gromacs, pymol crashed. Can you please help? Thank you in advance! -- Regards, Raag

Re: [PyMOL] PyMOL-users Digest, Vol 112, Issue 8

Thank you so much Tsejrk and Seera for your kind help!! Thomas replied. He said that I can load the .gro files too by giving a command on the terminal. PyMOL> cd your/working/directory PyMOL> load file.gro It worked!! Thank you so much, once again. I'm sharing his reply here so that in case any

[PyMOL] (no subject)

Hi! What is the command for superimposing a .gro file and a .pdb file in PyMOL? I tried opening the .gro file and then loading the .pdb file. Consequently, I could only see the latter and not the former. Thank you in advance! -- Regards, Raag

[PyMOL] superimposing and aligning

Hi! how do you align two molecules when you superimpose? Can you please tell me the exact command? Thank you so much and sorry for the bother! -- Regards, Raag -- ___ PyMOL-use

[PyMOL] plugin manager

Hi! I needed to install PyTMs but am unable to do so. I can't find the plugin manager. In the menu, after the wizard I have 'help' not 'plugins'. I installed the educational version of MacPyMOL in around Aug/Sep 2015. Looking forward to your help, Regards, Raag --

[PyMOL] PyTMs

Hi! PyTMs is wonderful and permits me to really play around with a lot of different PTMs! In PyTMs, I can find some of the PTMs that I need to work on (acetylation and phosphorylation) for my PhD. However, there are some PTMs that I need to work on for my PhD, but I can't find those features in P

[PyMOL] unable to install caver plugin

Hi! I'm using MacPyMOL and have been trying to install the Caver plugin. However, it gives an error saying that it has been installed but initialization failed. Please guide! Regards, Raag -- Check out the vibrant tech c

[PyMOL] Unable to install CAVER plugin

Hi! I'm using MacPyMOL (PyMOL 1.7.4.5 Edu Incentive Product) and have been trying to install the Caver plugin. However, it gives an error saying that it has been installed but initialization failed. Please help! Regards, Raag -

[PyMOL] show as cartoon: dashed lines

Hi! I predicted the structure of a heterodimer using Swiss Model. Then I simulated it using GROMACS. When I opened the .gro file in PyMOL, it appeared normal at first. However, when I chose show as cartoon, I got dashed lines. I have attached a screenshot of the same. This problem did not occur bef

[PyMOL] unable to produce publication quality images

Hi! I have been using pymol since 2015. I was able to make publication quality images back then. However, I can no longer use the ray command. I have pymol for eucational use. Looking forward to your kind help! Regards, Raag Saluja