Re: [PyMOL] Question on geometry option in replace command

Dear Lei, the best way to build a new molecule is via the builder in the GUI. The commands "replace" or "attach" are not well documented. I could reproduce your problem and I think PyMOL runs some kind of check routine after you issue a replace or attach command and it will reset the atomic

Re: [PyMOL] Anaconda python-bundle package documentation or help

Dear Csongor, as far as I know it is not well documented how you can access the python objects and its methods or data structures created by the PyMOL API. For many tasks one usually finds some information, often PyMOL or python scripts. Concerning your example of the hydrogen bonds determine

Re: [PyMOL] [pymol] Assembly

Dear Matthias, use: set assembly, 1 set all_states, 1 fetch 7epp GUI "generate symmetry mates" does not work as the unit cell is defined as: CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1 resulting in symmetry mates shifted by 1.0 Ang. in x y z. We need a "generate biological assem

Re: [PyMOL] How to install APBS on PyMol

Hi Luigi, I assume you are running Open source PyMOL 2.X and tried to install the apbsplugin.py file via the Plugin manager. I just tried this and got the same error from the Plugin manager. I am no expert here, but I assume this is related to the fact that this plugin uses the Tkinter GUI and

Re: [PyMOL] Dss when creating movie from dcd traj

Hi Effie, try to load the trajectory with the option discrete=1: load trajectory.dcd, discrete=1 Best, Norbert Am 09.11.2023 um 19:38 schrieb Effie Artikis: Hello, I’ve uploaded my MD simulation and am trying to create a movie but I’ve noticed that when I play the MD simulation, the second

Re: [PyMOL] How to delete/hide unwanted poses in Pymol?

Hi Luigi, that depends on how the data are read into PyMOL and how the coordinate files are structured. For example, if you read in a pdb file ligand1.pdb, which contains this ligand with different poses having different residue numbers and next you read in a second pdb file for the second l

Re: [PyMOL] Changing dashed aromatic circle to a proper circle

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Re: [PyMOL] help with PyMOL rename command

Dear wdela, usually each atom in a residue has a different atom name. If this is not the case, the rename command will rename the atoms, that do not have unique names within a residue. It appears as if you cannot specify which atom names the renamed atoms will get. If you want to change to spe

Re: [PyMOL] File attachments

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Re: [PyMOL] separate two molecule as an object from a complex of four molecules

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[PyMOL] hydrogen bond detection via the dist command and mode=2 option

Dear PyMOL users and experts, I wonder if anybody has insight into the following problem concerning the determination of hydrogen bonding interactions in PyMOL via the dist command with the mode=2 option. For an upcoming local PyMOL workshop, which I organize for PhD students, I tried to find

[PyMOL] Gaps in cartoon representation due to non-continuous residue numbers

Dear PyMOL experts, in GPCR crystal structures it is quite common to have fusions with lysozyme or BRIL in the third intracellular loop. The residue numbers of the inserted domains are often incremented by 1000. As a result, the two residues at the fusion point jump from for example 223 to 100

[PyMOL] stereo rotation lost with draw command

I want to render a stereo image using the "draw" command instead of ray tracing. Unfortunately, the stereo rotation is lost with the command and the image is flat. If this is not a bug, is there a way to change this behaviour? Norber