issue with VMD and pyrite

[Nasser]

I’m getting thies error after pasting this code in the VMD TKConsole " File rendering failed, check the VMD text console for errors".
can someone help me. I really need pyrite for my presentation but seems no one helps me out. I appreciate if someone make a video and showhow to start form scratch. how to use VMD to make OBJ file, import it into Blender and use pyrite to give motion to the protein. I really apprecite. It’s taking me alot of time to figure out but I wasn’t able to solve the issues yet.
I"m pasiting this code to the TKConsole:
set m {
{{1.0 0.0 0.0 0.0}
{0.0 1.0 0.0 0.0}
{0.0 0.0 1.0 0.0}
{0.0 0.0 0.0 1.0}}
{{1.0 0.0 0.0 0.0}
{0.0 1.0 0.0 0.0}
{0.0 0.0 1.0 0.0}
{0.0 0.0 0.0 1.0}}
{{1.0 0.0 0.0 0.0}
{0.0 1.0 0.0 0.0}
{0.0 0.0 1.0 0.0}
{0.0 0.0 0.0 1.0}}
{{1.0 0.0 0.0 0.0}
{0.0 1.0 0.0 0.0}
{0.0 0.0 1.0 0.0}
{0.0 0.0 0.0 1.0}}
}

for {set i 0} {$i < [molinfo num]} {incr i} {
molinfo ${i} set {center_matrix rotate_matrix scale_matrix global_matrix} $m
}

[Jacob Durrant]

Hi Nasser. Much thanks for your interest in Pyrite. I’d recommend using BlendMol to generate the mesh to then use in Pyrite, rather than trying to generate the mesh directly in VMD. One of the reasons we created BlendMol is so that users would have to bother with creating the mesh directly. Here’s a video that might help: https://git.durrantlab.pitt.edu/jdurrant/blendmol#video-s3-blendmolpyrite

Take care,

Jacob

[NASSER FAGHIH]

threre is something in your video that is confusing me.
first you upload "shroom2-rock1.first_frame.pdb". you get this file from protein data base or you made it in bledmol?
then you upload another file in pyrite "shroom2-rock1.traj.pdb". I’m confused how you generated this file? you used blendmol to generate this file?

[Jacob Durrant]

Hi Nasser. There are two steps. The first step is to generate a mesh of your protein. BlendMol is the best tool for that. You provide BlendMol with a single-frame PDB file (or a VMD state file), and it imports that file into Blender as a mesh. The PDB file can come from any source (e.g., the Protein Data Bank).

The second step is to animate the mesh by imparting to it the motions present in an MD trajectory file. That MD trajectory file needs to be a multiframe PDB file. (So the trajectory is also a PDB file.) You can convert other trajectory formats to the multiframe PDB format using VMD as well.

Unfortunately, both Blender and VMD are not very user-friendly programs. If you’re not familiar with those programs, you might want to consider other options for visualization, such as PyMol or Chimera.

Best of luck.

[NASSER FAGHIH]

Thank you Jacob for clarifying. I was wondering how I can make the MD trajectory file with DCD format? I searched online to find a tutorial video but I wasn’t able to. do you have any suggestions? Is it possible to make MD trajectory file by VMD or Pymol?

[Jacob Durrant]

Hi Nasser. VMD can do the conversion. Just load the trajectory into VMD, click on it’s name in the VMD Main window to select it, right click on the same name to pull up a context menu, click "Save Coordinates…", then put as your "Selected atoms" something like "protein", make sure the File type is set to pdb, and press the "Save…" button.

Here’s a link related to what you want to do, in case it helps: https://www.researchgate.net/post/How_to_write_pdb_file_of_protein_ligand_system_of_a_particular_frame_using_VMD

Take care.

[Author]

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