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I'm a structural biologist working for a small biotech. Very interested in alternatives to PyMOL and ChimeraX. Took it for a small spin, right away I'm unable t

I'm a structural biologist working for a small biotech. Very interested in alternatives to PyMOL and ChimeraX. Took it for a small spin, right away I'm unable to move with the mouse using the free cam. Also was unable to open a .pdb file that I had locally (fetching from RCSB worked though). Really cool work thus far though. what type of docking are you planning to support? Autodock? Or something from scratch?

landl0rd 1y ago
Second this question; would be really cool if we had solid support for some of the qvina2/qvina-w/gpuvina implementations too along with stuff like haddock for affinity-based protein-protein. P.S. putting this here since I can't edit prior comment; fails to build on mac. It looks like you may have local updated versions of dependency crates (bio_apis) not pushed to gh since I see things like missing `rcsb::load_validation_2fo_fc_cif`, `f32x8` (I assume this is SIMD?), derive(Debug) on ReqError, etc. even with your forked versions of the crates.
- the__alchemist 1y ago
  Good call; I just updated the dependencies, and removed the local patches on the latest Github. Should compile now on Mac/x86, but I can't test. Is the Mac in question ARM CPU? I ask because the `f32x8` missing you see shouldn't be affected by the local patches. I hard-coded SIMD for x86. The latest push attempts to gate SIMD so it will still compile on ARM, but I haven't tested it. Good call on the qvina2/qvina-w/gpuvina implementations!
the__alchemist 1y ago
Would love to solve the PDB file and cam errors. Is there a way you can share the .PDB? Or, if it's exactly the one available on RCSB, if you share the ident, I can download it and fix. Re free cam: Does the arc cam work? Do the movement keys in free cam work? Does right clicking to select an atom or residue work? Are you holding M1 when moving the mouse? Thank you! For docking, I initially wanted to do ADV integration, but am leaning more towards from-scratch.

landl0rd 1y ago

Second this question; would be really cool if we had solid support for some of the qvina2/qvina-w/gpuvina implementations too along with stuff like haddock for affinity-based protein-protein. P.S. putting this here since I can't edit prior comment; fails to build on mac. It looks like you may have local updated versions of dependency crates (bio_apis) not pushed to gh since I see things like missing `rcsb::load_validation_2fo_fc_cif`, `f32x8` (I assume this is SIMD?), derive(Debug) on ReqError, etc. even with your forked versions of the crates.

the__alchemist 1y ago
Good call; I just updated the dependencies, and removed the local patches on the latest Github. Should compile now on Mac/x86, but I can't test. Is the Mac in question ARM CPU? I ask because the `f32x8` missing you see shouldn't be affected by the local patches. I hard-coded SIMD for x86. The latest push attempts to gate SIMD so it will still compile on ARM, but I haven't tested it. Good call on the qvina2/qvina-w/gpuvina implementations!

the__alchemist 1y ago

Would love to solve the PDB file and cam errors. Is there a way you can share the .PDB? Or, if it's exactly the one available on RCSB, if you share the ident, I can download it and fix. Re free cam: Does the arc cam work? Do the movement keys in free cam work? Does right clicking to select an atom or residue work? Are you holding M1 when moving the mouse? Thank you! For docking, I initially wanted to do ADV integration, but am leaning more towards from-scratch.