search

scipion-em / scipion-em-cryosparc2

Plugin to use cryoSPARC2 programs within the Scipion framework
GNU General Public License v3.0
2 stars 0 forks source link

flex mesh prepare #171

Open rmarabini opened 1 week ago

rmarabini commented 1 week ago

Hi,

Flex mesh prepare visualize should offer the possibility of visualizing the created mesh.

For example, after the execution of the protocol the following files are created:

J37_flex_mesh.csg J37_map.mrc J37_mask.csg J37_mask_hard.cs J37_mesh.cs J37_mesh_pdb.pdb events.bson job.json J37_map.cs J37_mask.cs J37_mask.mrc J37_mask_hard.mrc J37_mesh.pkl J37_volume.csg gridfs_data job.log

What I need to see is

chimera J37_map.mrc J37_mesh_pdb.pdb

where the pdb file contains the mesh

pconesa commented 5 days ago

Does this receive a pdb and outputs a pdb with a mesh?

rmarabini commented 5 days ago

Hi,

The input is a 3D map (volume) and the output is a mesh of tetrahedrons. In purity the input is the protocol flex data prepare. Additionally, for display purposes it creates a PDB file. This file is a hack that allows chimera to visualize the mesh but is not used in any subsequent protocol.

Do not worry about this issue, I will add the visualization to the protocol and send a pull request. (I will create other pull request for https://github.com/scipion-em/scipion-em-cryosparc2/issues/170) but could you solve issue https://github.com/scipion-em/scipion-em-cryosparc2/issues/172

Thanks

Roberto