Arthur Zalevsky
The description of the hydrogen mass scaling in the documentation is a little bit vague. It seems that it is not a common hydrogen repartitioning approach (the subtraction part is...
The recent version of VCF-kit is unusable right after the installation: ``` [nknyazeva@head02 silwer]$ vk Traceback (most recent call last): File "/home/nknyazeva/.local/bin/vk", line 9, in load_entry_point('VCF-kit==0.1.6', 'console_scripts', 'vk')() File "/home/tools/python/Python-2.7/lib/python2.7/site-packages/pkg_resources/__init__.py",...
To improve the integration with raw crosslinking-MS data Andrea proposed adding an `evidence` or `provenance` column to the `_ihm_cross_link_list` table. Here is an example of the current API response: ```...
There are multiple types of restraints that are usually applied during modeling (like forcefields, excluded volume, or connectivity) that we do not record right now. In previous discussions, we considered...
We already have fields or tables for depositors to report EM3D, EM2D, and SAS fits values (basically, validation metrics) on a per-model basis: ` _ihm_3dem_restraint.cross_correlation_coefficient` field `_ihm_sas_restraint.chi_value` field ` _ihm_2dem_class_average_fitting`...
* For entries 165-198 (Andrea's collection), we can replace initial jPOST IDs with ProteomeExchange PXD-style IDs (JPST001851 to PXD036833). Andrea is ok with the change. * We should also enforce...
In the scenario when a residue is represented on multiple scales simultaneously: 1) martini-like (multiple beads per residue, `by-feature`) 2) Ca (on bead per residue, 'by-residue`) It's impossible to distinguish...
I couldn't find examples of `multi-residue` granularity. It seems that in all relevant entries (like NPC), it was replaced with `by-feature.` I think documentation regarding the selection of `by-residue,` `multi-residue`,...
`restraints.angles.as_JSON()` throws error. Steps to reproduce: ``` Apptainer> molprobity.molprobity probe=False coot=False prefix=1hao_mp pickle=True 1hao.cif Apptainer> mmtbx.python Python 3.7.16 | packaged by conda-forge | (default, Dec 13 2022, 23:24:55) [GCC 11.3.0]...