aalhossary/crosslinx

CrossLinX is the acronym of protein CrossLINks eXplorer.

crosslinx's Issues

Resolution lost in cryo-EM

There are a couple of dozen lines with Resolution = 0.
Each was cryo-EM with resolutions in the range 3.35 - 3.8 Å.
Somehow the resolution value is getting lost.

(3j8h, 3jaj) are available only in mmCIF.
(6hu9, 7o3e) are available as PDB files and have geometrically correct looking His-Tyr bonds.

Make it run in parallel

Use MPI wrapper to run several instances of the application on multiple machines.

Can also explore Java parallel capabilities.

Better to do it in CLI mode only, because it would be problematic to do it in GUI mode.

Renaming to CrossLinkX

Rename the generated jar, the window titles, the help and about section, and finally the repository itself.

Missed Cross Link in 5NGQ

5NGQ, chain E has DLS (di-acetyl-lysine) bonded to DCY206. So the acetyl fills the N-C gap, not an oxygen.
FG finds this one because FG is looking only for a Cys/Dcy/CSO sulfur gamma within 3.1 Å of any nitrogen that is not (a mainchain nitrogen or a sidechain nitrogen in (Asn/Gln or the D forms of those, Dsg/Dgn)). So the N can be in a ligand or a non-standard residue such as DLS.

Fetch and display electron density maps around putative interactions

Fetching the electron density map should be added to BioJava.
Then clicking a found cross link should focus on it (as in #1 ) and show the electron density map around the interaction

Add a list of found interactions per structure

Clicking one of the listed interactions should focus on that found interaction.
This can be a shorter JList below the found interactions JList.

ensure consistency with FGJM

All methods details are here
This link goes to an updated/clarified version, which has not yet been released in the forthcoming FGiJ version 3.71. In some cases, including His-Tyr, the rationale for the cutoff distance is explained.