James Krieger

longer compound IDs coming

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At current growth rates, we anticipate running out of three-character Chemical Component IDs by the end of 2023. After this point, the wwPDB will issue five-character alphanumeric accession codes for...

account for PDB FTP deprecation

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Dear all, The FTP protocol for file downloads has been losing popularity over the years in favor of HTTP/S. There are many advantages of HTTP/S including speed, statelessness, security (HTTPS),...

most versions of adjustText don't work

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We may want to stop supporting that feature completely

store hydrogen bonds between beta-strands

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The second part of the SHEET lines stores hydrogen bonds to previous beta-strands that indicate strand packing register e.g. 2tbv has the following. ``` SHEET 1 S1A 4 VAL A...

It looks like it's also possible to get Interpro families and Pfam families together, so we probably want to rename our function to searchInterproAndPfam and make it do that and...

This is a nice feature that gets triggered with altloc=None that makes separate coordinate sets for each altloc, copying shared atoms without altlocs across sets. It didn't previously work with...

parse GENESIS DCD

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Currently we get this error: ``` ----> 1 traj = parseDCD("Runs/002492_FlexProtGenesis/extra/output_000001.dcd") File ~/software/scipion3/software/em/ProDy/prody/trajectory/dcdfile.py:494, in parseDCD(filename, start, stop, step, astype) 473 def parseDCD(filename, start=None, stop=None, step=None, astype=None): 474 """Parse CHARMM format...

If two pdb files are loaded into ChimeraX, they can be joined into one file there, but it's not really a proper PDB file and ProDy doesn't read it properly...

It would be nice to include some way of building and reading from a graph based on Doruker et al 2002 (https://pubmed.ncbi.nlm.nih.gov/11913377/) It could also be good to have something...

At the moment, we only write secondary structure info