bgsu-rna / fr3d Goto Github PK

Im using zGetNTData to load .pdb files. Everything is ok when file is not so big but files like 1S72.pdb does not give any output, there are 0 interactions. Weird thing is that it is working on OS X with 4.0.3 octave but is not on Ubuntu 16.04 with octave 4.0.0, 4.0.2, 4.0.3, 4.2.0.

Can't download pdb files over http using urlread in R2007b.

I encountered a problem while reading file 488D.pdb. It enters infinite loop in file zBorderSS at line 121 and newer leaves. Used zAddNTData to read file.

affects zStackingOverlap.m

Need to make sure that FR3D properly handles biological assemblies of viral particles and doesn't run out of memory. The .pdb1 can be huge, for example 4ftb.pdb1 is about 38Mb, and I think I've seen even larger files.

In the file: zGetNTData, the warning has overlapping nucleotides and should be used with caution is produced when the array d, the atom distances has the condition
if d(min(10, length(d))) < 1
but in that case the base pairs are never computed!
In particular 1S72 fails with that condition.
Closing the if condition instead of the else
fixed the problem as here zGetNTData.txt.

I am not sure if side effects are produced.