PCA WebApp crash

[Barry Grant]

Using 7HVP and increasing the number of hits to 25 leads to an Align tab error: "missing value where TRUE/FALSE needed"

Also using 1GC1 crashes the app

[Lars Skjærven]

Nice. works when you reload after the crash :)

[Lars Skjærven]

found the problem. pushing a fix tomorrow

[Lars Skjærven]

The 7HVP cases was related to a hit 3GI0_B which only contains alt atom records. all of these were deleted since we use argument rm.alt=TRUE. Cases like these are omitted from the current version of the pca webapp, but I have added a message in the ALIGN tab.

[Barry Grant]

Thanks, the 1gc1 works now but I still get a user unintelligible "missing value where TRUE/FALSE needed" on the ALIGN tab while using 7hvp and increasing to 25 hits.

[Lars Skjærven]

hmm. so my fix only worked for the archive mode. seems to crash in pdbsplit() --> write.pdb(). should be fixed with a test in pdbsplit(). see latest commit

[Lars Skjærven]

trying again

[Barry Grant]

Sorry 3GI0_B still causes crash but now with two error msgs...

[Lars Skjærven]

hmm.. did you re-install bio3d? I made an update in the bio3d function pdbsplit()

# before update:
> get.pdb("3GI0")
> pdbsplit("3GI0.pdb", ids = c("3GI0_A", "3GI0_B"), overwrite=F)   

Error in if (check.lengths%%natom != 0) { : 
  missing value where TRUE/FALSE needed

# after update:
> pdbsplit("3GI0.pdb", ids = c("3GI0_A", "3GI0_B"), overwrite=F)   
[1] "split_chain/3GI0_A.pdb"
Warning message:
In pdbsplit("3GI0.pdb", ids = c("3GI0_A", "3GI0_B"), overwrite = F) :
  unmatched ids: 3GI0_B

# with rm.alt=F
> pdbsplit("3GI0.pdb", ids = c("3GI0_A", "3GI0_B"), overwrite=F, rm.alt=F)   
[1] "split_chain/3GI0_A.pdb" "split_chain/3GI0_B.pdb"

The part of pdbsplit() which has been updated:

if(length(new.pdb$xyz) > 0) {   ## <--- this line is added
   if(!file.exists(new.name) | overwrite )
      write.pdb(new.pdb, file = new.name, sse=TRUE)
   out <- c(out, new.name)
}

[Barry Grant]

yes that works, sorry!