error using nma.pdbs()

[Former user]

modes <- nma.pdbs(pdbs, rm.gaps=FALSE, ncore=4)

Details of Scheduled Calculation: ... 8 input structures ... storing 426 eigenvectors for each structure ... dimension of x$U.subspace: ( 498x426x8 ) ... coordinate superposition prior to NM calculation ... estimated memory usage of final 'eNMA' object: 13 Mb

| | 0% Error in modes.array[, , i] = tmp.modes$U : number of items to replace is not a multiple of replacement length

[Barry Grant]

Thank you for posting this issue. Could you please provide some additional information about where your pdbs input object came from and its content?

One possibility is to run the following commands and send me an email [e-mail] with the pdbs.RData file attached.

> # First send (via copy and paste in reply here) the output of calling 'pdbs', e.g.
> pdbs
                               1        .         .         .         .         50
[Truncated_Name:1]1rx2_A.pdb   MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLDKPVIMGRHTWESI
[Truncated_Name:2]1rx4_A.pdb   MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLDKPVIMGRHTWESI
[Truncated_Name:3]1rg7_A.pdb   MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLDKPVIMGRHTWESI
                               **************************************************
                               1        .         .         .         .         50
<cut>
Call:
  pdbaln(files = files)

Class:
  pdbs, fasta

Alignment dimensions:
  3 sequence rows; 159 position columns (159 non-gap, 0 gap)

+ attr: xyz, resno, b, chain, id, ali, resid, sse, call

> # Then if necessary email me this 'pdbs.RData' file.
> save(pdbs, file="pdbs.RData")

[Lars Skjærven]

Any more info on this? Would be good to dig into the pdbs object as Barry suggests here.

[Barry Grant]

I have not heard back from the poster so I am closing this issue. Please do re-open if required.