I have two different pdb formats that I am trying load into Assemble. One works and the other does not. The one that does not, is an output of an RNA prediction program called MC-Sym. I can put an example of each format (different H notation).

Normal (works):
ATOM 1 P GUA N 1 10.728 90.102 59.876 1.00 0.00 N1
ATOM 2 O1P GUA N 1 11.487 88.829 59.805 1.00 0.00 N1
ATOM 3 O2P GUA N 1 10.507 90.642 61.240 1.00 0.00 N1
ATOM 4 O5' GUA N 1 9.274 89.726 59.300 1.00 0.00 N1
ATOM 5 C5' GUA N 1 9.160 89.055 58.054 1.00 0.00 N1
ATOM 6 H5' GUA N 1 9.732 88.127 58.086 1.00 0.00 N1
ATOM 7 H5'' GUA N 1 9.572 89.685 57.262 1.00 0.00 N1
ATOM 8 C4' GUA N 1 7.708 88.714 57.709 1.00 0.00 N1
ATOM 9 H4' GUA N 1 7.720 88.101 56.807 1.00 0.00 N1
ATOM 10 O4' GUA N 1 7.082 87.964 58.752 1.00 0.00 N1
ATOM 11 C1' GUA N 1 5.861 88.590 59.133 1.00 0.00 N1
ATOM 12 H1' GUA N 1 5.065 87.848 59.212 1.00 0.00 N1
ATOM 13 N9 GUA N 1 5.960 89.255 60.462 1.00 0.00 N1
ATOM 14 C8 GUA N 1 6.898 89.096 61.459 1.00 0.00 N1
ATOM 15 H8 GUA N 1 7.829 88.566 61.300 1.00 0.00 N1
ATOM 16 N7 GUA N 1 6.553 89.611 62.616 1.00 0.00 N1
ATOM 17 C5 GUA N 1 5.318 90.213 62.353 1.00 0.00 N1
ATOM 18 C6 GUA N 1 4.414 90.962 63.190 1.00 0.00 N1
ATOM 19 O6 GUA N 1 4.496 91.233 64.388 1.00 0.00 N1
ATOM 20 N1 GUA N 1 3.299 91.418 62.523 1.00 0.00 N1
ATOM 21 H1 GUA N 1 2.631 91.964 63.039 1.00 0.00 N1
ATOM 22 C2 GUA N 1 3.053 91.153 61.220 1.00 0.00 N1
ATOM 23 N2 GUA N 1 2.119 91.838 60.635 1.00 0.00 N1
ATOM 24 H21 GUA N 1 1.715 92.591 61.159 1.00 0.00 N1
ATOM 25 H22 GUA N 1 2.077 91.747 59.635 1.00 0.00 N1
ATOM 26 N3 GUA N 1 3.818 90.426 60.428 1.00 0.00 N1
ATOM 27 C4 GUA N 1 4.955 89.991 61.043 1.00 0.00 N1
ATOM 28 C3' GUA N 1 6.854 89.949 57.412 1.00 0.00 N1
ATOM 29 H3' GUA N 1 7.254 90.833 57.916 1.00 0.00 N1
ATOM 30 C2' GUA N 1 5.502 89.544 57.987 1.00 0.00 N1
ATOM 31 H2'' GUA N 1 4.969 90.438 58.309 1.00 0.00 N1
ATOM 32 O2' GUA N 1 4.737 88.827 57.021 1.00 0.00 N1
ATOM 33 H2' GUA N 1 5.009 89.222 56.173 1.00 0.00 N1
ATOM 34 O3' GUA N 1 6.689 90.127 56.016 1.00 0.00 N1

MC-Sym (doesn't work):
ATOM 1 C1* G A 1 6.018 88.752 59.087 1.00 0.00
ATOM 2 C2* G A 1 5.463 89.763 58.083 1.00 0.00
ATOM 3 C3* G A 1 6.741 90.292 57.448 1.00 0.00
ATOM 4 C4* G A 1 7.677 89.150 57.476 1.00 0.00
ATOM 5 C5* G A 1 9.141 89.511 57.408 1.00 0.00
ATOM 6 H1* G A 1 5.419 87.843 59.040 1.00 0.00
ATOM 7 H2* G A 1 4.845 90.555 58.505 1.00 0.00
ATOM 8 H3* G A 1 6.933 91.270 57.888 1.00 0.00
ATOM 9 H4* G A 1 7.537 88.523 56.596 1.00 0.00
ATOM 10 O1P G A 1 11.920 89.802 57.300 1.00 0.00
ATOM 11 O2* G A 1 4.620 89.104 57.158 1.00 0.00
ATOM 12 O2P G A 1 12.063 87.766 58.629 1.00 0.00
ATOM 13 O3* G A 1 6.689 90.127 56.016 1.00 0.00
ATOM 14 O4* G A 1 7.375 88.521 58.750 1.00 0.00
ATOM 15 O5* G A 1 9.932 88.309 57.445 1.00 0.00
ATOM 16 P G A 1 11.523 88.373 57.388 1.00 0.00
ATOM 17 1H5* G A 1 9.404 90.153 58.249 1.00 0.00
ATOM 18 2H5* G A 1 9.345 90.061 56.489 1.00 0.00
ATOM 19 HO2* G A 1 4.277 89.747 56.534 1.00 0.00
ATOM 20 C2 G A 1 3.053 91.153 61.220 1.00 0.00
ATOM 21 C4 G A 1 4.955 89.991 61.043 1.00 0.00
ATOM 22 C5 G A 1 5.318 90.213 62.353 1.00 0.00
ATOM 23 C6 G A 1 4.414 90.962 63.190 1.00 0.00
ATOM 24 C8 G A 1 6.898 89.096 61.459 1.00 0.00
ATOM 25 H1 G A 1 2.631 91.964 63.039 1.00 0.00
ATOM 26 H8 G A 1 7.829 88.566 61.300 1.00 0.00
ATOM 27 N1 G A 1 3.299 91.418 62.523 1.00 0.00
ATOM 28 N2 G A 1 2.119 91.838 60.635 1.00 0.00
ATOM 29 N3 G A 1 3.818 90.426 60.428 1.00 0.00
ATOM 30 N7 G A 1 6.553 89.611 62.616 1.00 0.00
ATOM 31 N9 G A 1 5.960 89.255 60.462 1.00 0.00
ATOM 32 O6 G A 1 4.496 91.233 64.388 1.00 0.00
ATOM 33 1H2 G A 1 1.961 91.732 59.643 1.00 0.00
ATOM 34 2H2 G A 1 1.550 92.477 61.172 1.00 0.00

The main difference I see besides for example G vs. GUA for the resid notation, is the H atom naming notation. I am wondering if there is a work around for this, or can Assemble handle the different naming notations in these two different pdb files some how? Thanks!

Jeremy

ps: Here is the error output from Assemble:

Error


Message:
fr.unistra.ibmc.paradise.goloka.core.analysis.AnalysisException: fr.unistra.ibmc.paradise.goloka.core.io.FileParsingException: fr.unistra.ibmc.paradise.goloka.BiologicalSymbolException: Edge 3 unknown : . choose between H, S & W
Level:
SEVERE
Stack Trace:
fr.unistra.ibmc.paradise.goloka.core.io.FileParsingException: fr.unistra.ibmc.paradise.goloka.BiologicalSymbolException: Edge 3 unknown : . choose between H, S & W
fr.unistra.ibmc.paradise.goloka.core.io.RNAMLFileIO.parseFile(RNAMLFileIO.java:72)
fr.unistra.ibmc.paradise.goloka.services.analysis.rnaview.RnaviewAnalysis.run(RnaviewAnalysis.java:97)
fr.unistra.ibmc.paradise.goloka.services.analysis.RequestBehaviour$1AnalysisWorker.doInBackground(RequestBehaviour.java:81)
org.jdesktop.swingworker.SwingWorker$1.call(Unknown Source)
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
java.util.concurrent.FutureTask.run(FutureTask.java:138)
org.jdesktop.swingworker.SwingWorker.run(Unknown Source)
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
java.lang.Thread.run(Thread.java:619)