Hello,
I have just updated to JSmol 14.0.17, and I have found myself unable to
execute the script "set pdbaddhydrogens true" before loading a specific
structure (2YJP) without JSmol crashing with the following error:
"ERROR creating model: TypeError: f is undefined"
Specifically, the following commands are executed:
set pdbaddhydrogens;
set antialiasDisplay;load /pdbuploads/2yjp-0/2yjp.pdb;slab off; spin off;
trace off; set ambient 40; set specpower 40;select none; selectionHalos on;
The output produced is as follows, on the first run (after the first run,
the ETHANEDIOL and HOH calls do not show up):
pdbAddHydrogens = true
antialiasDisplay = true
fetching http://www.rcsb.org/pdb/files/ligand/EDO.cif
1,2-ETHANEDIOL
fetching http://www.rcsb.org/pdb/files/ligand/HOH.cif
WATER
File Error:ERROR creating model: TypeError: f is undefined
script ERROR: ERROR creating model: TypeError: f is undefined
----
load >> "/charmming/pdbuploads/admin/2yjp-0/2yjp.pdb" <<"
2yjp.pdb is 2YJP downloaded directly from PDB.org. The scripts I am
including in my HTML are:
" <script type="text/javascript"
src="/charmming/js/jsmol/js/JSmolCore.js"></script>
<script type="text/javascript"
src="/charmming/js/jsmol/js/JSmolApplet.js"></script>
<script type="text/javascript"
src="/charmming/js/jsmol/js/JSmolApi.js"></script>
<script type="text/javascript"
src="/charmming/js/jsmol/js/j2sjmol.js"></script>
<script type="text/javascript"
src="/charmming/js/jsmol/js/JSmol.full.js"></script>
<script type="text/javascript"
src="/charmming/js/jsmol/js/JSmoljQueryExt.js"></script>
"
This error only seems to occur with structures similar to 2YJP, with metal
ion ligands. I have tried 1YJP and 3TIM and they both get hydrogens
generated without errors. I have tried a molecule with a ligand, 1ATL,
which has the ligand OQI, and it had hydrogens added without error. I then
tried to load 1CKU, which has iron-sulfur clusters, and I got the same
error as before. I know 2YJP has a zinc ion ligand in its structure. Is
this what is breaking pdbaddhydrogens?
(Note: all of these structures were downloaded directly from PDB.org)
Also, I have noticed that pdbaddhydrogens does not add hydrogens to water
oxygens. Is this intended behavior?
-Vinushka Schalk
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