On 08/18/2015 07:06 AM, Robert Hanson wrote:
> http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/
>
> Now holds the latest test build that I hope will lead to Jmol 14.4.0
> release later this week or next.
>
> I would it if you would test it if you have a site and have the time to do
> that.
>
Bob, so far I have found the following problems:
1) Loading state with "%" in label
----- Example 1 ------
load =1deh;
select @1;
label "75%%";
write IMAGE PNGJ "test.png";
load "test.png"
script ERROR: java.lang.ArrayIndexOutOfBoundsException: 50
----line 37 command 37 of function _setfilestate:
load >> "1deh.pdb.gz" <<
----line 4 command 4 of function _setstate:
_setFileState
----line 303 command 9 of test.png|state.spt:
_setState
----
load "test.png"
-------------------------
It works if the command 'label "75%%";' is left out.
2) Loading state with mmCIF data loaded from file
---- Error message -----------
script compiler ERROR: invalid context for end {
----line 66 command 43 of tor1_direct.spt:
<<<<
------- State snippet - line 66 is last line ----------
function _setFileState() {
set allowEmbeddedScripts false;
set appendNew true;
set appletProxy "";
set applySymmetryToBonds false;
set autoBond false;
set axesOrientationRasmol true;
set bondRadiusMilliAngstroms 150;
set bondTolerance 0.45;
set defaultLattice {0.0 0.0 0.0};
set defaultLoadFilter "";
set defaultLoadScript "";
set defaultStructureDssp true;
set defaultVDW Auto;
set forceAutoBond false;
#set defaultDirectory
"/home/waldorf/rhuehne/xp_share/statistical_computing_2015/live_demo/jmol-14.3.16_2015.08.17";
#set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";;
#set loadLigandFormat "http://www.rcsb.org/pdb/files/ligand/%FILE.cif";;
#set smilesUrlFormat
"http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True";;
#set nihResolverFormat
"http://cactus.nci.nih.gov/chemical/structure/%FILE";;
#set pubChemFormat
"http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";;
#set edsUrlFormat
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";;
#set edsUrlFormatDiff
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE_diff.omap";;
#set edsUrlCutoff
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat";;
set bondingVersion 1;
set legacyAutoBonding false;
set legacyHAddition false;
set legacyJavaFloat false;
set minBondDistance 0.4;
set minimizationCriterion 0.001;
set minimizationSteps 100;
set multipleBondBananas false;
set pdbAddHydrogens false;
set pdbGetHeader false;
set pdbSequential false;
set percentVdwAtom 23;
set smallMoleculeMaxAtoms 40000;
set smartAromatic true;
{
var mmcifdata = "data_\n\n_database_PDB_rev.num
1\n\nloop_\n_atom_site.group_PDB\n_atom_site.id\n_atom_site.type_symbol\n_atom_site.label_alt_id\n_atom_site.pdbx_PDB_ins_code\n_atom_site.Cartn_x\n_atom_site.Cartn_y\n_atom_site.Cartn_z\n_atom_site.auth_seq_id\n_atom_site.auth_comp_id\n_atom_site.auth_asym_id\n_atom_site.auth_atom_id\n_atom_site.B_iso_or_equiv\nHETATM
1 F . ? 8.283288 0.5313158 5.485306 1 AF_GEN 1 F 0.0\nHETATM 2 O . ?
8.528945 3.1111236 9.93697 2 OB_INC 1 O 23\nHETATM 3 O . ? 6.0449963
8.852097 6.743042 3 OB_INC 1 O 21\nHETATM 4 O . ? 0.9487134 0.09274781
6.8239126 4 OB_INC 1 O 22\nHETATM 5 O . ? 4.817381 1.4741284 8.931922 5
OB_INC 1 O 25.2964\nHETATM 6 O . ? 7.227149 1.953963 2.3662586 6 OB_INC
1 O 21.2766\nHETATM 7 O . ? 3.7307687 6.521468 1.4611292 7 OB_INC 1 O
20.4255\nHETATM 8 O . ? 1.7012602 0.6498462 8.378336 8 OB_INC 1 O
22.314\nHETATM 9 O . ? 5.2661505 0.7180977 1.8682116 9 OB_INC 1 O
66.5289\nHETATM 10 O . ? 5.704546 7.329689 0.4776889 10 OB_INC 1 O
33.4694\nHETATM 11 O . ? 5.557795 5.6229663 0.24342775 11 OB_INC 1 O
19.2488\nHETATM 12 O . ? 5.0318737 8.574695 5.3713326 12 OB_INC 1 O
20.3\nHETATM 13 O . ? 5.2738314 1.5182424 1.6378951 13 OB_INC 1 O
21.6\nHETATM 14 O . ? 2.3375292 2.7180953 8.059456 14 OB_INC 1 O
48.7179\nHETATM 15 O . ? 6.9656067 7.771125 1.2366229 15 OB_INC 1 O
56.4103\nHETATM 16 O . ? 8.207472 3.2507496 6.00739 16 OB_INC 1 O
0\nHETATM 17 O . ? 7.4468565 5.045697 7.537592 17 OB_DEC 1 O
-41.8685\nHETATM 18 O . ? 6.303235 8.634991 7.192274 18 OB_INC 1 O
20\nHETATM 19 O . ? 9.483559 8.284061 8.199555 19 OB_INC 1 O 0\nHETATM
20 O . ? 4.152029 1.1701101 2.2749436 20 OB_INC 1 O 30\nHETATM 21 O . ?
4.770071 2.7501268 2.6243048 21 OB_INC 1 O 0\nHETATM 22 F . ? 9.550337
9.689629 7.4191 22 AF_OTF 1 F 0.0\nHETATM 23 F . ? 8.728293 8.193404
6.062113 23 AF_GEN 1 F 0.0\nHETATM 24 F . ? 2.0784569 8.377502 6.8328657
24 AF_GEN 1 F 0.0\nHETATM 25 F . ? 4.306638 1.8817282 3.2492442 25
AF_GEN 1 F 0.0\nHETATM 26 F . ? 9.330269 0.41205764 9.709152 26 AF_GEN 1
F
0.0\nloop_\n_struct_conn.id\n_struct_conn.conn_type_id\n_struct_conn.ptnr1_auth_asym_id\n_struct_conn.ptnr1_label_atom_id\n_struct_conn.ptnr1_auth_comp_id\n_struct_conn.ptnr1_auth_seq_id\n_struct_conn.ptnr2_auth_asym_id\n_struct_conn.ptnr2_label_atom_id\n_struct_conn.ptnr2_auth_comp_id\n_struct_conn.ptnr2_auth_seq_id\n1
covale 1 F AF_GEN 1 1 O OB_INC 2\n2 covale 1 F AF_GEN 1 1 O OB_INC 3\n3
covale 1 F AF_GEN 1 1 O OB_INC 4\n4 covale 1 F AF_GEN 1 1 O OB_INC 5\n5
covale 1 F AF_GEN 1 1 O OB_INC 6\n6 covale 1 F AF_GEN 1 1 O OB_INC 7\n7
covale 1 F AF_GEN 1 1 O OB_INC 8\n8 covale 1 F AF_GEN 1 1 O OB_INC 9\n9
covale 1 F AF_GEN 1 1 O OB_INC 10\n10 covale 1 F AF_GEN 1 1 O OB_INC
11\n11 covale 1 F AF_GEN 1 1 O OB_INC 12\n12 covale 1 F AF_GEN 1 1 O
OB_INC 13\n13 covale 1 F AF_GEN 1 1 O OB_INC 14\n14 covale 1 F AF_GEN 1
1 O OB_INC 15\n15 covale 1 F AF_GEN 1 1 O OB_INC 16\n16 covale 1 F
AF_GEN 1 1 O OB_DEC 17\n17 covale 1 F AF_GEN 1 1 O OB_INC 18\n18 covale
1 F AF_GEN 1 1 O OB_INC 19\n19 covale 1 F AF_GEN 1 1 O OB_INC 20\n20
covale 1 F AF_GEN 1 1 O OB_INC 21\n21 covale 1 O OB_INC 2 1 F AF_GEN
1\n22 covale 1 O OB_INC 3 1 F AF_GEN 1\n23 covale 1 O OB_INC 4 1 F
AF_GEN 1\n24 covale 1 O OB_INC 5 1 F AF_GEN 1\n25 covale 1 O OB_INC 6 1
F AF_GEN 1\n26 covale 1 O OB_INC 7 1 F AF_GEN 1\n27 covale 1 O OB_INC 7
1 F AF_OTF 22\n28 covale 1 O OB_INC 8 1 F AF_GEN 1\n29 covale 1 O OB_INC
9 1 F AF_GEN 23\n30 covale 1 O OB_INC 9 1 F AF_GEN 1\n31 covale 1 O
OB_INC 10 1 F AF_GEN 23\n32 covale 1 O OB_INC 10 1 F AF_GEN 24\n33
covale 1 O OB_INC 10 1 F AF_GEN 1\n34 covale 1 O OB_INC 11 1 F AF_GEN
1\n35 covale 1 O OB_INC 12 1 F AF_GEN 1\n36 covale 1 O OB_INC 13 1 F
AF_GEN 1\n37 covale 1 O OB_INC 14 1 F AF_GEN 1\n38 covale 1 O OB_INC 14
1 F AF_GEN 25\n39 covale 1 O OB_INC 15 1 F AF_GEN 1\n40 covale 1 O
OB_INC 16 1 F AF_GEN 1\n41 covale 1 O OB_DEC 17 1 F AF_GEN 1\n42 covale
1 O OB_DEC 17 1 F AF_GEN 26\n43 covale 1 O OB_INC 18 1 F AF_GEN 1\n44
covale 1 O OB_INC 19 1 F AF_GEN 1\n45 covale 1 O OB_INC 20 1 F AF_GEN
1\n46 covale 1 O OB_INC 21 1 F AF_GEN 1";
load "@mmcifdata" /*options*/ FILTER "addBonds"
};
}
-------------------------------------------------------
3) 'zoom [percent-zoom]' (from the documentation) doesn't work (also in
version 14.0.5)
---- Example 2 ---------
load =1deh;
zoom 120%;
script ERROR: number expected
----
zoom 120 >> % <<
------------------------
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany
Phone: +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail: [email protected]
Website: http://www.fli-leibniz.de
Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein
VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228
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