Lines Matching refs:files
44 # bug fix: PDB cryst1 record for NMR files not ignored
77 # bug fix: NWChem reader not reading files with lower-case-only atom names
107 # bug fix: AIMS files with empty lines preceding keyword lines are now recognized
111 # bug fix: CASTEP reader not understanding unit specifier in .cell files
185 # bug fix: isosurface not retrieving exact reference for jvxl files in state
195 # bug fix: isosurface reading of contoured JVXL files defaults to "nomesh nofill"
261 …: show structure not properly showing structure indices, IDs, or strand counts for PDB or CIF files
275 # * using IDTFConverter.exe, on Windows one can turn these files into VERY COMPACT U3D files.
456 # (as in certain cif files)
520 # new feature: MO LIST or SHOW MO LIST display listing of orbitals for all files
571 # bug fix: gzipped gzip file not read properly. (Jmol-FAH files)
749 # new feature: An XML reader for Materials Studio .xsd files http://accelrys.com/products/material…
843 # yes yes B yes atomType atom type (mol2, AMBER files) or atom name (other file types) -- Jmol 11.…
993 # --NMR files where you want just one model at a time and, once loaded, want to save the positions
1135 # bug fix: reading multiple files from a ZIP file collection, Jmol was forcing autobond
1154 # new feature: Spartan MO-Animation files can be read
1163 # bug fix -- trajectories with files having bonds can be a problem
1188 # bug fix: Spartan .spardir /input files not being read
1256 # bug fix: Some Spartan files not reading: Compound Document not properly finding root directory bl…
1269 # code: rewritten code for JvxlReader saves nx*ny*nz*8 bytes of memory on loading JVXL files
1272 # -- streamlined methods for converting CUBE data to JVXL files
1278 # bug fix: Mopac graphf UHF files not read properly for beta orbitals, or can't read file
1501 # then it will be read correctly. Binary pmesh files may be read with isosurface command.
1502 # new feature: pmesh files and inline scripts now can be colored and saved as JVXL files
1511 # new feature: fully remappable JVXL files
1572 # bug fix: AMBER topology file reading of IFBOX=2 files
1605 # new feature: set atomTypes "abcd=>C;efgh=>H" for reading mol2 and mdTop files
1638 …feature: (Application) -c option checks without loading files; -C option checks with loading files
1659 # new feature: independent JAR files for language localizations
1684 # creates a set of files movie0001.jpg, movie0002.jpg, etc. for frames in atomExpression
1694 # load files "u.mdtop" FILTER "![WAT],![URE]" COORD {0 -1 1} "mdcrd::u.mdcrd" ;
1701 # -- explicit format "mdcrd::" is required, because these files have no identifying characteristics
1702 # -- as many COORD keywords/coordinate files as desired can be included:
1704 # load files "u.mdtop" FILTER "![WAT],![URE]" COORD {0 -1 1} "mdcrd::u1.mdcrd" "mdcrd::u2.mdcrd"…
1767 # bug fix: CML files not properly loading symmetry
1780 # webexport help updated to reflect ability to handle files opened with "load append"
1899 # bug fix: adaptation for malformed PDB files (HEADER with nothing following it)
1933 # code: realignment of applet JAR files
1970 # bug fix: LOAD "..." nn loading of model numbers for PDB files should read real model number, no…
2007 # new feature: webexport now compresses data files over 512 MB
2016 # new feature: PRELIMINARY aniso_beta for cif files -- has not been checked for correct Ortep type …
2029 # new feature: webexport now cleans up scratch files on deletion of instances and program exit.
2128 # new feature: spacegroup/symmetry for CML files with <module> tags
2440 # bug fix: reading .mmol (biological unit) files such as
2456 # which overrides the default behavior and disallows reading of files from
2536 # new feature: set pdbSequential (default FALSE) for custom PDB files
2632 # filter terms -- only a crude filter here, only for PDB and mmCIF files:
2738 # ELLIPSOID command -- with symmetry and crude footballs, including PDB files
2894 # bug fix: isosurface reading/writing JVXL files having insideout keyword
2925 # So if initially there were two files loaded
2939 # bug fix: mol2 reader cannot read files with single-line comments
2946 # bug fix: WebExport with http:// files fails to save file
3126 # new feature: Spartan input files read as Odyssey format
3147 # new feature: reading of Spartan spinput files (uses Odyssey reader)
3149 # bug fix: PDB files with missing amino acid carbonyl O cause exception
3177 # new feature: allows zip files to be designated as default directoriesusing
3237 # bug fix: isosurface gridpoints "ch3cl_map.jvxl" -- gridpoints for jvxl files that are already map…
3240 # files: JUnitTest for scripts --
3242 # files at http://chemapps.stolaf.edu
3248 # bug fix: load "files" not properly loading zip files or files involving default directory
3274 # bug fix: frame 1.2 when file 1 only has one model displaying all files
3437 # bug fix: no special atom checks for PDB symmetry files
3480 …ug fix: WebExport not properly accessing files in more complicated situations (pmesh, isosurface, …
3573 # new feature: JmolManifest in a zip file directs which files to load and in what order
3574 # JmolManifest is simply a list of files, one per line.
3580 # 3) files must be on separate lines or separated by vertical bar | marks; no whitespace around na…
3581 # 4) files may be ZIP files themselves.
3583 # IGNORE_ERRORS --- process the file and do not stop if some files are not valid model files
3585 # EXCEPT_FILES --- process all files EXCEPT those given
3590 # bug fix: multimodel files could have connected atoms between different models.
3890 # new feature: write FILE (text-files only)
3892 #new feature webexport: automatic usage of a different path to the applet for local files to allow …
3966 # POV-Ray .pov files created by Jmol can be loaded as scripts
3974 # bug fix: 11.3.14+ does not write colormapped JVXL files
3995 # loading of PDB and CIF files containing site information
4164 # bug fix for WebPageMaker not writing files
4248 # automatic gzip of large structure/quantum files.
4250 # Minor fixes to instruction .html files.
4619 # bug fix: load multiple files inline causes null pointer exception
4643 # new feature: molecular dipole for Gaussian files
4720 # bug fix: reading of JVXL files for orbitals loses phase information
4735 # bug fix: Support for mol2 files with blank line after comments.
4743 # bug fix: odydata fix for files with \r\n for line ending
4852 # bug fix for Jvxl.jar standalone application not having complete set of class files (jvxl)
4897 # bug fix for load files losing structure and cartoons
4938 # bug fix for mo data misreading in smol files
4941 # bug fix for PDB files not supplying information about residues for the popup menu.
4968 # build: renames applet files JmolApplet0*.jar and JmolAppletSigned0*.jar
5083 # (1) "file:" allows reading of xy data from files for graphing f(x,y)
5201 # adds support for CAChe CSF files with MOPAC (AM1, PM3, etc.),
5206 # adds MOPAC 2007 graphf output reader (gpt2 files, MOPAC molecular orbitals)
5264 # fixes two nasty bugs relating to isosurfaces and JVXL files.
5265 # -- JVXL files created from molecular orbitals will show up with no color
5267 # -- JVXL files created from molecular orbitals will show unwanted cross-over
5303 # load files ..... # just a cleaner version of loading multiple files.
5394 # molecular electrostatic potential output files
5427 # or possibly in accompanying jar files, such as, perhaps, JmolPopupMenu.jar,