Jmol

[Jarom]

Jmol 14.15.1

Jmol – oprogramowanie do trójwymiarowej wizualizacji i animacji struktur chemicznych, krystalicznych, biomolekularnych oraz materiałowych.

źródło: Podstawy naukoznawstwa Tom 1 pod redakcją Pawła Kawalca, Piotra Lipskiego, Rafała Wodzisza.

Obsługiwane systemy operacyjne:

Instrukcja i historia zmian:

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Opcja 1.

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Opcja 2:

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Opcja 3:

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[Jarom]

Jmol 14.15.2

• bug fix: CIP chirality adds axial chirality (M/P[Ra/Sa], m/p[ra/sa]) for cumulenes
• bug fix: CIP chirality adds atropisomer chirality (M/P[Ra/Sa], m/p[ra/sa]) for biaryls
• bug fix: CIP chirality adds cumulene E/Z chirality
• lines
• validation data are at
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• validates for 160 structures (some duplicates; both cip_examples.zip and stereo_test_cases.sdf)
• validates for all cases considered:
• simple R/S and E/Z small-ring removal of E/Z
• parallel-strand Rule 4b and Rule 5 (Mata)
• pseudochiral r/s and m/p odd and even cumulenes
• atropisomers
• P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
• imine and diazine E/Z chirality

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[Jarom]

Jmol 14.15.3

• bug fix: SMARTS search for atropisomeric bond that is in an alicyclic ring fails (Fred Ziegler)
• used for M/P chirality check
• for example: load $c1cc2c3-c4c5CC2.c5ccc4C.c3(C)c1 select on smarts("a-a") calculate chirality print {*}.chirality.join("") MM
• bug fix: use of the less preferred name of Jmol token that has two optional forms ("fix" vs "fixed") as a VAR does not assign that variable name
• bug fix: set cartoonRibose misses the C1'-O4' and O3'-P(+1) edges
• bug fix: JVXL reader not reading Gaussian files with "1" in the third line, 5th field
• bug fix: CIP M/P chirality test: load "$2,2'-dibromobiphenyl"; calculate chirality; print {*}.chirality.join("")
• bug fix: CIP chirality nearly fully validated on ACD/Labs AY-236 set, with some unimplemented aspects

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[Jarom]

Jmol 14.16.1

• new feature: load =chebi/nnnnnn chEBI 2D molecule load, with minimal 100-step minimization
• bug fix: CML reader does not read 2D wedge/hash information
• bug fix: CIP fix for missing branch descriptors; 984 lines
• bug fix: CIP adds helicene M/P chirality - validated using CCDC structures HEXHEL02 HEXHEL03 HEXHEL04 ODAGOS ODAHAF -
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  code: CIP: additional simplification; code: CIP status: implementation complete, including: All subrules implemented fully: 1a, 1b, 2, 3, 4a, 4b, 4c, 5 R/S, E/Z, M/P (odd-cumulene and helicene), r/s, seqCis/seqTrans (as Z/E) fused benzenoid aromatic Mancude ring "Kekule weighted" atom number adjustments
• Added logic to Rule 1b: The root distance for a Kekule-ambiguous duplicate
• atom is its own sphere, not the sphere of its duplicated atom.

Stated more precisely:
Proposed amended Sequence Rule 1:

• (1a) higher atomic number precedes lower;
• (1b) in comparing two duplicate nodes, lower root distance precedes higher

root distance, where "root distance" is defined:

• (i) in the case of a duplicate atom for which the atomic number is averaged
• over two or more atoms in applying Rule 1a, the distance from the duplicate
• node itself to the root node; and
• (ii) in all other cases, the distance of its corresponding nonduplicated atom
• node to the root node.

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[Jarom]

Jmol 14.17.1

Jmol.___JmolDate="$Date: 2017-05-27 11:35:09 -0500 (Sat, 27 May 2017) $"
Jmol.___fullJmolProperties="src/org/jmol/viewer/Jmol.properties"

# THIS IS THE TRUNK - for development and release


# Developers: to add a description of changes you have made,
# add it on a line below the "Jmol.___JmolVersion=..." line.
# Don't use Jmol.___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
#
# A full Jmol/JSpecView/JSmol release requires the following:
#
# 1. Generate a new version number. This should be done as in the following examples,
# listed in order of appearance:
#
# previous new
#
# 14.8.10 14.8.11-beta-2016-12-20 a beta release of 14.8.11 with a timestamp for Dec 20, 2016
# 14.8.10 14.8.11 bug fixes only - patch level
# 14.8.10 14.9.0 new features - minor version level (tag for Maven, create branch)
# 14.8.10 15.0.0 new features - major version level (tag for Maven, create branch)
#
# The distinction between major and minor is arbitrary.
#
# Note that -beta releases will be to

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# while full releases will be to

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.
#
# 2. Create a new Jmol.___... line and remove "Jmol.___" from the line for the
# previous release; failure to do remove this line will use the original release number,
# not the new one, since this is a property file.
#
# 3. Commit this change.
#
# 4. Run jmol build.xml, signing the jar files (only main, not dist or doc; or the whole thing).
#
# 5. Run jsmol build_11_fromJmol.xml
#
# 6. Run jsmol build_12_fromJSpecView.xml
#
# 7. Refresh the JSmol project
#
# 8. Run jsmol build_13_tojs.xml
#
# 9. Run jmol build.xml again (just dist and doc; or the whole thing)
#
# 10. Run jmol/tools build-release.xml
#

# TODO: The problem is if I open a normal PDB file, select some atoms, use
# the DATA "property_occupancy" [some random numbers] end "property_occupancy"
# command, and then write a PDB file, all the occupancies are listed as 1.00
# instead of the occupancies I tried to assign in jmol.

# TODO: fix UNDO

Jmol.___JmolVersion="14.17.1" // 2017.05.27

new feature: atom property x.cipRule
-- CIP sequence rule deciding this center
-- one of 1a, 1b, 2, 3, 4a, 4b, 4c, 5, or blank

bug fix: polyhedra broken in Jmol 14.10.0

bug fix: finalizing CIP algorithm
-- adding spiro chirality from P-93.5.3
-- completing root path for auxiliary descriptors

bug fix: JSmol: JSME/JSmol 2D->3D fails when one H of a CH2 is explicitly wedge and the other H is implicit (not shown at all). (JSmolJME.js)

code:

/**
* A full validated relatively efficient implementation of Cahn-Ingold-Prelog
* rules for assigning R/S, M/P, and E/Z stereochemical descriptors. Based on
* IUPAC Blue Book rules of 2013.
*

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*
* Features include:
*
* - deeply validated
*
* - implemented in Java (Jmol) and JavaScript (JSmol)
*
* - only two Java classes; roughly 1000 lines
*
* - efficient, one-pass process for each center using a single finite digraph for all auxiliary descriptors
*
* - exhaustive processing of all 8 sequence rules (1a, 1b, 2, 3, 4a, 4b, 4c, 5)
*
* - includes R/S, r/s, M/P (axial, not planar), E/Z
*
* - covers any-length odd and even cumulenes
*
* - uses Jmol conformational SMARTS to detect atropisomers and helicenes
*
* - covers chiral phosphorus and sulfur, including trigonal pyramidal and tetrahedral
*
* - properly treats complex combinations of R/S, M/P, and seqCis/seqTrans centers (Rule 4b)
*
* - properly treats neutral-species resonance structures using fractional atomic mass and a modified Rule 1b
*
* - implements CIP spiro rule (BB P-93.5.3.1)
*
* - detects small rings (fewer than 8 members) and removes E/Z specifications for such
*
* - detects chiral bridgehead nitrogens
*
* - reports atom descriptor along with the rule that ultimately decided it
*
* Primary 236-compound Chapter-9 validation set (AY-236) provided by Andres
* Yerin, ACD/Labs (Moscow).
*
* Mikko Vainio also supplied a 64-compound testing suite (MV-64), which is
* available on SourceForge in the Jmol-datafiles directory.
* (

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).
*
* Additional test structures provided by John Mayfield.
*
* Additional thanks to the IUPAC Blue Book Revision project, specifically
* Karl-Heinz Hellwich for alerting me to the errata page for the 2013 IUPAC
* specs (

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), Gerry Moss
* for discussions, Andres Yerin for discussion and digraph checking.
*
* Many thanks to the members of the BlueObelisk-Discuss group, particularly
* Mikko Vainio, John Mayfield (aka John May), Wolf Ihlenfeldt, and Egon Willighagen, for
* encouragement, examples, serious skepticism, and extremely helpful advice.

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[Jarom]

Jmol 14.17.2

• bug fix: WRITE FILE not working when file has been cached.
• bug fix: array.find("regex...","") does not reset RegExp each time it runs RegExp.exec() so does not find all possibilities
• code: CIPChirality.java fully interfaced using SimpleNode and SimpleEdge

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[Jarom]

Jmol 14.18.1

• bug fix: CIP misses Rule 4b cases where a branching atom has R or S chirality.
• see test_bt_P4.mol and test_bt_O3.mol (BH64.65 and BH64.66)
• see AY236.179 (3D structure was diasteriomer, so I missed that)
• bug fix: WRITE MOL should not generate > <JMOL_PARTIAL_CHARGES> because it is not SDF format
• bug fix: WRITE SDF should generate > <JMOL_PARTIAL_CHARGES> with a trailing space
• bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for .[C@H]2 (new group and attached to a connection number)
• bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4
• new feature: WRITE SDF writes > <.... user data
• can be set using MODEL PROPERTY "molData" x where x is an associative array
• can be read using _M.molData new feature: associativeArray.pop()
• clears associativeArray
• new feature: assArray1.push(assArray2)
• adds all key/value entries in assArray2 to assArray1.
• new feature: assArray1 + assArray2
• adds all key/value entries into a new associative array.

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[Jarom]

Jmol 14.20.2

Jmol 14.20.2

• bug fix: CIPChirality adding presort for Rules 4a and 4c (test12.mol; 828 lines)
• bug fix: write SDF and write MOL do not set atom parity field
• bug fix: JavaScript JSmol broken for chirality due to bug in Clazz.clone(obj)
• bug fix: Upgrade of natural abundance average masses (no significant changes here): // all numbers except radionuclides from: // Atomic weights of the elements 2013 (IUPAC Technical Report) // Juris Meija, Tyler B. Coplen, Michael Berglund, Willi A. Brand, Paul De Bièvre, // Manfred Gröning, Norman E. Holden, Johanna Irrgeher, Robert D. Loss, Thomas Walczyk, // Thomas Prohaska Published Online: 2016-02-24 |

Jmol 14.19.1

• bug fix: CIPChirality: minor fixes for Rule 4b and 5 for BH64_012-015; better atropisomer check
• bug fix: SPIN QUATERNION
• bug fix: CENTERAT ABSOLUTE broken (since forever?)
• bug fix: SPIN QUATERNION {0 0 -1 0} still does a positive, not negative, rotation (solution is to apply a miniscule rotation of 1e-10 degrees)
• bug fix: script array context [3 -0] becomes [3], as in [3 - 0]
• new feature: WRITE "SDF" implements atom value V nnn ... information
• requires assigning the data property name "atom_values" in the model's molData property
• $ load $2,3-dichlorobutane
• $ molData = {"atom_values":"chirality"}
• $ model properties "molData" molData
• $ write diol.sdf

-- note that if the model already has a molData property, then use the following to append to it:

• $ molData = (_M.molData ? _M.molData : {})
• $ molData.atom_values = "chirality"
• $ model properties "molData" molData
• new feature: x = load("filename","JSON") -- loads JSON data into variable
• bug fix: SET ANTIALIASDISPLAY requires click [via resizeImage()]
• bug fix: CIP gives wrong alkene root distance for cyclopropene
• bug fix: WRITE of structure file does not report number of atoms and warn if selected is different from this molecule
• bug fix: WRITE MOL using format 10f.5 instead of 10f.4 for x, y, z coordinates
• bug fix: MOL/SDF files should truncate lines at 80 characters.

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[Jarom]

Jmol 14.20.3

bug fix: ROTATE should not stop spin if it does not initiate a spin
bug fix: CIPChirality tests for CIP1966#31,#32 douple spirans and C3 compounds
bug fix: CIPChirality for Rule 2 using atomic masses and not for duplicate atoms
bug fix: MOL file reading where isotope is indicated in atom line and V item
bug fix: MOL reader fails for H1, D, T isotopes indicated as symbols along with isotope difference

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[Jarom]

Jmol 14.20.4

• bug fix: SpartanSMOL reader for iSpartan files does not read charges or vibrational mode data
• bug fix: CIPChirality fix for BH64_075; adding Rule 3b.
• bug fix: CIPChirality new Rule 6 covers all special spiro cases and C3-symmetry bug fix: SMILES generator fails for [2H]/C=C/[1H]
• bug fix: write SDF fails for 1H. (Must use M ISO.) JmolVersion="14.20.3" // 2017.07.20 bug fix: ROTATE should not stop spin if it does not initiate a spin
• bug fix: CIPChirality tests for CIP1966#31,#32 douple spirans and C3 compounds
• bug fix: CIPChirality for Rule 2 using atomic masses and not for duplicate atoms
• bug fix: MOL file reading where isotope is indicated in atom line and V item
• bug fix: MOL reader fails for H1, D, T isotopes indicated as symbols along with isotope difference

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[Jarom]

Jmol 14.20.5

Jmol.___JmolVersion="14.20.5" // 2017.08.29
bug fix: isosurface intersect unitcell broken
bug fix: show spacegroup does not report H-M name

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[Jarom]

Jmol 14.20.6

Jmol.___JmolVersion="14.20.6"
bug fix: MO HOMO + n delivers HOMO + 2*n
code: more efficient CIPChirality using breadth-first scanning for chirality descriptors

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[Jarom]

Jmol 14.20.7

Jmol.___JmolVersion="14.20.7"
bug fix: calculate chirality broken for JSmol (missing Integer.compare)

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[Jarom]

Jmol 14.22.1

• new feature: draw BOUNDBOX BEST -- draws the best box around currently selected atoms
• bug fix: a.distance.min(b).min should not report 0 if a == b. (testing atom against itself should be skipped)
• bug fix: SHOW BEST ROTATION just shows the current rotation, not the best rotation to use to get to the best view
• bug fix: rotate BEST can fail with flat structures
• bug fix: LOAD "" FILE BOUNDBOX does not include all atoms

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[Jarom]

Jmol 14.23.1

• new feature: load "" fill UNITCELL PRIMITIVE (for files that are conventional)
• new feature: load "" fill UNITCELL CONVENTIONAL (for VASP files, which are primitive cells)
• bug fix: primitive unit cell incorrect for rhombohedral lattice space groups (trigonal R...; 146, 148, 155, 160, 161, 166, 167)
• bug fix: (AFLOW specific) CIF for trigonal and hexagonal cells (itn 143-194) should orient rotated 60 deg cw
• bug fix: LOAD ... SUPERCELL {2 2 2} broken

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