http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.3_2014.07.24.zip
is a pre-release update. 14.3.3 and 14.2.3 (synchronized) will be released
next week, prior to the BCCE meetin. Please test!
Several recently reported bug fixes and quite a few new features as well:
___JmolVersion="14.2.3_2014.07.23"
bug fix: write PDB fails
bug fix: 1-letter sequence for water showing as "I" not "?"
bug fix: SHOW SEQUENCE FALSE not giving 1-letter sequences
bug fix: for (i in x) where x is an associative array does not work
bug fix: DSSP analysis not returning information to console
bug fix: move and moveto cannot be in the same session
bug fix: x.func(y) as second operand in a boolean "and" operation
where the first operand evaluates to FALSE
(so that x.func(y) is never evaluated), triggers a script error.
bug fix: set atomPicking, setDrawPicking, pickLabel, pickingSpinRate
all should not be in state
bug fix: model kit menu does not allow setting of new element
bug fix: getproperty structureInfo can fail with phosphorus monomers
bug fix: PDB reader not placing compoundSource in model auxiliary info
new feature: getProperty(x,"[select a,b,c ....
- selection of specific keys to report in getProperty command
- does not require star-slash, which could mark end-of-comment
new feature: x.in(a,b,c,d...) # suggestion of Sameer Velankar
new feature: x.in([a,b,c,d])
- returns 0 (x not in group) or position 1-n
new feature: SQL NOCACHE flag
- prevents caching when using outside variables or functions
- can be anywhere in the
- example:
select within(annotations,"NOCACHE SCOP where myfunc(_dbName,
_domainName, _atoms)")
new feature: load *1cbs/all
- loads annotations from EBI along with mmCIF file
- query code is in org.jmol.dssx.DSSRParser for now
- enables seqid (_atom_site.label_seq_id) required for animation
- annotation information is in the JSON form (in all cases below,
additional key/value pairs are allowed):
{ "<pdbID>" : { <databaseInformation> } }
where <PdbID> is a lower-case PDB id such as 1crs or 1d66
and <databaseInformation> is one or more records:
"<databaseID>" : { <entryInfo> }
<dataBaseID> is a database identifier such as:
"CATH", "SCOP", "InterPro", "UniProt", "GO", "EC"
<entryInfo> is one or more records of the form:
"<entryID>" : { <entry> }
<entry> must at the very least contain:
"identifier" : "<some identifier>"
"mappings" : [ array of <mapping> ]
<mapping> must minimally be
{ "chain_id" : "<author chainIdentifier>" }
but is more likely to contain start/end records:
{ "chain_id" : "<author chainIdentifier>",
"start" : <residueRecord>,
"end" : <residueRecord>
}
<residueRecord> must minimally be:
{ "residue_number" : <mmCIF _atom_site.label_seq_id> }
but usually also contains "author_residue_number" and
"author_insertion_code".
- reports to console:
Annotations loaded:
CATH 2.40.128.20
EC
GO GO:0001972 GO:0005215 GO:0005501 GO:0005634 GO:0005730
GO:0005737 GO:0005783 GO:0006355 GO:0006810 GO:0007165 GO:0008289
GO:0008544 GO:0016918 GO:0019841 GO:0035115 GO:0042573 GO:0070062
InterPro IPR000463 IPR000566 IPR011038 IPR012674
Pfam PF00061
SCOP 50847
UniProt P29373
Use SHOW ANNOTATIONS for details.
new feature: SHOW ANNOTATIONS
- displays tab-separated annotation information
1cbs CATH 2.40.128.20 topology=Lipocalin
1cbs Pfam PF00061 identifier=Lipocalin / cytosolic
fatty-acid binding protein family
1cbs Pfam PF00061 description=Lipocalin / cytosolic
fatty-acid binding protein family
1cbs InterPro IPR012674 name=Calycin
1cbs InterPro IPR012674 identifier=Calycin
new feature: SHOW ANNOTATIONS "<annotationRecordIinfo>"
- selects specific records
- text-based matching in all fields
new feature: SHOW ANNOTATIONS "<annotationRecordIinfo> mappings"
- adds information about mapping
new feature: select within(annotation, "<query>")
- allows selection of atoms based on annotations.
- <query> can be:
- a databaseID:
select within(annotations,"InterPro")
- a specific databaseID.entryID:
select within(annotations,"InterPro.IPR012674 where
identifier='calycin'")
- a databaseID followed by a WHERE clause:
select within(annotations,"InterPro where identifier='calycin'")
select within(annotations,"InterPro where identifier like
'*-like*'")
any text information in the SHOW ANNOTATION report.
new feature: load *1cbs/all
new feature: load /pdbe/xxxx
-- loads CIF file http://www.ebi.ac.uk/pdbe/entry-files/download/xxxx.cif
-- can be abbreviated as "*":
load *1ai6
-- can be supplemented with annotations (TODO)
new feature: {*}.seqid
-- mmCIF only
-- settable using {*}.seqid = ....
-- from _atom_site.label_seq_id
-- a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
Data items in the ENTITY_POLY_SEQ category specify the sequence
of monomers in a polymer. Allowance is made for the possibility
of microheterogeneity in a sample by allowing a given sequence
number to be correlated with more than one monomer id - the
corresponding ATOM_SITE entries should reflect this heterogeneity.
new feature: eval(...)
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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