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Split standard nucleotides set A, C, G, T, U. into components: phosphate, sugar, nucleobase.
Nucleotide splitting will require attachment points rework and monomer coordinates' updates.:
Before the splitting:
After:
Fully expanded form:
For DNA nucleotides deoxyribose (d) should be used instead of ribose (r).
deoxyribose:
Please note that In molV3000 nucleotides' phosphate appears from the left side of ribose/deoxiribose.
By default biovia draw saves sequences into template atoms and adds corresponding nucleotides template:
CTAB:
M V30 BEGIN CTAB
M V30 COUNTS 2 1 1 0 1
M V30 BEGIN ATOM
M V30 1 A 1.9906 -2.7031 0 0 CLASS=RNA ATTCHORD=(2 2 Br) SEQID=1
M V30 2 G 2.9355 -2.7031 0 0 CLASS=RNA ATTCHORD=(2 1 Al) SEQID=2
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 1
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 DAT 1 ATOMS=(1 1) FIELDNAME="SMMX:sequence position data" -
M V30 FIELDDISP=" 1.9906 -2.7031 DA ALL 1 "
M V30 END SGROUP
M V30 END CTAB
Templates:
M V30 BEGIN TEMPLATE
M V30 TEMPLATE 1 RNA/AM V30 BEGIN CTAB
///skipped.
M V30 END CTABM V30 TEMPLATE 2 RNA/G
M V30 BEGIN CTAB
///skipped.
M V30 END CTAB
M V30 END TEMPLATE
Molfile loader should transform this into granular form:
CTAB:
M V30 BEGIN CTAB
M V30 COUNTS 3 2 0 0 0
M V30 BEGIN ATOM
M V30 1 P 0 0 0 0 CLASS=PHOSPHATE SEQID=1 ATTCHORD=(2 2 Br)
M V30 2 R 5 0 0 0 CLASS=SUGAR SEQID=2 SEQNAME=A ATTCHORD=(4 1 Al 3 Cx)
M V30 3 A 5 -4 0 0 CLASS=BASE SEQID=2 SEQNAME=A ATTCHORD=(2 2 Al)M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 END BOND
M V30 END CTAB
Templates:
M V30 BEGIN TEMPLATE
M V30 TEMPLATE 23 PHOSPHATE/P/P NATREPLACE=P
//skipped.
M V30 TEMPLATE 25 SUGAR/R/R NATREPLACE=R
//skipped
M V30 TEMPLATE 16 BASE/A/A NATREPLACE=A
//skipped
M V30 END TEMPLATE
Full CTAB V3000 form with support of the additional data-sgroups:
Split standard nucleotides set A, C, G, T, U. into components: phosphate, sugar, nucleobase.
Nucleotide splitting will require attachment points rework and monomer coordinates' updates.:
Before the splitting:
After:
Fully expanded form:
For DNA nucleotides deoxyribose (d) should be used instead of ribose (r).
deoxyribose:
Please note that In molV3000 nucleotides' phosphate appears from the left side of ribose/deoxiribose.
By default biovia draw saves sequences into template atoms and adds corresponding nucleotides template:
Templates:
Molfile loader should transform this into granular form:
CTAB:
Templates:
Full CTAB V3000 form with support of the additional data-sgroups:
SMMX:class
SMMX:NUCLEOTIDE_P5
SMMX:NUCLEOTIDE_BASE
SMMX:NUCLEOTIDE_SUGAR
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