X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-basic.html;h=238366c90f007d780ff3f520d098155e42b2b4ed;hb=b72ed01b68a8572022f912687db5be60b53c15cf;hp=44c3459176a340eaa74e4ab228b86463da90a4fc;hpb=9c970ce520ca5480fcd289c8ef32ed78284cde29;p=jalview.git
diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html
index 44c3459..238366c 100644
--- a/help/help/html/features/clarguments-basic.html
+++ b/help/help/html/features/clarguments-basic.html
@@ -315,11 +315,11 @@
The value can also be specified as a sub-value:
- jalview --open examples/uniref50.fa --structure [seqid=FER1+SPIOL,structureviewer=jmol,tempfac=plddt]examples/AlphaFold/AF-P00221-F1-model_v4.pdb + jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,structureviewer=jmol,tempfac=plddt]examples/AlphaFold/AF-P00221-F1-model_v4.pdbwhich is equivalent to
- jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --tempfac plddt --seqid FER1+SPIOL + jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --tempfac plddt --seqid FER1_SPIOL --structureviewer jmol@@ -540,7 +540,7 @@
‑‑bgcolour
- Only applies to ‑‑structureimage
. Specify a background colour for a structure image. The colour can be specified as a named colour recognised by Java (e.g. "white"
, "cyan"
) or as a #RRGGBB hash-6-digit-hex-string as used in web pages (e.g. "#ffffff"
, "#00ffff"
). Note that if you're using a hash in a bash-like shell then you should quote the string to avoid problems with it being interpreted as a comment character.
+ Only applies to ‑‑structureimage
. Specify a background colour for a structure image. The colour can be specified as a named colour recognised by Java (e.g. "white"
, "cyan"
) or as a RRGGBB 6 digit hex string (e.g. ffffff
, 00ffff
).
E.g. @@ -556,7 +556,7 @@
svg
, eps
, html
, biojs
)
- Jalview can export an alignment in Encapsulated PostScript (eps
), Scalable Vector Graphics (svg
), HTML (html
) or BioJSON -- another HTML format (biojs
), by using, e.g.
+ Jalview can export an alignment in Encapsulated PostScript (eps
), Scalable Vector Graphics (svg
), HTML (html
) or BioJSON -- another HTML format with an interactive MSA viewer (biojs
), by using, e.g.
jalview --open examples/uniref50.fa --colour gecos-flower --image printable.eps@@ -565,6 +565,7 @@ jalview --open examples/uniref50.fa --colour gecos-flower --image printable.eps jalview --open examples/uniref50.fa --colour gecos-flower --image printable.postscript --type eps jalview --open examples/uniref50.fa --colour gecos-flower --image [type=eps]printable.postscript + jalview --open examples/uniref50.fa --colour gecos-flower --image [type=biojs]printable.html