From: Ben Soares Date: Wed, 3 May 2023 16:18:55 +0000 (+0100) Subject: JAL-629 a bit more documentation X-Git-Tag: Release_2_11_4_0~348 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b8781bdce3e54b27102f53d1e3cb5fe2c9d27b6c;p=jalview.git JAL-629 a bit more documentation --- diff --git a/help/help/html/features/clarguments-ng.html b/help/help/html/features/clarguments-ng.html index 9b1e88d..4a173d2 100644 --- a/help/help/html/features/clarguments-ng.html +++ b/help/help/html/features/clarguments-ng.html @@ -79,7 +79,7 @@

Typical Use Cases

-

Opening files (--open, --append, --newframe)

+

Opening files (--open, --append, --new)

To simply open one or more alignment files in different frames just put the filenames as the first arguments: @@ -149,17 +149,17 @@ Note that whilst you can include a Jalview Project File (.jvp) as an --append value, the items in the file will always open in their original frames and not append to another.

-
--newframe
+
--new

- To append different sets of alignment files in different frames, use --newframe to move on to a new alignment frame: + To append different sets of alignment files in different frames, use --new to move on to a new alignment frame:

-  jalview --append these/filename*.fa --newframe --append other/filename*.fa
+  jalview --append these/filename*.fa --new --append other/filename*.fa
   

- --open is like using --newframe --append applied to every filename/URL given to --open + --open is like using --new --append applied to every filename/URL given to --open

@@ -270,7 +270,7 @@

- index: + index: You can alternatively specify the (zero-indexed) index of the sequence within the alignment, although this is less precise. So to attach the structure to the 8th sequence use:

   jalview --open examples/uniref50.fa --structure [7]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
@@ -290,7 +290,8 @@
   chimerax,
   
pymol. -
+

+

none and jmol will always be available, but to use the others you must have the appropriate software already set up on your computer and in Jalview. See the page Discovering and Viewing PDB and 3D-Beacons structures for more details.

   jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,viewer=none]examples/AlphaFold/AF-P00221-F1-model_v4.pdb