-
For ANY protein pdb files containing tryptophan (TRP), when converted to fasta format, TRP gets designated as X (unknown residue) instead of W, E.g.
babel 1HVR.pdb 1HVR.fasta.
This is for any pdb files, so I am not attaching anything. What worries me, is TRP recognized properly at all, or is it just an openbabel fasta conversion glitch?.
2009-07-10 14:13:20 UTC in Open Babel
-
For ANY protein pdb files containing tryptophan (TRP), when converted to fasta format, TRP gets designated as X (unknown residue) instead of W, E.g.
babel 1HVR.pdb 1HVR.fasta.
This is for any pdb files, so I am not attaching anything. What worries me, is TRP recognized properly at all, or is it just an openbabel fasta conversion glitch?.
2009-07-10 13:38:06 UTC in Open Babel
-
For ANY protein pdb files containing tryptophan (TRP), when converted to fasta format, TRP gets designated as X (unknown residue) instead of W, E.g.
babel 1HVR.pdb 1HVR.fasta.
This is for any pdb files, so I am not attaching anything. What worries me, is TRP recognized properly at all, or is it just an openbabel fasta conversion glitch?.
2009-07-10 09:09:26 UTC in Open Babel
-
Avogadro used to work on KDE 3.5, but after transition to KDE4 Avogadro fails to launch with an error:
avogadro: main/renderbuffer.c:2153: _mesa_reference_renderbuffer: Assertion `oldRb->Magic == 0xaabbccdd' failed.
Abort
I tried rebuilding from source, with the same result.
I am using:
AMD Athlon(tm) 64 Processor 3400+
cpu MHz : 2400.000
cache size : 512 KB...
2008-11-12 13:31:28 UTC in Avogadro
-
It seams that on some systems (I use Kubuntu Intrepid, AMD64) lrelease does not use options specified in makefiles.
A way around this is the following:
before doing make as you tried above,
in the files
build/libavogadro/src/CMakeFiles/avogadro-lib.dir/build.make
build/avogadro/src/CMakeFiles/avogadro-app.dir/build.make
find all lines with lrelease iin them and delete all options.
2008-11-12 13:21:22 UTC in Avogadro
