Jan wrote:
I've implemented preliminary altloc handling for CIF files in the
prototype.
See http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm
very nice
can also use
select *%
OK
to indicate "all atoms that have no alternate specification", so then
we have:
select *% or *%1 # conformation 1
select *% or *%2 # conformation 2
this didn't work for me:
jmolApplet0: unrecognized expression token:* : select *% or *%1
line#1 :: select *% or *%1
only
select *%1 or *%
is as expected.
which file are you using, Jan? This was a bug I spotted and fixed a day
or two ago.
This works at file:///E:/bhtest/proto/altloc.htm, right?
RasMol cartoons and such won't render quite correctly, I think. My
guess is that they will take either the first or the last
conformation only, but I don't have an example file to test that.
I think you must be using the wrong jar file. I'm going to have to start
dating these.
RasMol-->Jmol: exchanging ; by % would lead to the same result in Jmol
select 54 # all
select 54 and *;A # only AltLoc A part
select 54 and not *;B # AltLoc A part together with the common
backbone atoms
I also added %A for label display of the altloc identifier and added
"%n" to the %U label format
Those interested -- tell me what you think.
great, please add it to trunk and PDB file loader.
It is in both the CIF and PDB reader already in 10.x. That's about all I
can do. If it is destined for the trunk, Miguel will have to address the
underlying capabilities that were removed back in March. Please address
your request to Miguel.
Miguel, are you SURE there is this "run" business?
What are some more files we can test this on? (1skt is over 30 models
and 5 Mb -- any others?)
1h6d
a monster with almost no variation
1i54
nice -- an overlay of wireframe
http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm?model=alt/1i54.cif
shows these almost exactly identical
1i55
same here
1isc
nice iron compound; very slight variations.
http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm?model=alt/1isc.pdb
1jfb
1jfc
nice
http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm?model=alt/1jfb.cif
1jze
I love this one!
http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm?model=alt/1jze.cif
1jzj
http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm?model=alt/1jzj.cif
even nicer!
1k2o
excellent
1mng
Ah, this one is SUPERB. Another bug in CifReader. Do you see the
problem? I'll fix it.
http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm?model=alt/1mng.cif
Regards, Jan
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