Miguel wrote:
...
I fear that I will do a lot of work and that it will not meet people's
expectations.
but an implementation as in RasMol, simply to offer selection commands,
would solve the greatest needs.
Q: are you talking about Open RasMol?
Please explain how alt locs are supported.
RasMol2.7.2.1.1 supports altLoc selection
select *;A
would select all atoms with altLoc code A
RasMol2.7.2.1.1 in general (if the PDB file is OK, using the same atom
names but altLoc) didn't make ugly bondings e.g. the image is generated
by the following script:
load pdb 1plc.pdb
restrict [LYS]54
# one of the altLoc residues in this file
define exmpl selected
center exmpl
zoom 500
rotate y 90
select exmpl & *;A
cpk 50
# all the LYS54 altLoc A atoms
wireframe 20
select exmpl & (*.CA, *.CB;A)
wireframe 15
# the connecting bond from the altLoc A model to the main model
select exmpl & not *;A
# the main model
wireframe 10
write gif altLoc.gif
At the moment, a PDB file could not correctly be shown in Jmol lacking
altLoc support.
I do not understand how to implement any type of altLoc support that would
not break many things. For example, secondary structures ...
because altLoc is mainly used for local conformation change, especially
side chain orientation, the approximation only using the main model
would be OK.
In the future implementation of an equivalent of the RasMol structure
command
structure
the command should only apply to the current selection and on load, the
main model should be the current selection, that will not brake the
approximation above.
By the way, automatic beta-sheet assignment may be a bit too relaxed,
e.g. 1ppa
Regards, Jan
I am not going to work on alternateLocations until someone comes to me
with a specific well-thought-out proposal on how it should be
implemented.
I vote for a minimal implementation without model generation, but
allowing selection of altLoc.
Please propose a specific minimal implementation.
Miguel
