Hi all,
I'm trying to load biological assemblies into my script. From old bulletin
board messages I figured out that multiplex=1 would output the biological
assembly as different states and objects. I worked out that cmd.group()
would give a single object with multiple states. Then cmd.create() would
make one object with one state. Unfortunately if you group a monomer with
one state it gives you a selection of 0 atoms. There is a whole bunch of
arithmetic on the back end of the script crashes with a divide by zero
error for the monomeric ones. I thought I'd be smart and use count_states
to build a conditional loop but I don't think I"m using it correctly
because it isn't passing the multiple states into the loop.
Is there some requirement that I'm missing or not seeing here?
This might be easier to explain if I snip from scripts...
#Outputs the monomers correctly but doesn't account for the biological
assembly so I get false negatives
cmd.set("all_states", 1)
for file in glob("*.pdb1"):
cmd.load(file,'prot')
cmd.select('allLigands', "het and (not resn HOH)") etc.
#Outputs the multimers correctly but gives a divide by zero error for the
monomers
cmd.set("all_states", 1)
for file in glob("*.pdb1"):
cmd.load(file,'prot', multiplex =1)
cmd.group('ens', 'prot'+'*')
cmd.create('BA', 'ens')
cmd.select('allLigands', "het and (not resn HOH)") etc.
#Outputs the monomers correctly but doesn't pass multimers into the
conditional loop. I've also tried moving the cmd.group() before the if
loop. That didn't work either.
cmd.set("all_states", 1)
for file in glob("*.pdb1"):
cmd.load(file,'prot', multiplex=1)
if cmd.count_states('prot') > 1:
cmd.group('ens', 'prot')
cmd.create('BA', 'ens')
cmd.delete('ens')
cmd.select('allLigands', "het and (not resn HOH)") etc.
Any help would be appreciated. I swear this is the last time I'll bother
you. Thanks again.
Katherine
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