Try:
select !(n. ca | n. c | n. n | n. o)
Cheers,
JTM
"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly accelerated."
Linus Pauling, Nobel Laureate 1954
"...everything that living
I believe that you need to make these new objects to correct the problem,
at least this is a quick fix that I have done in the past. There may be a
more elegant solution:
load my.pdb, obj1
load my.pdb, obj2
[whatever to each obj]
When loaded separately you don't have this problem.
Cheers,
JTM
I find mpeg encoder from Berkeley works fantastic and very fast. The only
problem is if you want to add frames from another source that may not be
exactly the same frame size. For just putting frames together I haven't
found anything faster or easier with a great quality output.
Cheers,
JTM
"We
select [ligand name and/or chain] and n. [atom name]
For instance, if your ligand is chain c and you want to select the atom
named C21 in the pdb file:
select c. c & n. c21
or if your ligand has a residue name like "BME" or something similar then
you could do:
select r. bme & n. c21
Cheers,
JT
Hello:
The bond distance is hard coded, as far as I know there is no way to
change it without recompiling the program. The "unbond" command works
very well though and you can put it into a script when you read in the pdb
so that you don't have to redo it every time.
unbond [atom selection 1], [a
Use the translate command to move selected parts of the protein. There
are lots of posts in the archives for more info.
Cheers,
JTM
"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly
Hello:
Not exactly sure what you are asking here but if you want to calculate the
distance moved you could use the distance command:
distance atomx, atomy
to tell you how far atoms in the residues has moved.
you can also calculate dihedrals (ie/ X values) using the dihedral command
dihedral name_
hide nonbonded
should remove these. They must be in your pdb file somewhere: waters,
metals something.
Cheers,
JTM
"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly accelerated."
L
Use the "translate" command to move one/both of the pdb molecules until
they superimpose. Just interpolate the distance depending on how many
frames you want to do and the distance separated.
Cheers,
JTM
"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic
