Manual Structure Calculation Using CYANA: Difference between revisions
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(Created page with '== Manual structure calculation with CYANA 2.1 == Manual structure calculation is performed similar to the automated calculation. # Create a new work…') |
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=== '''CALC.cya''' === | === '''CALC.cya''' === | ||
<pre>peaks := n_cons,ali_cons,aro_cons # names of peak lists | |||
< | |||
peaks := n_cons,ali_cons,aro_cons # names of peak lists | |||
prot := $name # names of proton lists | prot := $name # names of proton lists | ||
tolerance := 0.05,0.02,0.4 # chemical shift tolerances | tolerance := 0.05,0.02,0.4 # chemical shift tolerances | ||
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overview $name.ovw structures=20 pdb # write overview file and coordinates | overview $name.ovw structures=20 pdb # write overview file and coordinates | ||
#overview $name.ovw structures=20 significant=1 pdb | #overview $name.ovw structures=20 significant=1 pdb | ||
</ | </pre> | ||
Here <tt>expand=0</tt> is needed to correctly interpret UPLs created with CALIBA. | Here <tt>expand=0</tt> is needed to correctly interpret UPLs created with CALIBA. | ||
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Macro <tt>flip.cya</tt> can be used to flip the side chains Glu, Asp, Phe and Tyr to reduce RMSD in the final calculation. | Macro <tt>flip.cya</tt> can be used to flip the side chains Glu, Asp, Phe and Tyr to reduce RMSD in the final calculation. | ||
Overview by default will report only violation in at least <tt>structures/3</tt> conformers, and in this particular case these are six. To have all violations reported add <tt>significant=1</tt>. | Overview by default will report only violation in at least <tt>structures/3</tt> conformers, and in this particular case these are six. To have all violations reported add <tt>significant=1</tt>. | ||
Macro <tt>peakcheck</tt> verifies AtomList and peaklists for consistency and is very useful when manually assigned peaks are used. | |||
It is important to set peak volumes to their absolute values before calling caliba for calibration. | |||
-- Main.AlexEletski - 10 Jul 2007 | -- Main.AlexEletski - 10 Jul 2007 | ||
Revision as of 05:18, 1 November 2009
Manual structure calculation with CYANA 2.1
Manual structure calculation is performed similar to the automated calculation.
- Create a new working subdirectory (structure/cyana21/calc3)
- Copy init.cya, XXXX.seq, XXXX.prot into this directiory.
- Export the latest peaklists, like n-cons, ali-cons and aro-cons.
- Copy the latest stereofound.cya from the latest GridSearch run.
- (Optional) Copy the talos.aco file
- Download the CALC.cya file (see below). Modify peaklist names, calibration parameters and tolerances.
- Run calculation with CYANA 2.1 on a workstation or U2 cluster
CALC.cya
peaks := n_cons,ali_cons,aro_cons # names of peak lists
prot := $name # names of proton lists
tolerance := 0.05,0.02,0.4 # chemical shift tolerances
# order: 1H(a), 1H(b), 13C/15N(b), 13C/15N(a)
if (master) then
# ---- check consistency of peak and chemical shift lists----
peakcheck peaks=$peaks prot=$prot
# ---- calibration ----
read prot $prot
read peaks n_cons
peaks set volume=abs(volume)
caliba bb=2.0E+06 sc=2.0E+05 methyl=4.0E+04
write upl n
read peaks ali_cons
peaks set volume=abs(volume)
caliba bb=2.5E+06 sc=4.3E+05 methyl=2.0E+05
write upl ali
read peaks aro_cons
peaks set volume=abs(volume)
caliba bb=1.7E+06 sc=2.4E+05 methyl=6.0E+04
write upl $name-in.upl
stereofound
distance modify
write upl $name.upl
end if
synchronize
# ---- structure calculation ----
expand=0
read seq $name.seq # re-read sequence to initialize
read upl $name.upl # read upper distance limits
#read aco talos.aco # read angle constraints
seed=5671 # random number generator seed
calc_all structures=100 command=anneal steps=10000 # calculate 100 conformers
flip # align side chains for lower RMSD
overview $name.ovw structures=20 pdb # write overview file and coordinates
#overview $name.ovw structures=20 significant=1 pdb
Here expand=0 is needed to correctly interpret UPLs created with CALIBA.
Macro flip.cya can be used to flip the side chains Glu, Asp, Phe and Tyr to reduce RMSD in the final calculation.
Overview by default will report only violation in at least structures/3 conformers, and in this particular case these are six. To have all violations reported add significant=1.
Macro peakcheck verifies AtomList and peaklists for consistency and is very useful when manually assigned peaks are used.
It is important to set peak volumes to their absolute values before calling caliba for calibration.
-- Main.AlexEletski - 10 Jul 2007