And to save it, add this python block

python
for PDB in PDBs:
    cmd.save("%s-K.pdb"%PDB,"%s"%PDB)
python end

Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE
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Mobil:
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2011/9/22 Troels Emtekær Linnet <tlinnet@gmail.com>
# Firs load files in dirextory with: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
# load_sep.py
# Load multiple PDB files into a multiple PyMOL objects
#  e.g. load_sep prot_*.pdb, prot
# will create objects with names, prot1, prot2, prot3, etc.

# Now the rest
cd /home/tlinnet/Desktop

# Test protein
fetch 4INS, async=0

# Get all loaded PDB object names in pymol
PDBs = cmd.get_names()

python
### We need to find a way to get the information of chain and resi from the loaded list
### Create empty list
ProtChainResiList = []
for PDB in PDBs:
    #print PDB
    ### Get the ID numbers of CA atom in protein
    CAindex = cmd.identify("%s and name CA"%PDB)
    for CAid in CAindex:
        ### We need to find a way to get the information of chain and resi from ID
        pdbstr = cmd.get_pdbstr("%s and id %s"%(PDB,CAid))
        pdbstr_lines = pdbstr.splitlines()
        chain = pdbstr_lines[0].split()[4]
        resi = pdbstr_lines[0].split()[5]
        #print "CAid: %s Chain: %s resi: %s"%(CAid, chain,resi)
        ProtChainResiList.append([PDB,chain,resi])
#for entry in ProtChainResiList:
#    print entry
python end

### We devide it up in several python blocks, so python dont speed ahead:
python
### Start the wizard
cmd.wizard("mutagenesis")
###### REMOVE [0:3]
for p,c,r in ProtChainResiList[0:4]:
    #print p,c,r
    cmd.do("refresh_wizard")
    cmd.get_wizard().set_mode("LYS")
    selection="/%s//%s/%s"%(p,c,r)
    #print selection
    cmd.get_wizard().do_select(selection)
    ### Select frame 1, which is most probable
    cmd.frame(1)
    cmd.get_wizard().apply()
### Stop the wizard
cmd.set_wizard("done")
python end

Troels Emtekær Linnet



2011/9/22 Fabio Gozzo <fgozzo@gmail.com>
Hi Pymolers,

I need to perform a batch operation but I need a help with script modification.
A have a set (~100) of pdb files that I would like to mutate all residues to lysine. I modified mutate02.py script in pymol to perform this task, but I would need two extra "features":

1) the script would need to save the file with a different name. For example, load test.pdb, mutate all residues to lysine and then save the mutated version to test_K.pdb
2) the script would need to perform this task for all the pdb files in a directory.

Right now, I am not concerned about the possible rotamers of lysine, any lysine rotamer would work.
Could anyone give a hint on how to do it ?
Thanks !
Fabio.


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