Re: [PyMOL] Mutate residues in batch mode
And to save it, add this python block
python
for PDB in PDBs:
cmd.save("%s-K.pdb"%PDB,"%s"%PDB)
python end
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Karl-Liebknecht-Straße 53, 2 RE
Re: [PyMOL] Mutate residues in batch mode
# 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
> 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.
>
>
>
> --
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
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All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1___
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[PyMOL] Mutate residues in batch mode
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. -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
