I am trying to calculate cysteine pka of a large dataset of proteins.
I can use the software propka entring PDB code one by one.
Does anybody did it with a large datataset of PDB?
Thank you
Bonjour Stephane thank you for your answer
The "example 3" should do the job. Have you ever used this script ?
It is not clear to me the how the PDBs are listed
"1DSB","*","30" , 1DSB is the PDB but what are * and the number. Mayb the number is the amino acid, but what if I whant all the residues. Moreover I do not understand why in the string
resis =...only part of the listed PDB are recalled.
Regards
The first parameter is the molecule ID, the second the chain ID (* for "all chains"), the third the residue or range of residues
propka(molecule="NIL",chain="*",resi="0",resn="NIL",method="upload",logtime=time.strftime("%m%d",time.localtime()),server_wait=3.0,version="v3.1",verbose="no",showresult="no",pkafile="NIL")
thank you annemarie
do you know why in the example 3 the line:
resis = [["1DSB","*","30"],["1ERT","*","32"]]
has only two entris of the 11 declared in the previouos line?
Of the many parameters, you need to explicitly set only the ones you want to set different from the default value..
From the script:
"propka(molecule="NIL",chain="*",resi="0",resn="NIL",method="upload",logtime=time.strftime("%m%d",time.localtime()),server_wait=3.0,version="v3.1",verbose="no",showresult="no",pkafile="NIL")
# method : method=upload is default. This sends .pdb file and request result from propka server.
## method=file will only process a manual .pka file, and write a pymol command file. No use of mechanize.
## If one points to an local .pka file, then method is auto-changed to method=file. This is handsome in off-line environment, ex. teaching or seminar.
# pkafile: Write the path to .pka file. Ex: pkafile=./Results_propka/4ins_.pka
# molecule : name of the molecule. Ending of file is assumed to be .pdb
# chain : which chains are saved to file, before molecule file is send to server. Separate with "." Ex: chain=A.b
# resi : Select by residue number, which residues should be printed to screen and saved to the log file: /Results_propka/_Results.log.
## Separate with "." or make ranges with "-". Ex: resi=35.40-50
# resn : Select by residue name, which residues should be printed to screen and saved to the log file: /Results_propka/_Results.log.
## Separate with "." Ex: resn=cys.tyr
# logtime : Each execution give a set of files with the job id=logtime. If logtime is not provided, the current time is used.
## Normal it usefull to set it empty. Ex: logtime=_
# verbose : Verbose is switch, to turn on messages for the mechanize section. This is handsome to see how mechanize works, and for error searching.
# showresult : Switch, to turn on all results in pymol command window. Ex: showresult=yes
# server_wait=10.0 is default. This defines how long time between asking the server for a result. Set no lower than 3 seconds."