Propka - Revision history

Tlinnet: /* Known bugs */

2011-08-22T10:58:51Z

Known bugs

Tlinnet: /* ScriptVersion */

2011-08-22T10:38:03Z

ScriptVersion

Tlinnet: /* Python Code */

2011-08-22T10:37:22Z

Python Code

Tlinnet: /* Known bugs */

2011-08-22T10:30:51Z

Known bugs

Tlinnet: /* Changelog */

2011-08-22T09:40:28Z

Changelog

Tlinnet: /* Changelog */

2011-08-22T08:32:49Z

Changelog

Tlinnet: /* ScriptVersion */

2011-08-22T08:27:18Z

ScriptVersion

Tlinnet at 08:26, 22 August 2011

2011-08-22T08:26:40Z

Show changes

Tlinnet: /* Changelog */

2011-08-22T08:22:02Z

Changelog

Tlinnet: /* Changelog */

2011-08-22T08:02:06Z

Changelog

@@ Line 953: / Line 953: @@
 * The propka server sometimes use another naming scheme for Ligands. These Ligands will not be pka labelled or shown in pymol. The results will still downloaded to "/.Results_propka/file.pka"
 *# This can be reproduced with 1BJ6. Here the propka webpage predicts the pka values for the ligands: AN7,GN1,CN3,CO2,GO2, but the .pdb file names these ligands: DA,DA,DC,DG.
-* Alternative configurations of a Ligand is at the moment a problem, and will not shown. For example 1HXB and the ligand ROC. The script extraxt AROC and BROC from pymol, which does match with the .pka file. Try save the protein with only one configuration of the Ligand.
+* Alternative configurations of a Ligand is at the moment a problem, and will not shown. For example 1HXB and the ligand ROC.

@@ Line 907: / Line 907: @@
 == ScriptVersion ==
-Current_Version=20110822
+Current_Version=20110823
 == Changelog ==

@@ Line 272: / Line 272: @@
 def 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"):
-	Script_Version="20110822"
+	Script_Version="20110823"
 	### First we have to be sure, we give reasonable arguments
 	if pkafile!="NIL":
@@ Line 725: / Line 725: @@
 			else: comment=""
 			### Make the selection for which atom to copy
-			newselection = ("/%s//%s/%s/%s"%(newmolecule,chain,resn,atom))
+			ligselection = ("/%s and chain %s and resn %s and name %s"%(newmolecule,chain,resn,atom))
-			protselect = ("%sLig_%s%s%s"%(newmolecule,chain,resn,atom))
+			ligselect = ("%sLig_%s%s%s"%(newmolecule,chain,resn,atom))
-			result_pka_pymol.write("cmd.select('%s','%s')\n"%(protselect,newselection))
+			result_pka_pymol.write("cmd.select('%s','%s')\n"%(ligselect,ligselection))
-			result_pka_pymol.write("cmd.show('sticks','byres %s')\n"%(protselect))
+			result_pka_pymol.write("cmd.show('sticks','byres %s')\n"%(ligselect))
 			### The temporary name
 			tempname = ("%s%s%s%s"%(pkamolecule,chain,resn,atom))
 			tempnamelabel = ("%s%s%s%s"%(pkalabelmolecule,chain,resn,atom))
-			tempselect= ("/%s//%s/%s"%(tempname,chain,resn))
+			tempselect= ("/%s and chain %s and resn %s"%(tempname,chain,resn))
-			tempselectlabel= ("/%s//%s/%s"%(tempnamelabel,chain,resn))
+			tempselectlabel= ("/%s and chain %s and resn %s"%(tempnamelabel,chain,resn))
 			### Copy the atom, call it by the residue name
-			result_pka_pymol.write("cmd.create('%s','%s',quiet=1)\n"%(tempname,newselection))
+			result_pka_pymol.write("cmd.create('%s','%s',quiet=1)\n"%(tempname,ligselection))
 			### Alter the name and the b value of the newly created atom
 			result_pka_pymol.write("cmd.alter('%s','b=%s')\n"%(tempselect,pka))
@@ Line 803: / Line 804: @@
 				if not Check_bonding_partners(bonding_partners, l[8])[0]:
 					NBname,cutoff=BondTypeName(dictio[l[8][:3]],NBbond)
-					fromselection = ("/%s//%s/%s/%s"%(newmolecule,chain,resn,atom))
+					fromselection = ("/%s and chain %s and resn %s and name %s"%(newmolecule,chain,resn,atom))
 					toselection = ("/%s//%s/%s/%s"%(newmolecule,NBchain,NBresi,NBname))
 					if l[8][:3]=='NTR':
 						extind=cmd.identify("chain %s and name N"%(NBchain))[0]
 						toselection = ("/%s and id %s and name N"%(newmolecule,extind))
 					if l[8][:3]=='CTR':
 						extind=cmd.identify("chain %s and name C"%(NBchain))[-1]
 						toselection = ("/%s and id %s and name C"%(newmolecule,extind))
 					distname = ("%s_%s%s%s%s%s_%s_%s"%(newmolecule,chain,resn,atom,NBchain,NBresi,NBbond,pkachange))
 					result_pka_pymol.write("cmd.distance('%s','%s','%s'%s)\n"%(distname,fromselection,toselection,cutoff))
@@ Line 818: / Line 821: @@
 				if Check_bonding_partners(bonding_partners, l[8])[0]:
 					cutoff=""; NBresn = Check_bonding_partners(bonding_partners, l[8])[1]; NBname=l[8][len(NBresn):]+"*"
-					fromselection = ("/%s//%s/%s/%s"%(newmolecule,chain,resn,atom))
+					fromselection = ("/%s and chain %s and resn %s and name %s"%(newmolecule,chain,resn,atom))
 					toselection = ("/%s and chain %s and resn %s and name %s"%(newmolecule,NBchain,NBresn,NBname))
 					if verbose == 'yes': print("Ligand->Ligand: (%s) -> (%s)"%(fromselection, toselection))

@@ Line 950: / Line 950: @@
 * The propka server sometimes use another naming scheme for Ligands. These Ligands will not be pka labelled or shown in pymol. The results will still downloaded to "/.Results_propka/file.pka"
 *# This can be reproduced with 1BJ6. Here the propka webpage predicts the pka values for the ligands: AN7,GN1,CN3,CO2,GO2, but the .pdb file names these ligands: DA,DA,DC,DG.
 [[Category:Script_Library]]
 [[Category:Structural_Biology_Scripts]]
 [[Category:Biochemical_Scripts]]

@@ Line 907: / Line 907: @@
 == Changelog ==
 * 20110822
 *# Made the naming scheme consistent, so one can work with multiple proteins, and the grouping still works.
 *# Bonds to N-terminal and C-terminal did not show up. Fixed.

@@ Line 898: / Line 898: @@
 == Changelog ==
 * 20110822
-*: 1) Made the naming scheme consistent, so one can work with multiple proteins, and the grouping still works.
+*# Made the naming scheme consistent, so one can work with multiple proteins, and the grouping still works.
-*: 2) Bonds to N-terminal and C-terminal did not show up. Fixed.
+*# Bonds to N-terminal and C-terminal did not show up. Fixed.
-*: 3) If one just write "propka", the "last" molecule in the pymol object list is now assumed, instead of the first. This makes mutagenesis analysis easier.
+*# If one just write "propka", the "last" molecule in the pymol object list is now assumed, instead of the first. This makes mutagenesis analysis easier.
-*: 4) The pka difference from assumed standard values are now also displayed. Standard values are set to: pkadictio = {'ASP':3.9, 'GLU':4.3, 'ARG':12.0, 'LYS':10.5, 'HIS':6.0, 'CYS':8.3, 'TYR':10.1}
+*# The pka difference from assumed standard values are now also displayed. Standard values are set to: pkadictio = {'ASP':3.9, 'GLU':4.3, 'ARG':12.0, 'LYS':10.5, 'HIS':6.0, 'CYS':8.3, 'TYR':10.1}
-*: 5) The menu size is made bigger, so it can fit the long names for the bonding partners.
+*# The menu size is made bigger, so it can fit the long names for the bonding partners. There's also a slider that you can drag using the mouse
 * 20110821
-*: 1) The resn function was made wrong, only taking the last item of list. Fixed.
+*# The resn function was made wrong, only taking the last item of list. Fixed.
-*: 2) resn= can now also be print to screen/log for ligands like ATP. Ex: resn=CYS.ATP.TRP
+*# resn= can now also be print to screen/log for ligands like ATP. Ex: resn=CYS.ATP.TRP
-*: 3) Ligands are now also written to the "stripped-file". "./Results_propka/PDB.stripped"
+*# Ligands are now also written to the "stripped-file". "./Results_propka/PDB.stripped"
-*: 4) Bonds are now also made for Ligands.
+*# Bonds are now also made for Ligands.
 * 20110820
-*: 1) If one points to a result .pka file, then "method" is automatically set to "method=file".
+*# If one points to a result .pka file, then "method" is automatically set to "method=file".
-*: 2) Added the ability for pka values for ligands
+*# Added the ability for pka values for ligands
-*: 3) Bonds are now generated for the pka atoms.
+*# Bonds are now generated for the pka atoms.
-*: 4) The color scheme is changed from "rainbow" to "red_white_blue". This is easier to interpret.
+*# The color scheme is changed from "rainbow" to "red_white_blue". This is easier to interpret.
 ** CC: COULOMBIC INTERACTION. Color is red.
 ** SH: SIDECHAIN HYDROGEN BOND. Color is brightorange.
@@ Line 920: / Line 921: @@
 * 20110817
-*: 1) If just invoking with "propka", it will select the first molecule. And now it is possible also to write. "propka all".
+*# If just invoking with "propka", it will select the first molecule. And now it is possible also to write. "propka all".
-*: 2) Removed the "raise UserWarning" if the script is oudated. Only a warning message is printed.
+*# Removed the "raise UserWarning" if the script is oudated. Only a warning message is printed.
 * 20110816
-*: 1) Made the execution of the pymol command script silent, by only using cmd.API. This will raise a Warning, which can be ignored.
+*# Made the execution of the pymol command script silent, by only using cmd.API. This will raise a Warning, which can be ignored.
-*: 2) Built-in a Script version control, to inform the user if the propka script is updated on this page
+*# Built-in a Script version control, to inform the user if the propka script is updated on this page
-*: 3) The alternate attribute for the labeling atoms are reset. It was found pymol objected altering names for atoms which had alternate positions/values.
+*# The alternate attribute for the labeling atoms are reset. It was found pymol objected altering names for atoms which had alternate positions/values.
-*: 4) Reorganized the input order, which means that: molecule=all is default.
+*# Reorganized the input order, which means that: molecule=all is default.
 === Known bugs ===
 * Bonds can be multiplied from amino acids to Ligands like ZN or ATP. Assume the shortest bond to be correct.
-*: ZN: This is caused, since ZN has no ID number and when there are several in the same chain. This can be reproduced for 1HP1, bond: A41ZNCC. Here it shows to bonds, where only the shortes is correct. No fix possible.
+*# ZN: This is caused, since ZN has no ID number and when there are several in the same chain. This can be reproduced for 1HP1, bond: A41ZNCC. Here it shows to bonds, where only the shortes is correct. No fix possible.
-*: ATP: This is caused, since propka sometimes eats the ending of the atom name. In the .pdb file is written O3', which propka represents like O3. Therefore a wildcard "*" is generel inserted, which can cause multiple bonds to the ATP molecule. This can be reproduced for 1HP1, bond: A504ATPSH. Here multiple bonds are made to all the O3*,O2* atoms. No fix possible.
+*# ATP: This is caused, since propka sometimes eats the ending of the atom name. In the .pdb file is written O3', which propka represents like O3. Therefore a wildcard "*" is generel inserted, which can cause multiple bonds to the ATP molecule. This can be reproduced for 1HP1, bond: A504ATPSH. Here multiple bonds are made to all the O3*,O2* atoms. No fix possible.
 * The propka server sometimes use another naming scheme for Ligands. These Ligands will not be pka labelled or shown in pymol. The results will still downloaded to "/.Results_propka/file.pka"
-*: This can be reproduced with 1BJ6. Here the propka webpage predicts the pka values for the ligands: AN7,GN1,CN3,CO2,GO2, but the .pdb file names these ligands: DA,DA,DC,DG.
+*# This can be reproduced with 1BJ6. Here the propka webpage predicts the pka values for the ligands: AN7,GN1,CN3,CO2,GO2, but the .pdb file names these ligands: DA,DA,DC,DG.
 [[Category:Script_Library]]
 [[Category:Structural_Biology_Scripts]]
 [[Category:Biochemical_Scripts]]