Re: [ccp4bb] HETATM automated chain assignment
Dear Romain, I already ask this question to someone of the pdb staff during a deposition process, and he answer me that it is an in house program and they don't distribute theirs in house programs, so if this direction hit your mind, you can forget it directly. Meow... 2013/2/15 Talon Romain > Hello to the CCP4 bulletin board community, > > I would like to know if I could find a tool to automatically assign HETATM > atom (or even, water molecules) to the nearest protein chain ? > > In my case, I have 4 protein chains in the asymmetric unit : A, B, C and > D. I would like to assign each ions and each ligands (which are numerous) > with the chain letter of the nearest residue that coordinate them. > Usually, I rename everything by hand but as the in-house program of the > PDBe AutoDep deposition tool automatically do that... > > I beg your pardon if this question has just been posted here. I didn't > find any tool either in the CCP4 Suite or in the "Extensions" and > "Calculate" menus of the Coot program (v0.7). > > Best regards. > > Romain Talon >
Re: [ccp4bb] HETATM automated chain assignment
Have a look at sortwater. http://www.ccp4.ac.uk/html/sortwater.html If you want to use it for non-water ions in addition to waters, you would need to run it a second time for each of the atom types using the water keyword to define the residue type and atom name. Also, it won't work for multi-atom ions, but could work for Na, Cl, K, Mg, Ca etc Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Talon Romain Sent: Friday, February 15, 2013 8:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] HETATM automated chain assignment Hello to the CCP4 bulletin board community, I would like to know if I could find a tool to automatically assign HETATM atom (or even, water molecules) to the nearest protein chain ? In my case, I have 4 protein chains in the asymmetric unit : A, B, C and D. I would like to assign each ions and each ligands (which are numerous) with the chain letter of the nearest residue that coordinate them. Usually, I rename everything by hand but as the in-house program of the PDBe AutoDep deposition tool automatically do that... I beg your pardon if this question has just been posted here. I didn't find any tool either in the CCP4 Suite or in the "Extensions" and "Calculate" menus of the Coot program (v0.7). Best regards. Romain Talon
[ccp4bb] HETATM automated chain assignment
Hello to the CCP4 bulletin board community, I would like to know if I could find a tool to automatically assign HETATM atom (or even, water molecules) to the nearest protein chain ? In my case, I have 4 protein chains in the asymmetric unit : A, B, C and D. I would like to assign each ions and each ligands (which are numerous) with the chain letter of the nearest residue that coordinate them. Usually, I rename everything by hand but as the in-house program of the PDBe AutoDep deposition tool automatically do that... I beg your pardon if this question has just been posted here. I didn't find any tool either in the CCP4 Suite or in the "Extensions" and "Calculate" menus of the Coot program (v0.7). Best regards. Romain Talon
