[ccp4bb] Coot chain ID
Dear All, I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did the Merge Molecules and did the refinement. In output PDB file the chain ID sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM numbering is starting from ligand (Chain B instead of Chain A). How can I make the sequence A, B and C (Protein, ligand and SO4). Best wishes Dipankar This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] Coot chain ID
Dipankar, A little bit of cut-and-paste in a good text editor will sort that out fairly easily. Tony. Sent from my iPhone On 14 Apr 2012, at 07:54, Dipankar Manna dipanka...@aurigene.commailto:dipanka...@aurigene.com wrote: Dear All, I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did the “Merge Molecules” and did the refinement. In output PDB file the chain ID sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM numbering is starting from ligand (Chain B instead of Chain A). How can I make the sequence A, B and C (Protein, ligand and SO4). Best wishes Dipankar This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] Coot chain ID
In Coot you can use Extensions - Modelling - Reorder Chains Bernahrd -- Bernhard Lechtenberg PhD student Huntington lab University of Cambridge Department of Haematology Cambridge Institute for Medical Research Wellcome Trust/MRC Building, Hills Road Cambridge, CB2 0XY United Kingdom -Original Message- From: Dipankar Manna dipanka...@aurigene.com Reply-to: Dipankar Manna dipanka...@aurigene.com To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot chain ID Date: Sat, 14 Apr 2012 06:55:10 + Dear All, I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did the “Merge Molecules” and did the refinement. In output PDB file the chain ID sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM numbering is starting from ligand (Chain B instead of Chain A). How can I make the sequence A, B and C (Protein, ligand and SO4). Best wishes Dipankar This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] Coot chain ID
Edit, or use coot to reorder chains If you read that edited pdb into pdbset pdbset xyzin edited.pdb xyzout edited-and-renumbered.pdb end I think the renumbering happens automatically.. Eleanor On 14 April 2012 09:46, Bernhard Lechtenberg bc...@cam.ac.uk wrote: In Coot you can use Extensions - Modelling - Reorder Chains Bernahrd -- Bernhard Lechtenberg PhD student Huntington lab University of Cambridge Department of Haematology Cambridge Institute for Medical Research Wellcome Trust/MRC Building, Hills Road Cambridge, CB2 0XY United Kingdom -Original Message- From: Dipankar Manna dipanka...@aurigene.com Reply-to: Dipankar Manna dipanka...@aurigene.com To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot chain ID Date: Sat, 14 Apr 2012 06:55:10 + Dear All, I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did the “Merge Molecules” and did the refinement. In output PDB file the chain ID sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM numbering is starting from ligand (Chain B instead of Chain A). How can I make the sequence A, B and C (Protein, ligand and SO4). Best wishes Dipankar This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
