Re: [ccp4bb] Adding a residue with an insertion code
Hi Jared and all, There is also a JAVA program called PDBeditor by Jonas Lee that may make the PDB editing part a little easier or less error prone: http://sourceforge.net/projects/pdbeditorjl/ I did a little test and find it pretty useful, especially for those who do not have access to a text editor that supports column editing mode (or those who haven’t yet get acquainted with notepad++). It allows you to select certain blocks in the PDB based on certain criteria, and edit properties of certain residues together, e.g., adding “A” to column 27 of residue 101. HTH Zhijie From: Sampson, Jared Sent: Wednesday, January 14, 2015 3:48 PM To: Zhijie Li Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Adding a residue with an insertion code Thanks to Paul and Zhijie for the suggestions. In the past, I’ve also renumbered everything from 1 (using pdbset) for the duration of refinement, then renumbered the structure at the end. For that, I would use either pdbset and a text editor (which is somewhat tedious, as there are several insertion positions in either the Kabat or Chothia numbering schemes, although Matt Franklin suggested to me off-list that their usage in new PDB deposits has been declining), or if I’m not feeling particularly secretive about the structure, via Andrew Martin's Abnum server (http://www.bioinf.org.uk/abs/abnum/), although that’s only good for antibody structures, of course. In any case, insertion codes are the exception to the rule, and I don’t particularly mind the workarounds every now and then. I just wanted to make sure I wasn’t missing an easier way to do it. :) Thanks again, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jan 14, 2015, at 12:52 PM, Zhijie Li zhijie...@utoronto.ca wrote: Hi Jared, The only thing that comes to my mind that might help a little is to use pdbset to renumber your residues. Then you only need to change residue 101 to 100A manually in a text editor (unfortunately I could not find a program that does that). Here are the steps I would take: 1) build the model with normal numbering, i.e., the concerned region would be 100,101,102; 2) manually change 101 to 100A in text editor; 3) pdbset xyzin old.pdb xyzout new.pdb renumber increment –1 102 to 500 chain A !move everything up starting from 102 end You can make a little shell script file for step 3, to save some typing/typo. (see attachment for an example) Zhijie From: Sampson, Jared Sent: Wednesday, January 14, 2015 11:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Adding a residue with an insertion code Along the same lines as Dialing’s recent post about inserting a residue, I’d like to ask: Is it possible to insert a residue with an insertion code in the residue number? For example, what’s the best way to insert residue 100A between residues 100 and 101? This situation arises frequently for me in antibody CDR loops, for example. I ran into it most recently just last week, and Coot wouldn’t allow this kind of insertion, even though the consecutively numbered residues were too far apart to be covalently linked. (In the terminal window, it explained that residue was not at a terminus.”) My workaround has been either to increment the residue numbers of the C-terminal portion of the chain, then renumber manually in a text editor; or, to position a lone amino acid in approximately the right spot, save the coordinates, copy them manually into the working PDB and adjust the numbering in a text editor, reload the PDB in Coot, and real space refine the loop with the insertion. Any suggestions for how to do this more efficiently? Thanks! Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jan 14, 2015, at 9:54 AM, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: If the residues are consecutively numbered (Calculate Renumber residues), and are assigned the same chain ID (Calculate Change Chain ID), Coot might surprise you and link them on its own. On Wed, Jan 14, 2015 at 9:39 AM, Zhijie Li zhijie...@utoronto.ca wrote: Have you done it? 1) Click “add residue...” 2) Click that “real space refine zone” button. You will see what will happen. From: Dialing Pretty Sent: Wednesday, January 14, 2015 9:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal Dear All, Suppose I delete a residue ( residue 100 for example) for outlier refinement, then I add the same residue at the C-terminal of residue 99 (by Add terminal residue function of the Coot). By coot, how can I connect the C-terminal of residue 100 to the N-terminal of residue 101? I am looking forward to getting your reply. DIaling renumber.sh
Re: [ccp4bb] Adding a residue with an insertion code
Thanks to Paul and Zhijie for the suggestions. In the past, I’ve also renumbered everything from 1 (using pdbset) for the duration of refinement, then renumbered the structure at the end. For that, I would use either pdbset and a text editor (which is somewhat tedious, as there are several insertion positions in either the Kabat or Chothia numbering schemes, although Matt Franklin suggested to me off-list that their usage in new PDB deposits has been declining), or if I’m not feeling particularly secretive about the structure, via Andrew Martin's Abnum server (http://www.bioinf.org.uk/abs/abnum/), although that’s only good for antibody structures, of course. In any case, insertion codes are the exception to the rule, and I don’t particularly mind the workarounds every now and then. I just wanted to make sure I wasn’t missing an easier way to do it. :) Thanks again, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jan 14, 2015, at 12:52 PM, Zhijie Li zhijie...@utoronto.camailto:zhijie...@utoronto.ca wrote: Hi Jared, The only thing that comes to my mind that might help a little is to use pdbset to renumber your residues. Then you only need to change residue 101 to 100A manually in a text editor (unfortunately I could not find a program that does that). Here are the steps I would take: 1) build the model with normal numbering, i.e., the concerned region would be 100,101,102; 2) manually change 101 to 100A in text editor; 3) pdbset xyzin old.pdb xyzout new.pdb renumber increment –1 102 to 500 chain A !move everything up starting from 102 end You can make a little shell script file for step 3, to save some typing/typo. (see attachment for an example) Zhijie From: Sampson, Jaredmailto:jared.samp...@nyumc.org Sent: Wednesday, January 14, 2015 11:04 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Adding a residue with an insertion code Along the same lines as Dialing’s recent post about inserting a residue, I’d like to ask: Is it possible to insert a residue with an insertion code in the residue number? For example, what’s the best way to insert residue 100A between residues 100 and 101? This situation arises frequently for me in antibody CDR loops, for example. I ran into it most recently just last week, and Coot wouldn’t allow this kind of insertion, even though the consecutively numbered residues were too far apart to be covalently linked. (In the terminal window, it explained that residue was not at a terminus.”) My workaround has been either to increment the residue numbers of the C-terminal portion of the chain, then renumber manually in a text editor; or, to position a lone amino acid in approximately the right spot, save the coordinates, copy them manually into the working PDB and adjust the numbering in a text editor, reload the PDB in Coot, and real space refine the loop with the insertion. Any suggestions for how to do this more efficiently? Thanks! Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jan 14, 2015, at 9:54 AM, Emilia C. Arturo (Emily) ec...@drexel.edumailto:ec...@drexel.edu wrote: If the residues are consecutively numbered (Calculate Renumber residues), and are assigned the same chain ID (Calculate Change Chain ID), Coot might surprise you and link them on its own. On Wed, Jan 14, 2015 at 9:39 AM, Zhijie Li zhijie...@utoronto.camailto:zhijie...@utoronto.ca wrote: Have you done it? 1) Click “add residue...” 2) Click that “real space refine zone” button. You will see what will happen. From: Dialing Prettymailto:03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk Sent: Wednesday, January 14, 2015 9:24 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal Dear All, Suppose I delete a residue ( residue 100 for example) for outlier refinement, then I add the same residue at the C-terminal of residue 99 (by Add terminal residue function of the Coot). By coot, how can I connect the C-terminal of residue 100 to the N-terminal of residue 101? I am looking forward to getting your reply. DIaling renumber.sh
Re: [ccp4bb] Adding a residue with an insertion code
Hi Jared, The only thing that comes to my mind that might help a little is to use pdbset to renumber your residues. Then you only need to change residue 101 to 100A manually in a text editor (unfortunately I could not find a program that does that). Here are the steps I would take: 1) build the model with normal numbering, i.e., the concerned region would be 100,101,102; 2) manually change 101 to 100A in text editor; 3) pdbset xyzin old.pdb xyzout new.pdb renumber increment –1 102 to 500 chain A !move everything up starting from 102 end You can make a little shell script file for step 3, to save some typing/typo. (see attachment for an example) Zhijie From: Sampson, Jared Sent: Wednesday, January 14, 2015 11:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Adding a residue with an insertion code Along the same lines as Dialing’s recent post about inserting a residue, I’d like to ask: Is it possible to insert a residue with an insertion code in the residue number? For example, what’s the best way to insert residue 100A between residues 100 and 101? This situation arises frequently for me in antibody CDR loops, for example. I ran into it most recently just last week, and Coot wouldn’t allow this kind of insertion, even though the consecutively numbered residues were too far apart to be covalently linked. (In the terminal window, it explained that residue was not at a terminus.”) My workaround has been either to increment the residue numbers of the C-terminal portion of the chain, then renumber manually in a text editor; or, to position a lone amino acid in approximately the right spot, save the coordinates, copy them manually into the working PDB and adjust the numbering in a text editor, reload the PDB in Coot, and real space refine the loop with the insertion. Any suggestions for how to do this more efficiently? Thanks! Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jan 14, 2015, at 9:54 AM, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: If the residues are consecutively numbered (Calculate Renumber residues), and are assigned the same chain ID (Calculate Change Chain ID), Coot might surprise you and link them on its own. On Wed, Jan 14, 2015 at 9:39 AM, Zhijie Li zhijie...@utoronto.ca wrote: Have you done it? 1) Click “add residue...” 2) Click that “real space refine zone” button. You will see what will happen. From: Dialing Pretty Sent: Wednesday, January 14, 2015 9:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal Dear All, Suppose I delete a residue ( residue 100 for example) for outlier refinement, then I add the same residue at the C-terminal of residue 99 (by Add terminal residue function of the Coot). By coot, how can I connect the C-terminal of residue 100 to the N-terminal of residue 101? I am looking forward to getting your reply. DIaling renumber.sh Description: Binary data
