Re: [ccp4bb] Comparison of Water Positions across PDBs
Hmmm..does that mean that the journals are now the ultimate authority of what stays in the PDB? I find this slightly irritating and worthy of change. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat Echols Sent: Dienstag, 5. November 2013 15:09 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs On Tue, Nov 5, 2013 at 12:22 AM, Bernhard Rupp hofkristall...@gmail.com wrote: Given their otherwise almost paranoid sensitivity to ultimate author authority (resulting in things like still having 2hr0 etc in the bank because certain authors go AWOL or ignore major issues) In defense of the PDB, it's not just the authors who went AWOL in that case - it is ultimately the responsibility of the journals to retract clearly fraudulent publications. -Nat
Re: [ccp4bb] Comparison of Water Positions across PDBs
On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp hofkristall...@gmail.comwrote: Hmmm….does that mean that the journals are now the ultimate authority of what stays in the PDB? I find this slightly irritating and worthy of change. http://www.wwpdb.org/UAB.html It is the current wwPDB (Worldwide PDB) policy that entries can be made obsolete following a request from the people responsible for publishing it (be it the principal author or journal editors). I'm not sure I understand why things should be any different; the PDB is not advertising itself as anything other than an archival service, unlike the journals which are supposed to be our primary mechanism of quality control. -Nat
Re: [ccp4bb] Comparison of Water Positions across PDBs
I've remained silent as this thread evolved into a discussion of how the PDB deals with water names and numbers. But Nat's comment about the PDB not advertising itself as anything other than an archival service finally prodded me into saying something. Something I've slowly come to realize is that the PDB, while it started as an archive, has developed into a working database. That's why they (the PDB workers/organizers/managers) have gotten into this mode where they change things from the original deposited files. I learned several years ago that the PDB is willing to change the atom names in a ligand from those previously used in the published literature. This was done in the name of consistency and essentially made the PDB files into database entries, rather than archival files since the atom names no longer matched the atom names used in the papers. Given the difficulties I had in discussing this with the annotaters, I've come to realize that as soon as I hit the submit button on a PDB submission, I've lost control over what will appear in the distributed file. In a way, it's been liberating to reach that point. It reduces my sense of responsibility for the contents of the file. Ron On Wed, 6 Nov 2013, Nat Echols wrote: On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp hofkristall...@gmail.com wrote: Hmmm….does that mean that the journals are now the ultimate authority of what stays in the PDB? I find this slightly irritating and worthy of change. http://www.wwpdb.org/UAB.html It is the current wwPDB (Worldwide PDB) policy that entries can be made obsolete following a request from the people responsible for publishing it (be it the principal author or journal editors). I'm not sure I understand why things should be any different; the PDB is not advertising itself as anything other than an archival service, unlike the journals which are supposed to be our primary mechanism of quality control. -Nat
Re: [ccp4bb] Comparison of Water Positions across PDBs
Dear all, there is a tool to identify invariant water molecules in homologous protein structures and the tool can be accessed via http://cluster.physics.iisc.ernet.in/3dss/ best, Sekar Thanks Bernhard you have helpfully distinguished between the two processes - there is certainly a movement of waters to symmetry replacements closer to a chain - and that gets documented in Remark 525 of the PDB file returned to authors - although then it is stripped out, I think, before the entry is released. But generally a renumbering is applied to all the waters - these are not actually moved but are re-ordered. And of course the number count of them may change - in order to accommodate any waters that are swapped in or out of the chain during the symmetry operation. Currently I don't think authors are given access to an audit of what is happening - they can of course check their favourite waters by a superimposition. Still have to say best way to avoid errors would be to check symmetry and re-order at the end of refinement, pre-deposition. All the best Martyn From: Bernhard Rupp hofkristall...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 4 November 2013, 14:50 Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs As far as confusion as a result of PDB renumbering is concerned: It was useful to run the old REM525 standalone program (I think I got it from PDBe/Kim Hendrick) at the end of solvent building. It does what the PDB did with water renumbering when creating the REMARK 525 (probably based on ccp4 contact with additions). Is there an updated standalone PDB tool available one can use these days to avoid at least that issue? Thx, BR From:CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of MARTYN SYMMONS Sent: Montag, 4. November 2013 15:17 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Thank you for that, Rachel Even though the tone of your comment does not suggest that you want to carry on a dialogue about this, I thought I would reply in any case - since dialogue is what this forum is supposed to be about. Thing is, I was sort of looking for an explanation of why the rule was adopted that waters were to be renumbered from N to C terminus. If this is not functioning to put the waters in register across a set of related structures then it seems somewhat arbitrary. And other schemes might be suggested to be better for the usability and interpretation of the structural data. In some cases there are only a few waters but in many structures the wwPDB partners renumber hundreds. And this process makes it difficult for authors to check the final deposited structure against the output of their refinement. I have to say that I agree with other contributors to this thread. It would be much better to let the refinement program authors agree on a default water numbering scheme. And then maintain that through deposition. I thought of six possible schemes before breakfast... one of my favourites was to order by B-factor - which might appeal to crystallographers. Another was to give priority to those in the coordination sphere of any metal ions - these actually get priority in the PDB as they are included in the LINKS records above the coordinates. These coordinated waters are often refined together with the metals and so it would make sense to move them closer to their friendly ion. And of course one other clearly suitable option would be to leave the waters in the authors' preferred order - chosen with help from their refinement suite. This is what happens during deposition with the residues of the polymers - (provided the authors chainids are suitably chosen). Following your link the rule for polymers is that: 'If the coordinate residue numbers, as provided by the author, are unique and sequential within a particular chain ID, the residues will not be renumbered.' I'm presuming that if the authors have a preferred suitable set of water numbers then that would be maintained similarly? Perhaps that is what is happening in the cases I notice that do not follow wwPDB rules? On Friday I was looking at TIRAP structures and in 3ub2 the protein construct starts at residue 78 and its final residue is 221 - but the associated DTT is labelled back at residue 1 in the same chain. Then the first ten out of eleven waters are residues 2 to 11 but then oddly the eleventh water is residue 222. Is there a difference in this C-terminal water compared with the N-terminal ones? I imagined it was perhaps maintained to fit in with the associated publication - or maybe started out life modelled as a metal ion - unfortunately I can find no mention of it in the paper. But, regardless of this distracting feature, surely this entry does not conform to the expected numbering scheme you mentioned
Re: [ccp4bb] Comparison of Water Positions across PDBs
On Tue, Nov 5, 2013 at 12:22 AM, Bernhard Rupp hofkristall...@gmail.comwrote: Given their otherwise almost paranoid sensitivity to ultimate author authority (resulting in things like still having 2hr0 etc in the bank because certain authors go AWOL or ignore major issues) In defense of the PDB, it's not just the authors who went AWOL in that case - it is ultimately the responsibility of the journals to retract clearly fraudulent publications. -Nat
Re: [ccp4bb] Comparison of Water Positions across PDBs
Thank you for that, Rachel Even though the tone of your comment does not suggest that you want to carry on a dialogue about this, I thought I would reply in any case - since dialogue is what this forum is supposed to be about. Thing is, I was sort of looking for an explanation of why the rule was adopted that waters were to be renumbered from N to C terminus. If this is not functioning to put the waters in register across a set of related structures then it seems somewhat arbitrary. And other schemes might be suggested to be better for the usability and interpretation of the structural data. In some cases there are only a few waters but in many structures the wwPDB partners renumber hundreds. And this process makes it difficult for authors to check the final deposited structure against the output of their refinement. I have to say that I agree with other contributors to this thread. It would be much better to let the refinement program authors agree on a default water numbering scheme. And then maintain that through deposition. I thought of six possible schemes before breakfast... one of my favourites was to order by B-factor - which might appeal to crystallographers. Another was to give priority to those in the coordination sphere of any metal ions - these actually get priority in the PDB as they are included in the LINKS records above the coordinates. These coordinated waters are often refined together with the metals and so it would make sense to move them closer to their friendly ion. And of course one other clearly suitable option would be to leave the waters in the authors' preferred order - chosen with help from their refinement suite. This is what happens during deposition with the residues of the polymers - (provided the authors chainids are suitably chosen). Following your link the rule for polymers is that: 'If the coordinate residue numbers, as provided by the author, are unique and sequential within a particular chain ID, the residues will not be renumbered.' I'm presuming that if the authors have a preferred suitable set of water numbers then that would be maintained similarly? Perhaps that is what is happening in the cases I notice that do not follow wwPDB rules? On Friday I was looking at TIRAP structures and in 3ub2 the protein construct starts at residue 78 and its final residue is 221 - but the associated DTT is labelled back at residue 1 in the same chain. Then the first ten out of eleven waters are residues 2 to 11 but then oddly the eleventh water is residue 222. Is there a difference in this C-terminal water compared with the N-terminal ones? I imagined it was perhaps maintained to fit in with the associated publication - or maybe started out life modelled as a metal ion - unfortunately I can find no mention of it in the paper. But, regardless of this distracting feature, surely this entry does not conform to the expected numbering scheme you mentioned as the wwPDB standard: polymer - heterogen - water? Yours perplexedly Martyn From: Rachel Kramer Green kra...@rcsb.rutgers.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, 1 November 2013, 20:18 Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs In PDB format files, each polymer is assigned a unique chain ID. Chain IDs for all bound moieties and waters are assigned based on their proximity (number of contacts) to the nearest polymer. Once the polymers and non-polymer residues associated with them are assigned chain IDs, they are also assigned unique residue numbering with the order polymer residues, ligands and then waters. Please see: http://www.wwpdb.org/procedure.html#toc_4 The wwPDB has established this rule to improve the usability and interpretation of the structural data. Assigning the same chain ID for all moieties associated with a polymer enables rapid and uniform identification of feature analysis. Sincerely, Rachel Green Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu Twitter: https://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB On 10/30/2013 8:09 AM, Eugene Krissinel wrote: This is to be answered by PDB people, who definitely read BB :) Would be nice to have a tool common between CCP4/Phenix and the PDB which sorts this out Eugene On 30 Oct 2013, at 12:09, Andreas Förster wrote: Dear all, this water discussion is flowing increasingly towards a place where I feel a bit out of my depth. What is the convention for numbering water molecules? Is there preference for: - putting waters into a separate chain (W for water or S for solvent)? - splitting waters according to the peptide chains in the structure? - appending all waters to chain A? Thanks. Andreas On 30/10/2013 11:57, MARTYN SYMMONS wrote: At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue
Re: [ccp4bb] Comparison of Water Positions across PDBs
As far as confusion as a result of PDB renumbering is concerned: It was useful to run the old REM525 standalone program (I think I got it from PDBe/Kim Hendrick) at the end of solvent building. It does what the PDB did with water renumbering when creating the REMARK 525 (probably based on ccp4 contact with additions). Is there an updated standalone PDB tool available one can use these days to avoid at least that issue? Thx, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of MARTYN SYMMONS Sent: Montag, 4. November 2013 15:17 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Thank you for that, Rachel Even though the tone of your comment does not suggest that you want to carry on a dialogue about this, I thought I would reply in any case - since dialogue is what this forum is supposed to be about. Thing is, I was sort of looking for an explanation of why the rule was adopted that waters were to be renumbered from N to C terminus. If this is not functioning to put the waters in register across a set of related structures then it seems somewhat arbitrary. And other schemes might be suggested to be better for the usability and interpretation of the structural data. In some cases there are only a few waters but in many structures the wwPDB partners renumber hundreds. And this process makes it difficult for authors to check the final deposited structure against the output of their refinement. I have to say that I agree with other contributors to this thread. It would be much better to let the refinement program authors agree on a default water numbering scheme. And then maintain that through deposition. I thought of six possible schemes before breakfast... one of my favourites was to order by B-factor - which might appeal to crystallographers. Another was to give priority to those in the coordination sphere of any metal ions - these actually get priority in the PDB as they are included in the LINKS records above the coordinates. These coordinated waters are often refined together with the metals and so it would make sense to move them closer to their friendly ion. And of course one other clearly suitable option would be to leave the waters in the authors' preferred order - chosen with help from their refinement suite. This is what happens during deposition with the residues of the polymers - (provided the authors chainids are suitably chosen). Following your link the rule for polymers is that: 'If the coordinate residue numbers, as provided by the author, are unique and sequential within a particular chain ID, the residues will not be renumbered.' I'm presuming that if the authors have a preferred suitable set of water numbers then that would be maintained similarly? Perhaps that is what is happening in the cases I notice that do not follow wwPDB rules? On Friday I was looking at TIRAP structures and in 3ub2 the protein construct starts at residue 78 and its final residue is 221 - but the associated DTT is labelled back at residue 1 in the same chain. Then the first ten out of eleven waters are residues 2 to 11 but then oddly the eleventh water is residue 222. Is there a difference in this C-terminal water compared with the N-terminal ones? I imagined it was perhaps maintained to fit in with the associated publication - or maybe started out life modelled as a metal ion - unfortunately I can find no mention of it in the paper. But, regardless of this distracting feature, surely this entry does not conform to the expected numbering scheme you mentioned as the wwPDB standard: polymer - heterogen - water? Yours perplexedly Martyn _ From: Rachel Kramer Green kra...@rcsb.rutgers.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, 1 November 2013, 20:18 Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs In PDB format files, each polymer is assigned a unique chain ID. Chain IDs for all bound moieties and waters are assigned based on their proximity (number of contacts) to the nearest polymer. Once the polymers and non-polymer residues associated with them are assigned chain IDs, they are also assigned unique residue numbering with the order polymer residues, ligands and then waters. Please see: http://www.wwpdb.org/procedure.html#toc_4 The wwPDB has established this rule to improve the usability and interpretation of the structural data. Assigning the same chain ID for all moieties associated with a polymer enables rapid and uniform identification of feature analysis. Sincerely, Rachel Green _ Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu Twitter: https://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB On 10/30/2013 8:09 AM, Eugene Krissinel wrote: This is to be answered by PDB people, who definitely read BB :) Would be nice to have a tool common between CCP4/Phenix and the PDB which sorts this out
Re: [ccp4bb] Comparison of Water Positions across PDBs
Thanks Bernhard you have helpfully distinguished between the two processes - there is certainly a movement of waters to symmetry replacements closer to a chain - and that gets documented in Remark 525 of the PDB file returned to authors - although then it is stripped out, I think, before the entry is released. But generally a renumbering is applied to all the waters - these are not actually moved but are re-ordered. And of course the number count of them may change - in order to accommodate any waters that are swapped in or out of the chain during the symmetry operation. Currently I don't think authors are given access to an audit of what is happening - they can of course check their favourite waters by a superimposition. Still have to say best way to avoid errors would be to check symmetry and re-order at the end of refinement, pre-deposition. All the best Martyn From: Bernhard Rupp hofkristall...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 4 November 2013, 14:50 Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs As far as confusion as a result of PDB renumbering is concerned: It was useful to run the old REM525 standalone program (I think I got it from PDBe/Kim Hendrick) at the end of solvent building. It does what the PDB did with water renumbering when creating the REMARK 525 (probably based on ccp4 contact with additions). Is there an updated standalone PDB tool available one can use these days to avoid at least that issue? Thx, BR From:CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of MARTYN SYMMONS Sent: Montag, 4. November 2013 15:17 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Thank you for that, Rachel Even though the tone of your comment does not suggest that you want to carry on a dialogue about this, I thought I would reply in any case - since dialogue is what this forum is supposed to be about. Thing is, I was sort of looking for an explanation of why the rule was adopted that waters were to be renumbered from N to C terminus. If this is not functioning to put the waters in register across a set of related structures then it seems somewhat arbitrary. And other schemes might be suggested to be better for the usability and interpretation of the structural data. In some cases there are only a few waters but in many structures the wwPDB partners renumber hundreds. And this process makes it difficult for authors to check the final deposited structure against the output of their refinement. I have to say that I agree with other contributors to this thread. It would be much better to let the refinement program authors agree on a default water numbering scheme. And then maintain that through deposition. I thought of six possible schemes before breakfast... one of my favourites was to order by B-factor - which might appeal to crystallographers. Another was to give priority to those in the coordination sphere of any metal ions - these actually get priority in the PDB as they are included in the LINKS records above the coordinates. These coordinated waters are often refined together with the metals and so it would make sense to move them closer to their friendly ion. And of course one other clearly suitable option would be to leave the waters in the authors' preferred order - chosen with help from their refinement suite. This is what happens during deposition with the residues of the polymers - (provided the authors chainids are suitably chosen). Following your link the rule for polymers is that: 'If the coordinate residue numbers, as provided by the author, are unique and sequential within a particular chain ID, the residues will not be renumbered.' I'm presuming that if the authors have a preferred suitable set of water numbers then that would be maintained similarly? Perhaps that is what is happening in the cases I notice that do not follow wwPDB rules? On Friday I was looking at TIRAP structures and in 3ub2 the protein construct starts at residue 78 and its final residue is 221 - but the associated DTT is labelled back at residue 1 in the same chain. Then the first ten out of eleven waters are residues 2 to 11 but then oddly the eleventh water is residue 222. Is there a difference in this C-terminal water compared with the N-terminal ones? I imagined it was perhaps maintained to fit in with the associated publication - or maybe started out life modelled as a metal ion - unfortunately I can find no mention of it in the paper. But, regardless of this distracting feature, surely this entry does not conform to the expected numbering scheme you mentioned as the wwPDB standard: polymer - heterogen - water? Yours perplexedly Martyn From:Rachel Kramer Green kra...@rcsb.rutgers.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, 1 November 2013, 20:18 Subject
Re: [ccp4bb] Comparison of Water Positions across PDBs
In PDB format files, each polymer is assigned a unique chain ID. Chain IDs for all bound moieties and waters are assigned based on their proximity (number of contacts) to the nearest polymer. Once the polymers and non-polymer residues associated with them are assigned chain IDs, they are also assigned unique residue numbering with the order polymer residues, ligands and then waters. Please see: http://www.wwpdb.org/procedure.html#toc_4 The wwPDB has established this rule to improve the usability and interpretation of the structural data. Assigning the same chain ID for all moieties associated with a polymer enables rapid and uniform identification of feature analysis. Sincerely, Rachel Green Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu Twitter: https://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB On 10/30/2013 8:09 AM, Eugene Krissinel wrote: This is to be answered by PDB people, who definitely read BB :) Would be nice to have a tool common between CCP4/Phenix and the PDB which sorts this out Eugene On 30 Oct 2013, at 12:09, Andreas Förster wrote: Dear all, this water discussion is flowing increasingly towards a place where I feel a bit out of my depth. What is the convention for numbering water molecules? Is there preference for: - putting waters into a separate chain (W for water or S for solvent)? - splitting waters according to the peptide chains in the structure? - appending all waters to chain A? Thanks. Andreas On 30/10/2013 11:57, MARTYN SYMMONS wrote: At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue they are nearest from N to C terminus along each chain. This renumbering started when waters were assigned to macromolecular chains rather than getting a chain id of their own. I have failed to find the rationale explained in any PDB documents - but it could be motivated by this sort of consideration when waters from different chains or entries are to be compared. Having said that I do not know if there are any cases where this approach has successfully matched waters. .. However an associated step which is certainly a help is that, in the case of multiple chains, the crystal symmetry is applied to replace waters with their symmetry equivalent position if it is closer to a different chain. I believe a freely available program implementing a similar approach is WATERTIDY in CCP4 which might be a good place to start. It gives a pretty complete output, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] Comparison of Water Positions across PDBs
On 30/10/13 12:32, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Andreas, I am not sure there is a convention, but there has been a decision. When you deposit a structure with the PDB, they place all ligands including water molecules to the respective nearest macromolecular chain. I found this rather annoying the other day as I looked at the polymerase structure and wanted to take a look at the Zn-atoms. Instead of navigating through chain Z, where probably many crystallographers would have put them, I had to check the PDB (text) file for the correct chain and residue number and enter this into the 'goto'-field of coot. If I understand some people correctly, this is not a shortcoming of the PDB-format, but of the software developer developing the software I used. So I am waiting for the next version of coot/mmdb with voice recognition where I can just say Coot, please centre on the next Zn in this structure. Or at least opening a pop-up window saying This is you coot speaking. This structure contains 6 Zn atoms, and I feel that you are interested in looking at their environment. Please click 'yes' to centre on the next Zn-atom I think is most suitable for you to look at ;-) How about Ctrl-L (het-group navigation)? Paul.
Re: [ccp4bb] Comparison of Water Positions across PDBs
For detailed examination of this topic, see: Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. Steiner, T. (2000). Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica. Journal of Molecular Biology 296, 713-735. http://www.ncbi.nlm.nih.gov/pubmed/10669619 best regards, Joel On 30 Oct 2013, at 01:35, Ed Pozharski epozh...@umaryland.edumailto:epozh...@umaryland.edu wrote: http://www.ccp4.ac.uk/html/watertidy.html On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Comparison of Water Positions across PDBs
Well - years ago I wrote a program called watertidy to do just this - but it asigned waters as OH0 OH1 OH2 with a according to what atom it was H bonded too, and those names are not now permitted.. My way now is to read in a completed homologous structure - use SSM to fit it over the new one - extract the HOHs from structure 1 - add them to structure 2 - do some refinement and use COOT to decide which ones are valid - the density fit picture shows wonderful red bars for wrong'uns - then add more again using coot.. Eleanor On 30 October 2013 06:49, Joel Sussman joel.suss...@weizmann.ac.il wrote: For detailed examination of this topic, see: Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. Steiner, T. (2000). Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica. Journal of Molecular Biology 296, 713-735. http://www.ncbi.nlm.nih.gov/pubmed/10669619 best regards, Joel On 30 Oct 2013, at 01:35, Ed Pozharski epozh...@umaryland.edu wrote: http://www.ccp4.ac.uk/html/watertidy.html On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Comparison of Water Positions across PDBs
At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue they are nearest from N to C terminus along each chain. This renumbering started when waters were assigned to macromolecular chains rather than getting a chain id of their own. I have failed to find the rationale explained in any PDB documents - but it could be motivated by this sort of consideration when waters from different chains or entries are to be compared. Having said that I do not know if there are any cases where this approach has successfully matched waters. .. However an associated step which is certainly a help is that, in the case of multiple chains, the crystal symmetry is applied to replace waters with their symmetry equivalent position if it is closer to a different chain. I believe a freely available program implementing a similar approach is WATERTIDY in CCP4 which might be a good place to start. It gives a pretty complete output, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn From: Joel Sussman joel.suss...@weizmann.ac.il To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 30 October 2013, 6:49 Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs For detailed examination of this topic, see: Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. Steiner, T. (2000). Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica. Journal of Molecular Biology 296, 713-735. http://www.ncbi.nlm.nih.gov/pubmed/10669619 best regards, Joel On 30 Oct 2013, at 01:35, Ed Pozharski epozh...@umaryland.edu wrote: http://www.ccp4.ac.uk/html/watertidy.html On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Comparison of Water Positions across PDBs
Dear all, this water discussion is flowing increasingly towards a place where I feel a bit out of my depth. What is the convention for numbering water molecules? Is there preference for: - putting waters into a separate chain (W for water or S for solvent)? - splitting waters according to the peptide chains in the structure? - appending all waters to chain A? Thanks. Andreas On 30/10/2013 11:57, MARTYN SYMMONS wrote: At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue they are nearest from N to C terminus along each chain. This renumbering started when waters were assigned to macromolecular chains rather than getting a chain id of their own. I have failed to find the rationale explained in any PDB documents - but it could be motivated by this sort of consideration when waters from different chains or entries are to be compared. Having said that I do not know if there are any cases where this approach has successfully matched waters. .. However an associated step which is certainly a help is that, in the case of multiple chains, the crystal symmetry is applied to replace waters with their symmetry equivalent position if it is closer to a different chain. I believe a freely available program implementing a similar approach is WATERTIDY in CCP4 which might be a good place to start. It gives a pretty complete output, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] Comparison of Water Positions across PDBs
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Andreas, I am not sure there is a convention, but there has been a decision. When you deposit a structure with the PDB, they place all ligands including water molecules to the respective nearest macromolecular chain. I found this rather annoying the other day as I looked at the polymerase structure and wanted to take a look at the Zn-atoms. Instead of navigating through chain Z, where probably many crystallographers would have put them, I had to check the PDB (text) file for the correct chain and residue number and enter this into the 'goto'-field of coot. If I understand some people correctly, this is not a shortcoming of the PDB-format, but of the software developer developing the software I used. So I am waiting for the next version of coot/mmdb with voice recognition where I can just say Coot, please centre on the next Zn in this structure. Or at least opening a pop-up window saying This is you coot speaking. This structure contains 6 Zn atoms, and I feel that you are interested in looking at their environment. Please click 'yes' to centre on the next Zn-atom I think is most suitable for you to look at ;-) Best, Tim On 10/30/2013 01:09 PM, Andreas Förster wrote: Dear all, this water discussion is flowing increasingly towards a place where I feel a bit out of my depth. What is the convention for numbering water molecules? Is there preference for: - putting waters into a separate chain (W for water or S for solvent)? - splitting waters according to the peptide chains in the structure? - appending all waters to chain A? Thanks. Andreas On 30/10/2013 11:57, MARTYN SYMMONS wrote: At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue they are nearest from N to C terminus along each chain. This renumbering started when waters were assigned to macromolecular chains rather than getting a chain id of their own. I have failed to find the rationale explained in any PDB documents - but it could be motivated by this sort of consideration when waters from different chains or entries are to be compared. Having said that I do not know if there are any cases where this approach has successfully matched waters. .. However an associated step which is certainly a help is that, in the case of multiple chains, the crystal symmetry is applied to replace waters with their symmetry equivalent position if it is closer to a different chain. I believe a freely available program implementing a similar approach is WATERTIDY in CCP4 which might be a good place to start. It gives a pretty complete output, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFScPxSUxlJ7aRr7hoRAi1TAKDrjtWhH5sCw/3kwPimT/0WVE4oWwCgovPM 4bWow+/SfAp46XnoxD5UJXE= =YXln -END PGP SIGNATURE-
Re: [ccp4bb] Comparison of Water Positions across PDBs
Dear Elise, Try the 3Dss server (http://cluster.physics.iisc.ernet.in/3dss/). You can superimpose up to 20 structures and look for invariant waters. Cheers, Uli --- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.goh...@mdc-berlin.de http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
Re: [ccp4bb] Comparison of Water Positions across PDBs
This is to be answered by PDB people, who definitely read BB :) Would be nice to have a tool common between CCP4/Phenix and the PDB which sorts this out Eugene On 30 Oct 2013, at 12:09, Andreas Förster wrote: Dear all, this water discussion is flowing increasingly towards a place where I feel a bit out of my depth. What is the convention for numbering water molecules? Is there preference for: - putting waters into a separate chain (W for water or S for solvent)? - splitting waters according to the peptide chains in the structure? - appending all waters to chain A? Thanks. Andreas On 30/10/2013 11:57, MARTYN SYMMONS wrote: At deposition the PDB runs a script that renumbers authors' waters according to a scheme based on the residue they are nearest from N to C terminus along each chain. This renumbering started when waters were assigned to macromolecular chains rather than getting a chain id of their own. I have failed to find the rationale explained in any PDB documents - but it could be motivated by this sort of consideration when waters from different chains or entries are to be compared. Having said that I do not know if there are any cases where this approach has successfully matched waters. .. However an associated step which is certainly a help is that, in the case of multiple chains, the crystal symmetry is applied to replace waters with their symmetry equivalent position if it is closer to a different chain. I believe a freely available program implementing a similar approach is WATERTIDY in CCP4 which might be a good place to start. It gives a pretty complete output, detailing residues actually H-bonded to the waters, and you could parse that for further analysis and comparisons. Best wishes. Martyn -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London -- Scanned by iCritical.
Re: [ccp4bb] Comparison of Water Positions across PDBs
Elise - after looking into a related problem for some time, I've come to the conclusion it's a bit harder than it seems. Two obstacles: (1) there is no good coordinate system for partitioning the overall solvent volume (fraction of unit cell not occupied by protein density) into suitable neighborhoods (2) experimental support for water placement in deposited structures varies from sound to wishful thinking - with no single useful credibility metric ( a helpful review : http://www.ncbi.nlm.nih.gov/pubmed/8081736 ) The path I've gone down for (1) is to : (a) compute the distance field from the molecular surface and skeletonize it. This will give you the outer boundary of surrounding solvent (eg if you blew up the molecular surfaces like balloons, the surface defined by where the balloons touch); (b) carve up the resulting volume as appropriate, eg radial shells from the molecular surface for outer regions modeled as bulk solvent, atom-specific expansion of the molecular surface for regions occupied by modeled waters/ions. This is quite a bit of work (or so it seemed) but it enables you to segment the overall solvent volume into regions of interest and then calculate density of ordered waters/ions across structures (bearing in mind that much of modeled solvent may not be real). For sorting out non-bonding contacts there is a very nice and fast class, MAtomNonBond, in Kevin Cowtan's clipper library. For the distance field and skeletonization/medial-axis computation you might want to look at fast-marching implementations. Good luck! Alastair --- On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship
[ccp4bb] Comparison of Water Positions across PDBs
Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship
Re: [ccp4bb] Comparison of Water Positions across PDBs
Downloading structures of the same homologous family with blast. Then superimpose them on a reference structure. You may then try to look at over lapping water molecules On 30 Oct 2013 02:23, Elise B ek...@case.edu wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship
Re: [ccp4bb] Comparison of Water Positions across PDBs
Hi Elise, How about taking the homologue structure with highest number of waters and use it to run molecular replacement on all other datasets? Then you could keep only the good waters (manually unfortunately) which will ensure they will all have the same numbers. Probably not the fastest way but it should give what I think you were asking for? HTWorks D From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Swastik Phulera [swastik.phul...@gmail.com] Sent: 29 October 2013 21:16 To: ccp4bb Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Downloading structures of the same homologous family with blast. Then superimpose them on a reference structure. You may then try to look at over lapping water molecules On 30 Oct 2013 02:23, Elise B ek...@case.edumailto:ek...@case.edu wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Comparison of Water Positions across PDBs
Hi Elise, Not exactly what you are asking for, but lsqman will compare waters between structures with a cut-off. (However, it will not renumber the waters as you wanted) http://xray.bmc.uu.se/usf/lsqman_man.html#S71 If you want to look at waters related by NCS in a single PDB file with multiple macromolecule chains, then you can use sortwater which will renumber NCS related waters with the same residue number but different chain identifiers. (I think watncs also does a similar thing, but I have not used it). Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom Bellini Sent: Tuesday, October 29, 2013 3:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Hi Elise, How about taking the homologue structure with highest number of waters and use it to run molecular replacement on all other datasets? Then you could keep only the good waters (manually unfortunately) which will ensure they will all have the same numbers. Probably not the fastest way but it should give what I think you were asking for? HTWorks D From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Swastik Phulera [swastik.phul...@gmail.com] Sent: 29 October 2013 21:16 To: ccp4bb Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Downloading structures of the same homologous family with blast. Then superimpose them on a reference structure. You may then try to look at over lapping water molecules On 30 Oct 2013 02:23, Elise B ek...@case.edumailto:ek...@case.edu wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Comparison of Water Positions across PDBs
http://www.ccp4.ac.uk/html/watertidy.html On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
