Re: [ccp4bb] correlated alternate confs - validation?
Just a quick thought that might be a workaround solution within the PDB format restrictions: In NMR structures there are often multiple conformations stored in different MODEL sections - this should in principle be possible for x-ray structures as well, shouldn't it? Of course this is a waste of space, as you have to duplicate all atoms and not only the ones that are included in multiple conformations, and not all features might be handled by validation tools, but with the limitations of the current PDB format there are not many ways to encode this anyway. Best regards, Thomas
Re: [ccp4bb] correlated alternate confs - validation?
As an additional comment on the issue of spatially correlated disorder, SHELX (and possibly other programs) has an elegant way of handling bump generation between disordered atoms. SHELX will only generate a bump if two atoms are in van der Waals conflict AND their occupancies sum to 1.1 or greater. This is on top of an exclusion for atoms from different altloc (non-zero part) numbers, and has the attraction of enforcing a physically reasonable model in any event. This approach requires no information about the correlated group membership of the atoms, although as George Sheldrick pointed out, this can be handled using free variables in SHELX. I bring this up because several current validation programs do not take correlated disorder into account when generating clashes, and I wish that an occupancy check would be more widely implemented. Best regards, Mark Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu On 7/25/14 2:51 AM, Thomas Lütteke thomas.luett...@vetmed.uni-giessen.de wrote: Just a quick thought that might be a workaround solution within the PDB format restrictions: In NMR structures there are often multiple conformations stored in different MODEL sections - this should in principle be possible for x-ray structures as well, shouldn't it? Of course this is a waste of space, as you have to duplicate all atoms and not only the ones that are included in multiple conformations, and not all features might be handled by validation tools, but with the limitations of the current PDB format there are not many ways to encode this anyway. Best regards, Thomas
Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?
From a practical point of view, a solution for documenting grouped occupancy refinement should at minimum allow (a) easy automatic harvesting from the respective refinement log files, and (b) equally easy extraction from the PDB/cif format to replicate the same refinement (c)not mess up legacy code/format or use undocumented 'features' How this is best implemented is probably not trivial (except the REMARK kludge) and needs the data base/integrity/validation experts. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dusan turk Sent: Donnerstag, 24. Juli 2014 05:32 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation? Hello, A solution exists also for PDB records: As a consequence of a discussion with George which took place years ago, I have taken the liberty to extend the PDB record length of 80 characters and use additional characters to specify the group ID and their members list number and provided an interface to manipulate them. Thereby the PDB limitations were extended to adopt the SHELX philosophy of treating combined groups of any composition. ATOM 1 N GLY A 1 -31.334 -24.247 23.250 0.54 34.05 1A N 1 0 ATOM 2477 N GLY A 1 -29.650 -24.643 23.839 0.46 41.88 1B N 1 1 The records with our the group extension are not members of groups with partial occupancy. These two records shown are members of group ID 1, the atom in the first record belongs to group ID 1 members list number 0 and the second to group ID 1 and members list no 1. (The members lists begin with 0.) On Jul 24, 2014, at 1:02 AM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: Von: CCP4 bulletin board [ mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: mailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com http://www.skype.com/
Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [flame] It's all there in the shelx format. If someone would write a wrapper to translate it into mmCIF, everybody would be happy with the least necessary effort [/flame] ;-) Cheers, Tim On 07/24/2014 10:46 AM, Bernhard Rupp wrote: From a practical point of view, a solution for documenting grouped occupancy refinement should at minimum allow (a) easy automatic harvesting from the respective refinement log files, and (b) equally easy extraction from the PDB/cif format to replicate the same refinement (c)not mess up legacy code/format or use undocumented 'features' How this is best implemented is probably not trivial (except the REMARK kludge) and needs the data base/integrity/validation experts. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dusan turk Sent: Donnerstag, 24. Juli 2014 05:32 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation? Hello, A solution exists also for PDB records: As a consequence of a discussion with George which took place years ago, I have taken the liberty to extend the PDB record length of 80 characters and use additional characters to specify the group ID and their members list number and provided an interface to manipulate them. Thereby the PDB limitations were extended to adopt the SHELX philosophy of treating combined groups of any composition. ATOM 1 N GLY A 1 -31.334 -24.247 23.250 0.54 34.05 1A N 1 0 ATOM 2477 N GLY A 1 -29.650 -24.643 23.839 0.46 41.88 1B N 1 1 The records with our the group extension are not members of groups with partial occupancy. These two records shown are members of group ID 1, the atom in the first record belongs to group ID 1 members list number 0 and the second to group ID 1 and members list no 1. (The members lists begin with 0.) On Jul 24, 2014, at 1:02 AM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: Von: CCP4 bulletin board [ mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: mailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com http://www.skype.com/ - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFT0NuIUxlJ7aRr7hoRAuorAKDaX42345ovf1SIrVIPzAuO1g1UkwCglBsF NoX6cxLs99wWwd0KZyaZ9XE= =buQc -END PGP SIGNATURE-
Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?
Not sure why this qualifies as a flame or who you want to flame - seems reasonable but needs to be done so that the data items are extracted consistently from all programs and can be interpreted again by the refinement (or validation) programs independently of which program they came from. Insular kludges probably won't do. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Donnerstag, 24. Juli 2014 12:10 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation? -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [flame] It's all there in the shelx format. If someone would write a wrapper to translate it into mmCIF, everybody would be happy with the least necessary effort [/flame] ;-) Cheers, Tim On 07/24/2014 10:46 AM, Bernhard Rupp wrote: From a practical point of view, a solution for documenting grouped occupancy refinement should at minimum allow (a) easy automatic harvesting from the respective refinement log files, and (b) equally easy extraction from the PDB/cif format to replicate the same refinement (c)not mess up legacy code/format or use undocumented 'features' How this is best implemented is probably not trivial (except the REMARK kludge) and needs the data base/integrity/validation experts. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dusan turk Sent: Donnerstag, 24. Juli 2014 05:32 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation? Hello, A solution exists also for PDB records: As a consequence of a discussion with George which took place years ago, I have taken the liberty to extend the PDB record length of 80 characters and use additional characters to specify the group ID and their members list number and provided an interface to manipulate them. Thereby the PDB limitations were extended to adopt the SHELX philosophy of treating combined groups of any composition. ATOM 1 N GLY A 1 -31.334 -24.247 23.250 0.54 34.05 1A N 1 0 ATOM 2477 N GLY A 1 -29.650 -24.643 23.839 0.46 41.88 1B N 1 1 The records with our the group extension are not members of groups with partial occupancy. These two records shown are members of group ID 1, the atom in the first record belongs to group ID 1 members list number 0 and the second to group ID 1 and members list no 1. (The members lists begin with 0.) On Jul 24, 2014, at 1:02 AM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: Von: CCP4 bulletin board [ mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: mailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com http://www.skype.com/ - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFT0NuIUxlJ7aRr7hoRAuorAKDaX42345ovf1SIrVIPzAuO1g1UkwCglBsF NoX6cxLs99wWwd0KZyaZ9XE= =buQc -END PGP SIGNATURE-
Re: [ccp4bb] correlated alternate confs - validation?
Hi Bernhard, The validation of alternates is indeed quite poor and any improvements would probably depend on proper annotation by the depositor, particularly in complex correlated cases. For your model I would probably make the two waters alternates of each other. That way, it is easier to select out one of the two alternate conformations. Cheers, Robbie Sent from my Windows Phone Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups' geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar. occupancy refine AfaIct this does what I want. True? Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 mailto:b...@ruppweb.org b...@ruppweb.org mailto:b...@hofkristallamt.org b...@hofkristallamt.org http://www.ruppweb.org/ http://www.ruppweb.org/ ---
Re: [ccp4bb] correlated alternate confs - validation?
I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups’ geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar… occupancy refine AfaIct this does what I want. True? Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ ---
Re: [ccp4bb] correlated alternate confs - validation?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups’ geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar… occupancy refine AfaIct this does what I want. True? Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTz7qjUxlJ7aRr7hoRAs9cAKD4LFul9cmKYgsV5n6o3LZqTgHI6wCfZ4fS 2CdyyS0zWMjryhZrwgA2mZk= =iogi -END PGP SIGNATURE-
Re: [ccp4bb] correlated alternate confs - validation?
?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar occupancy refine AfaIct this does what I want. True? -- -- Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ -- - - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTz7qjUxlJ7aRr7hoRAs9cAKD4LFul9cmKYgsV5n6o3LZqTgHI6wCfZ4fS 2CdyyS0zWMjryhZrwgA2mZk= =iogi -END PGP SIGNATURE-
Re: [ccp4bb] correlated alternate confs - validation?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, That's right, the definition is not in the PDB, but REFMAC sensibly handles it this way. It is certainly a short-coming if not bug in the PDB (definition). Best, Tim On 07/23/2014 04:49 PM, Bernhard Rupp wrote: ?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar occupancy refine AfaIct this does what I want. True? -- - -- Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ -- - - - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTz85KUxlJ7aRr7hoRAoeqAKCGBTg8nowXCCFfbp9kfZsCYr2fHgCgoJhp CPPMzM1r6DEZv2DJi4vwXmI= =bMXr -END PGP SIGNATURE-
Re: [ccp4bb] correlated alternate confs - validation?
I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 23 Jul 2014, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, That's right, the definition is not in the PDB, but REFMAC sensibly handles it this way. It is certainly a short-coming if not bug in the PDB (definition). Best, Tim On 07/23/2014 04:49 PM, Bernhard Rupp wrote: ?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar occupancy refine AfaIct this does what I want. True? -- - -- Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ -- - - - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTz85KUxlJ7aRr7hoRAoeqAKCGBTg8nowXCCFfbp9kfZsCYr2fHgCgoJhp CPPMzM1r6DEZv2DJi4vwXmI= =bMXr
Re: [ccp4bb] correlated alternate confs - validation?
On Wed, Jul 23, 2014 at 3:25 AM, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: The practice at the PDB after deposition used to be to remove water alternate position indicators - although obviously to keep their partial occupancies. This has not been my experience - see for example: http://www.rcsb.org/pdb/files/2GKG.pdb which was deposited as a PDB file, not mmCIF. -Nat
Re: [ccp4bb] correlated alternate confs - validation?
An additional problem is existence of alternative conformations close to rotational axis that violate crystal symmetry. If we want to describe such correlated alternative configurations, we need to describe also how they transform by such rotational axis. This problems may also exists also for other packing contacts; however, for conformations close to rotational axis, symmetry operator cannot preserve conformer ID, and this issue cannot be avoided. Zbyszek Otwinowski I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groupsâ geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar⦠occupancy refine AfaIct this does what I want. True? Bernhard Rupp k.-k. Hofkristallamt 001 (925) 209-7429 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
Re: [ccp4bb] correlated alternate confs - validation?
I think there has been historically some glitch in the deposition of some refmac altloc waters So for example 4a9x from Buster is annotated correctly REMARK 3 PROGRAM : BUSTER 2.11.2 HETATM 9407 O HOH A2517 -22.429 1.144 -35.218 1.00 29.73 O HETATM 9408 O AHOH A2518 -18.933 -9.507 -28.753 0.50 3.00 O HETATM 9409 O BHOH A2518 -20.467 -9.093 -29.900 0.50 16.03 O so the A and B altloc retained. But for example in 4ac7 REMARK 3 PROGRAM : REFMAC 5.6.0117 where these two waters look like they originally were deposited as altloc waters HETATM 6205 O HOH A2043 -3.612 86.934 100.843 0.50 25.12 O ANISOU 6205 O HOH A2043 2630 2166 4747 -153 68 1496 O HETATM 6206 O HOH A2044 -3.506 85.122 100.190 0.50 22.20 O ANISOU 6206 O HOH A2044 3710 2476 2248862188 16 O and these two HETATM 6328 O HOH B2073 -1.182 117.989 73.544 0.50 15.63 O ANISOU 6328 O HOH B2073 2509 1684 1745408173289 O HETATM 6329 O HOH B2074 -0.561 117.641 72.161 0.50 14.37 O ANISOU 6329 O HOH B2074 2023 1187 2247107123 -211 O These waters also end up being annotated as close contacts in Remark 500 - which would not have happened if they had retained their altlocs. REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. ... REMARK 500 OHOH A 2043 OHOH A 2044 1.93 REMARK 500 OHOH B 2073 OHOH B 2074 1.56 Probably other examples can be retrieved but this latter file dates from my time at the PDBe and so may have been mangled at my hands. In my defence I think it is owing to the annotation step when the waters are renumbered to fit with the associated macromolecule N to C (for proteins). I think the script that was originally developed for this was not able to deal with waters with the same number but differing altlocs. Also alternate positions in this step can be associated with different residues by reason of being closer to one or other bit of chain. In this case they can have very different numbers - or chains. I think this can be handled better in the new mmCif-based annotation system with the cooperation of refinement program authors. all the best Martyn Martyn Symmons Cambridge Original message From : f...@bernstein-plus-sons.com Date : 23/07/2014 - 16:20 (GMTDT) To : CCP4BB@JISCMAIL.AC.UK Subject : Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 23 Jul 2014, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, That's right, the definition is not in the PDB, but REFMAC sensibly handles it this way. It is certainly a short-coming if not bug in the PDB (definition). Best, Tim On 07/23/2014 04:49 PM, Bernhard Rupp wrote: ?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would
Re: [ccp4bb] correlated alternate confs - validation?
Dear Frances, I don't think that you can put the blame entirely on the 80 column limitation. The program SHELX76 was limited to 80 columns because the input came as punched cards. It introduced a simple concept, the /free variables/, that are frequently used to represent occupancies and can be used to to build complicated networks of disordered residues with interdependent occupancies. Restraints may be applied to linear sums of these free variables. Ever since, small molecule crystallographers have used this concept to refine the disorders that they frequently encounter. Best wishes, George On 07/23/2014 05:20 PM, Frances C. Bernstein wrote: I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 23 Jul 2014, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bernhard, That's right, the definition is not in the PDB, but REFMAC sensibly handles it this way. It is certainly a short-coming if not bug in the PDB (definition). Best, Tim On 07/23/2014 04:49 PM, Bernhard Rupp wrote: ?? Refmac knows because of the group definition, otherwise I cannot force grouped occupancy refinement. There is no definition in PDB that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of (whatever) residue/water. BR -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] correlated alternate confs - validation? Hi Bernhard, do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: I would probably make the two waters alternates of each other. Quite possible, but the group definition, i.e. to which alt conf. side chain they belong, would need to be preserved, too. BR Cheers, Robbie Sent from my Windows Phone _ Van: Bernhard Rupp Verzonden: 23-7-2014 10:19 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] correlated alternate confs - validation? Hi Fellows, something that may eventually become an issue for validation and reporting in PDB headers: using the Refmac grouped occupancy keyword I was able to form and refine various networks of correlated alternate conformations - it seems to works really well at least in a 1.6 and 1.2 A case I tried. Both occupancy and B-factors refine to reasonable values as expected/guessed from e-density and environment. Respect thanks for implementing this probably underutilized secret. This opens a question for validation: Instead of pretty much ignoring any atoms below occupancy of 1, one can now validate each of the network groups geometry and density fit separately just as any other set of coordinates. I think with increasing data quality, resolution, and user education such refinements will become more frequent (and make a lot more sense than arbitrarily setting guessed independent hard occupancies/Bs that are not validated). Maybe some common format for (annotating) such correlated occupancy groups might eventually become necessary. Best, BR PS: Simple example shown below: two alternate confs of residue 338 which correlate with one water atom each in chain B, with corresponding partial occupancy (grp1: A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). occupancy group id 1 chain A residue 338 alt A occupancy group id 1 chain B residue 5 occupancy group id 2 chain A residue 338 alt B occupancy group id 2 chain B residue 16 occupancy group alts complete 1 2 . more similar occupancy refine AfaIct this does what I want. True
[ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation?
Hello, A solution exists also for PDB records: As a consequence of a discussion with George which took place years ago, I have taken the liberty to extend the PDB record length of 80 characters and use additional characters to specify the group ID and their members list number and provided an interface to manipulate them. Thereby the PDB limitations were extended to adopt the SHELX philosophy of treating combined groups of any composition. ATOM 1 N GLY A 1 -31.334 -24.247 23.250 0.54 34.05 1A N 1 0 ATOM 2477 N GLY A 1 -29.650 -24.643 23.839 0.46 41.88 1B N 1 1 The records with our the group extension are not members of groups with partial occupancy. These two records shown are members of group ID 1, the atom in the first record belongs to group ID 1 members list number 0 and the second to group ID 1 and members list no 1. (The members lists begin with 0.) On Jul 24, 2014, at 1:02 AM, CCP4BB automatic digest system lists...@jiscmail.ac.uk wrote: Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the PDB format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS Jozef Stefan e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem. Mol. Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com
