Re: [ccp4bb] Invisible atoms in ligands
Thank you Pavel for the clarification! What I was really trying to point out is that a missing atom, occ=0.00 and occ=0.01 are not as similar as one might naiively think. Also, if you put a ligand into a pocket and the occupancy refines to 0, that does not necessarily mean the ligand is partially occupied. If the pocket is actually filled with flat bulk solvent, then you expect the ligand occupancy to be non-zero, simply because something is better than nothing. However, if the bulk solvent mask were somehow smarter and filled the pocket of a, say, 60% occupied ligand with flat bulk density at 40% the level of bulk density used far away from any atoms, then one might actually see the occupancy of a bogus ligand refine to zero. That is, a ligand built into a pocket that is truly empty (filled with flat bulk solvent) and then occupancy refined would actually be a competition between two alternative hypotheses: 1) ligand in the pocket, 2) nothing but solvent in the pocket. If the occupancy of the ligand refines to zero in this context, then you can be quite confident that it didn't bind, at least not in the given orientation. I fully realize that the implementation of this is easier said than done, but perhaps it would be worth the effort? -James Holton MAD Scientist On 6/16/2014 3:04 PM, Pavel Afonine wrote: Hi James, a remark: different programs may treat occ=0 differently. In phenix.refine (phenix.maps, etc) atoms with zero occupancy will be ignored for bulk-solvent mask calculation, unless you ask to do otherwise. For example, this means that if you want to calculate a ligand OMIT map both options - removing the ligand from PDB file; - setting its occupancy to zero and making sure mask does not ignore occ=0 atoms) are a) not equivalent and b) both not good. In first case (removing atoms from file) bulk-solvent will flatten residual map (as you pointed out). In second case bulk-solvent will be excluded in a very specific area, so that residual (green) density you see there may be either just bulk-solvent or ligand in question or a mixture; obviously not a very useful information! This highlights the fundamental problem of flat bulk-solvent model the way it's currently used. Pavel On Sun, Jun 15, 2014 at 3:01 PM, James Holton jmhol...@lbl.gov mailto:jmhol...@lbl.gov wrote: The principle difference between occ=0 and omitting the atom entirely is that occ=0 atoms exclude bulk solvent. Or at least they do for typical operation of contemporary refinement programs. So, by defining occ=0 you are forcing all map voxels within ~0.6A or so of your invisible atom to be vacuum. If you omit it, then the bulk solvent may flood in, perhaps enough to pull the fo-fc peak down below 3x rms. How much the bulk solvent floods in depends on how nearby atoms exclude the bulk solvent, and this, in turn, depends on which refinement program you are using. Different bulk solvent implementations use different radii, shrink parameters, etc. In addition, bulk solvent always bleeds a bit into surrounding areas because the solvent B factor is never zero. The real problem, I think, is that for any voxel of the map there is ALWAYS something there. The only question is: what is it? Is there a 100% occupied ligand? 100% occupied solvent? Two conformers of the ligand? Or is it some mixture of all these? If you are asking these questions I think it is most likely a mixture, and mixtures are hard to model. What is worse, mixtures of a partially-occupied ligand with bulk solvent taking up the slack is currently impossible to model. We will have to wait for partial-occupancy-bulk-solvent to be implemented before we can build representations of these alternative hypotheses and and test them with competitive occupancy refinement. The bulk solvent is actually a very good example of something for which we see no evidence in our electron density maps, yet we model it in because 1) we know it must be there, and 2) it makes our R factors lower. What more could you want? -James Holton MAD Scientist On 6/13/2014 7:45 PM, Frank von Delft wrote: Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx
Re: [ccp4bb] Invisible atoms in ligands
Hi All, I had an interesting case recently where a Cl atom of a chlorophenyl moiety went missing in a structure (primary X-ray damage was the suspected culprit). Small molecule Mass Spec suggested the atom was there to start with but it was quite obviously missing in the maps (1.9Ang) and the des-chloro refined much better. I was asked to replace the missing atom as it was seen as misleading because all the assay and biophysical data was generated with the chlorophenyl compound; this after all, is what the X-ray model was supporting. I did wonder where the Cl atom ended up and in what state. David Hargreaves Associate Principal Scientist _ AstraZeneca Discovery Sciences, Structure Biophysics Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.commailto:name.surn...@astrazeneca.com Please consider the environment before printing this e-mail From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: 13 June 2014 10:45 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Invisible atoms in ligands Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
Re: [ccp4bb] Invisible atoms in ligands
Dear James You seem to be discounting the possibility of a true vacuum inside a structure, which is obviously not the same thing as 'something' (bulk solvent or whatever). I accept that this is unlikely in the case of ligand binding sites exposed to solvent, or indeed any site on the outer surface of the molecule, since any vacuum in that situation would be unstable against the ingress of water molecules, but it is possible in the case of fully-enclosed cavities (i.e. 'inner surface') that are normally inaccessible to water. I don't know if anyone has done a systematic survey of this, i.e. looking for cavities where the density appears to be actually zero (taking into account F000 of course), or at least significantly lower compared with the bulk solvent density (where the assumed value of F000 wouldn't affect the result). Cheers -- Ian On 16 June 2014 07:37, James Holton jmhol...@lbl.gov wrote: Thank you Pavel for the clarification! What I was really trying to point out is that a missing atom, occ=0.00 and occ=0.01 are not as similar as one might naiively think. Also, if you put a ligand into a pocket and the occupancy refines to 0, that does not necessarily mean the ligand is partially occupied. If the pocket is actually filled with flat bulk solvent, then you expect the ligand occupancy to be non-zero, simply because something is better than nothing. However, if the bulk solvent mask were somehow smarter and filled the pocket of a, say, 60% occupied ligand with flat bulk density at 40% the level of bulk density used far away from any atoms, then one might actually see the occupancy of a bogus ligand refine to zero. That is, a ligand built into a pocket that is truly empty (filled with flat bulk solvent) and then occupancy refined would actually be a competition between two alternative hypotheses: 1) ligand in the pocket, 2) nothing but solvent in the pocket. If the occupancy of the ligand refines to zero in this context, then you can be quite confident that it didn't bind, at least not in the given orientation. I fully realize that the implementation of this is easier said than done, but perhaps it would be worth the effort? -James Holton MAD Scientist On 6/16/2014 3:04 PM, Pavel Afonine wrote: Hi James, a remark: different programs may treat occ=0 differently. In phenix.refine (phenix.maps, etc) atoms with zero occupancy will be ignored for bulk-solvent mask calculation, unless you ask to do otherwise. For example, this means that if you want to calculate a ligand OMIT map both options - removing the ligand from PDB file; - setting its occupancy to zero and making sure mask does not ignore occ=0 atoms) are a) not equivalent and b) both not good. In first case (removing atoms from file) bulk-solvent will flatten residual map (as you pointed out). In second case bulk-solvent will be excluded in a very specific area, so that residual (green) density you see there may be either just bulk-solvent or ligand in question or a mixture; obviously not a very useful information! This highlights the fundamental problem of flat bulk-solvent model the way it's currently used. Pavel On Sun, Jun 15, 2014 at 3:01 PM, James Holton jmhol...@lbl.gov wrote: The principle difference between occ=0 and omitting the atom entirely is that occ=0 atoms exclude bulk solvent. Or at least they do for typical operation of contemporary refinement programs. So, by defining occ=0 you are forcing all map voxels within ~0.6A or so of your invisible atom to be vacuum. If you omit it, then the bulk solvent may flood in, perhaps enough to pull the fo-fc peak down below 3x rms. How much the bulk solvent floods in depends on how nearby atoms exclude the bulk solvent, and this, in turn, depends on which refinement program you are using. Different bulk solvent implementations use different radii, shrink parameters, etc. In addition, bulk solvent always bleeds a bit into surrounding areas because the solvent B factor is never zero. The real problem, I think, is that for any voxel of the map there is ALWAYS something there. The only question is: what is it? Is there a 100% occupied ligand? 100% occupied solvent? Two conformers of the ligand? Or is it some mixture of all these? If you are asking these questions I think it is most likely a mixture, and mixtures are hard to model. What is worse, mixtures of a partially-occupied ligand with bulk solvent taking up the slack is currently impossible to model. We will have to wait for partial-occupancy-bulk-solvent to be implemented before we can build representations of these alternative hypotheses and and test them with competitive occupancy refinement. The bulk solvent is actually a very good example of something for which we see no evidence in our electron density maps, yet we model it in because 1) we know it must be there, and 2) it makes our R factors lower. What more could you want?
Re: [ccp4bb] Invisible atoms in ligands
Dear Ian, This has been discussed in a review and related articles by Brian Matthews and Liljun Liu: Matthews BW, Liu L. A review about nothing: are apolar cavities in proteins really empty? Protein Sci. 2009 Mar;18(3):494-502. doi: 10.1002/pro.61. Review. PubMed PMID: 19241368; PubMed Central PMCID: PMC2760356. Daniel Le 16/06/2014 11:32, Ian Tickle a écrit : Dear James You seem to be discounting the possibility of a true vacuum inside a structure, which is obviously not the same thing as 'something' (bulk solvent or whatever). I accept that this is unlikely in the case of ligand binding sites exposed to solvent, or indeed any site on the outer surface of the molecule, since any vacuum in that situation would be unstable against the ingress of water molecules, but it is possible in the case of fully-enclosed cavities (i.e. 'inner surface') that are normally inaccessible to water. I don't know if anyone has done a systematic survey of this, i.e. looking for cavities where the density appears to be actually zero (taking into account F000 of course), or at least significantly lower compared with the bulk solvent density (where the assumed value of F000 wouldn't affect the result). Cheers -- Ian On 16 June 2014 07:37, James Holton jmhol...@lbl.gov mailto:jmhol...@lbl.gov wrote: Thank you Pavel for the clarification! What I was really trying to point out is that a missing atom, occ=0.00 and occ=0.01 are not as similar as one might naiively think. Also, if you put a ligand into a pocket and the occupancy refines to 0, that does not necessarily mean the ligand is partially occupied. If the pocket is actually filled with flat bulk solvent, then you expect the ligand occupancy to be non-zero, simply because something is better than nothing. However, if the bulk solvent mask were somehow smarter and filled the pocket of a, say, 60% occupied ligand with flat bulk density at 40% the level of bulk density used far away from any atoms, then one might actually see the occupancy of a bogus ligand refine to zero. That is, a ligand built into a pocket that is truly empty (filled with flat bulk solvent) and then occupancy refined would actually be a competition between two alternative hypotheses: 1) ligand in the pocket, 2) nothing but solvent in the pocket. If the occupancy of the ligand refines to zero in this context, then you can be quite confident that it didn't bind, at least not in the given orientation. I fully realize that the implementation of this is easier said than done, but perhaps it would be worth the effort? -James Holton MAD Scientist On 6/16/2014 3:04 PM, Pavel Afonine wrote: Hi James, a remark: different programs may treat occ=0 differently. In phenix.refine (phenix.maps, etc) atoms with zero occupancy will be ignored for bulk-solvent mask calculation, unless you ask to do otherwise. For example, this means that if you want to calculate a ligand OMIT map both options - removing the ligand from PDB file; - setting its occupancy to zero and making sure mask does not ignore occ=0 atoms) are a) not equivalent and b) both not good. In first case (removing atoms from file) bulk-solvent will flatten residual map (as you pointed out). In second case bulk-solvent will be excluded in a very specific area, so that residual (green) density you see there may be either just bulk-solvent or ligand in question or a mixture; obviously not a very useful information! This highlights the fundamental problem of flat bulk-solvent model the way it's currently used. Pavel On Sun, Jun 15, 2014 at 3:01 PM, James Holton jmhol...@lbl.gov mailto:jmhol...@lbl.gov wrote: The principle difference between occ=0 and omitting the atom entirely is that occ=0 atoms exclude bulk solvent. Or at least they do for typical operation of contemporary refinement programs. So, by defining occ=0 you are forcing all map voxels within ~0.6A or so of your invisible atom to be vacuum. If you omit it, then the bulk solvent may flood in, perhaps enough to pull the fo-fc peak down below 3x rms. How much the bulk solvent floods in depends on how nearby atoms exclude the bulk solvent, and this, in turn, depends on which refinement program you are using. Different bulk solvent implementations use different radii, shrink parameters, etc. In addition, bulk solvent always bleeds a bit into surrounding areas because the solvent B factor is never zero. The real problem, I think, is that for any voxel of the map there is ALWAYS something there. The only question is: what is it? Is there a 100% occupied ligand? 100% occupied solvent? Two conformers of the ligand? Or is it some mixture
Re: [ccp4bb] Invisible atoms in ligands
Dear Daniel Thanks for the info. I knew that Brian Matthews' group had done some work in this area. Cheers -- Ian On 16 June 2014 11:16, Daniel Picot daniel.pi...@ibpc.fr wrote: Dear Ian, This has been discussed in a review and related articles by Brian Matthews and Liljun Liu: Matthews BW, Liu L. A review about nothing: are apolar cavities in proteins really empty? Protein Sci. 2009 Mar;18(3):494-502. doi: 10.1002/pro.61. Review. PubMed PMID: 19241368; PubMed Central PMCID: PMC2760356. Daniel Le 16/06/2014 11:32, Ian Tickle a écrit : Dear James You seem to be discounting the possibility of a true vacuum inside a structure, which is obviously not the same thing as 'something' (bulk solvent or whatever). I accept that this is unlikely in the case of ligand binding sites exposed to solvent, or indeed any site on the outer surface of the molecule, since any vacuum in that situation would be unstable against the ingress of water molecules, but it is possible in the case of fully-enclosed cavities (i.e. 'inner surface') that are normally inaccessible to water. I don't know if anyone has done a systematic survey of this, i.e. looking for cavities where the density appears to be actually zero (taking into account F000 of course), or at least significantly lower compared with the bulk solvent density (where the assumed value of F000 wouldn't affect the result). Cheers -- Ian On 16 June 2014 07:37, James Holton jmhol...@lbl.gov wrote: Thank you Pavel for the clarification! What I was really trying to point out is that a missing atom, occ=0.00 and occ=0.01 are not as similar as one might naiively think. Also, if you put a ligand into a pocket and the occupancy refines to 0, that does not necessarily mean the ligand is partially occupied. If the pocket is actually filled with flat bulk solvent, then you expect the ligand occupancy to be non-zero, simply because something is better than nothing. However, if the bulk solvent mask were somehow smarter and filled the pocket of a, say, 60% occupied ligand with flat bulk density at 40% the level of bulk density used far away from any atoms, then one might actually see the occupancy of a bogus ligand refine to zero. That is, a ligand built into a pocket that is truly empty (filled with flat bulk solvent) and then occupancy refined would actually be a competition between two alternative hypotheses: 1) ligand in the pocket, 2) nothing but solvent in the pocket. If the occupancy of the ligand refines to zero in this context, then you can be quite confident that it didn't bind, at least not in the given orientation. I fully realize that the implementation of this is easier said than done, but perhaps it would be worth the effort? -James Holton MAD Scientist On 6/16/2014 3:04 PM, Pavel Afonine wrote: Hi James, a remark: different programs may treat occ=0 differently. In phenix.refine (phenix.maps, etc) atoms with zero occupancy will be ignored for bulk-solvent mask calculation, unless you ask to do otherwise. For example, this means that if you want to calculate a ligand OMIT map both options - removing the ligand from PDB file; - setting its occupancy to zero and making sure mask does not ignore occ=0 atoms) are a) not equivalent and b) both not good. In first case (removing atoms from file) bulk-solvent will flatten residual map (as you pointed out). In second case bulk-solvent will be excluded in a very specific area, so that residual (green) density you see there may be either just bulk-solvent or ligand in question or a mixture; obviously not a very useful information! This highlights the fundamental problem of flat bulk-solvent model the way it's currently used. Pavel On Sun, Jun 15, 2014 at 3:01 PM, James Holton jmhol...@lbl.gov wrote: The principle difference between occ=0 and omitting the atom entirely is that occ=0 atoms exclude bulk solvent. Or at least they do for typical operation of contemporary refinement programs. So, by defining occ=0 you are forcing all map voxels within ~0.6A or so of your invisible atom to be vacuum. If you omit it, then the bulk solvent may flood in, perhaps enough to pull the fo-fc peak down below 3x rms. How much the bulk solvent floods in depends on how nearby atoms exclude the bulk solvent, and this, in turn, depends on which refinement program you are using. Different bulk solvent implementations use different radii, shrink parameters, etc. In addition, bulk solvent always bleeds a bit into surrounding areas because the solvent B factor is never zero. The real problem, I think, is that for any voxel of the map there is ALWAYS something there. The only question is: what is it? Is there a 100% occupied ligand? 100% occupied solvent? Two conformers of the ligand? Or is it some mixture of all these? If you are asking these questions I think it is most likely a mixture, and mixtures are hard to
Re: [ccp4bb] Invisible atoms in ligands
The principle difference between occ=0 and omitting the atom entirely is that occ=0 atoms exclude bulk solvent. Or at least they do for typical operation of contemporary refinement programs. So, by defining occ=0 you are forcing all map voxels within ~0.6A or so of your invisible atom to be vacuum. If you omit it, then the bulk solvent may flood in, perhaps enough to pull the fo-fc peak down below 3x rms. How much the bulk solvent floods in depends on how nearby atoms exclude the bulk solvent, and this, in turn, depends on which refinement program you are using. Different bulk solvent implementations use different radii, shrink parameters, etc. In addition, bulk solvent always bleeds a bit into surrounding areas because the solvent B factor is never zero. The real problem, I think, is that for any voxel of the map there is ALWAYS something there. The only question is: what is it? Is there a 100% occupied ligand? 100% occupied solvent? Two conformers of the ligand? Or is it some mixture of all these? If you are asking these questions I think it is most likely a mixture, and mixtures are hard to model. What is worse, mixtures of a partially-occupied ligand with bulk solvent taking up the slack is currently impossible to model. We will have to wait for partial-occupancy-bulk-solvent to be implemented before we can build representations of these alternative hypotheses and and test them with competitive occupancy refinement. The bulk solvent is actually a very good example of something for which we see no evidence in our electron density maps, yet we model it in because 1) we know it must be there, and 2) it makes our R factors lower. What more could you want? -James Holton MAD Scientist On 6/13/2014 7:45 PM, Frank von Delft wrote: Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx
Re: [ccp4bb] Invisible atoms in ligands
Hi James, a remark: different programs may treat occ=0 differently. In phenix.refine (phenix.maps, etc) atoms with zero occupancy will be ignored for bulk-solvent mask calculation, unless you ask to do otherwise. For example, this means that if you want to calculate a ligand OMIT map both options - removing the ligand from PDB file; - setting its occupancy to zero and making sure mask does not ignore occ=0 atoms) are a) not equivalent and b) both not good. In first case (removing atoms from file) bulk-solvent will flatten residual map (as you pointed out). In second case bulk-solvent will be excluded in a very specific area, so that residual (green) density you see there may be either just bulk-solvent or ligand in question or a mixture; obviously not a very useful information! This highlights the fundamental problem of flat bulk-solvent model the way it's currently used. Pavel On Sun, Jun 15, 2014 at 3:01 PM, James Holton jmhol...@lbl.gov wrote: The principle difference between occ=0 and omitting the atom entirely is that occ=0 atoms exclude bulk solvent. Or at least they do for typical operation of contemporary refinement programs. So, by defining occ=0 you are forcing all map voxels within ~0.6A or so of your invisible atom to be vacuum. If you omit it, then the bulk solvent may flood in, perhaps enough to pull the fo-fc peak down below 3x rms. How much the bulk solvent floods in depends on how nearby atoms exclude the bulk solvent, and this, in turn, depends on which refinement program you are using. Different bulk solvent implementations use different radii, shrink parameters, etc. In addition, bulk solvent always bleeds a bit into surrounding areas because the solvent B factor is never zero. The real problem, I think, is that for any voxel of the map there is ALWAYS something there. The only question is: what is it? Is there a 100% occupied ligand? 100% occupied solvent? Two conformers of the ligand? Or is it some mixture of all these? If you are asking these questions I think it is most likely a mixture, and mixtures are hard to model. What is worse, mixtures of a partially-occupied ligand with bulk solvent taking up the slack is currently impossible to model. We will have to wait for partial-occupancy-bulk-solvent to be implemented before we can build representations of these alternative hypotheses and and test them with competitive occupancy refinement. The bulk solvent is actually a very good example of something for which we see no evidence in our electron density maps, yet we model it in because 1) we know it must be there, and 2) it makes our R factors lower. What more could you want? -James Holton MAD Scientist On 6/13/2014 7:45 PM, Frank von Delft wrote: Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: - for amino acid sidechains, their presence is implied in the residue name. - for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx
[ccp4bb] Invisible atoms in ligands
Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx
Re: [ccp4bb] Invisible atoms in ligands
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Frank, if you can calculate their position, i.e. it is part of a rigid group, I would leave it. If it is flexible, I would remove it because the reader of my deposited structure may not be a crystallographer and misinterpret the result. If it is obvious that some atoms are missing, it is even better because it is more likely to make the reader think about the reasons why part of the ligand is not displayed in the model. Cheers, Tim On 06/13/2014 11:45 AM, Frank von Delft wrote: Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx - -- - -- 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/ iD8DBQFTmsx7UxlJ7aRr7hoRAhxOAJ9YXwdr4kZULidLAdzTgEjdZwfXNQCeKYTA 9vSeeDh7eq2v4CwBII64wn8= =uviV -END PGP SIGNATURE-
Re: [ccp4bb] Invisible atoms in ligands
Hi Frank, I agree with what Tim has just posted. Personally I would not think occupancy=0, since this would mean the atom is not where you placed it (i.e. nowhere near). This could be useful if all your ligand has the same partial occupancy or, if you have multiple poses, the sum of occupancies of the single atoms equals that of the whole ligand. None of the above seems to fit your case. Another possibility is to define the whole ligand and letting the B-factors for those atoms go very high, but this provides an information on coordinates which some would just take for granted... if that structure ends up in the PDB, the less experienced readers would be tempted to say that x,y,z are the coordinates of that atom, which we would know from the B factors they are not. Since a PDB file contains a model (i.e. our understanding and interpretation of the electron density maps), omitting those atoms seems to me the more correct way. Having said so, I agree some important information is missing, but this can be explained in the paper supporting the entry. If the structure is only for internal use, then people dealing with it should be warned and the insanely-high B-factors option might be preferable. Hope this helps, Ciao Marco 2014-06-13 10:45 GMT+01:00 Frank von Delft frank.vonde...@sgc.ox.ac.uk: Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: - for amino acid sidechains, their presence is implied in the residue name. - for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx
Re: [ccp4bb] Invisible atoms in ligands
Hi Tim, The problem with missing atoms in ligands is that you cannot use the coordinates for any follow-up calculation that requires ligand topology (e.g. restraint generation). That forces you to rely on the annotation of the compound, for instance at the PDB. That can be quite messy and leaves extra room for errors and misunderstandings. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Friday, June 13, 2014 12:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Frank, if you can calculate their position, i.e. it is part of a rigid group, I would leave it. If it is flexible, I would remove it because the reader of my deposited structure may not be a crystallographer and misinterpret the result. If it is obvious that some atoms are missing, it is even better because it is more likely to make the reader think about the reasons why part of the ligand is not displayed in the model. Cheers, Tim On 06/13/2014 11:45 AM, Frank von Delft wrote: Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx - -- - -- 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/ iD8DBQFTmsx7UxlJ7aRr7hoRAhxOAJ9YXwdr4kZULidLAdzTgEjdZwfXNQCeKYT A 9vSeeDh7eq2v4CwBII64wn8= =uviV -END PGP SIGNATURE-
Re: [ccp4bb] Invisible atoms in ligands
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Robbie, maybe it is good not to use coordinates for calculations if you cannot measure the coordinates? Cheers, Tim On 06/13/2014 12:35 PM, Robbie Joosten wrote: Hi Tim, The problem with missing atoms in ligands is that you cannot use the coordinates for any follow-up calculation that requires ligand topology (e.g. restraint generation). That forces you to rely on the annotation of the compound, for instance at the PDB. That can be quite messy and leaves extra room for errors and misunderstandings. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Friday, June 13, 2014 12:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands Hi Frank, if you can calculate their position, i.e. it is part of a rigid group, I would leave it. If it is flexible, I would remove it because the reader of my deposited structure may not be a crystallographer and misinterpret the result. If it is obvious that some atoms are missing, it is even better because it is more likely to make the reader think about the reasons why part of the ligand is not displayed in the model. Cheers, Tim On 06/13/2014 11:45 AM, Frank von Delft wrote: Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx - -- - -- 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/ iD8DBQFTmuJyUxlJ7aRr7hoRAjdqAJ95tqbDlWhqW01lAuVvLwsMIAkv1wCaA0Bk O0z7t7Bl7O7amDF9CxM0CI0= =QSdy -END PGP SIGNATURE-
Re: [ccp4bb] Invisible atoms in ligands
Hi Tim, The problem I see with including atoms with no density is that the one place you can guarantee those atoms are not (at 100% occupancy), is at the coordinates assigned to them. I would argue that the scientific inaccuracy of such a model should outweigh the desire to use the coordinates for downstream calculations. A better solution may be for the PDB to require us to submit the PDB and CIF file we generate for the full ligand in addition to the protein PDB file which may only contain a truncated portion of the ligand as part of the model. I prefer omitting the atoms in the same way I do for the protein model and for the same reasons. I accept this makes it potentially more troublesome for downstream users as things stand, although would argue that there is greater potential for harm if the unsuspecting user believes the atomic positions are correct, where a ligand (or protein) atom has been modeled into a region with no density. Best, Isaac Westwood On 13 June 2014 11:35, Robbie Joosten robbie_joos...@hotmail.com wrote: Hi Tim, The problem with missing atoms in ligands is that you cannot use the coordinates for any follow-up calculation that requires ligand topology (e.g. restraint generation). That forces you to rely on the annotation of the compound, for instance at the PDB. That can be quite messy and leaves extra room for errors and misunderstandings. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Friday, June 13, 2014 12:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Frank, if you can calculate their position, i.e. it is part of a rigid group, I would leave it. If it is flexible, I would remove it because the reader of my deposited structure may not be a crystallographer and misinterpret the result. If it is obvious that some atoms are missing, it is even better because it is more likely to make the reader think about the reasons why part of the ligand is not displayed in the model. Cheers, Tim On 06/13/2014 11:45 AM, Frank von Delft wrote: Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx - -- - -- 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/ iD8DBQFTmsx7UxlJ7aRr7hoRAhxOAJ9YXwdr4kZULidLAdzTgEjdZwfXNQCeKYT A 9vSeeDh7eq2v4CwBII64wn8= =uviV -END PGP SIGNATURE-
Re: [ccp4bb] Invisible atoms in ligands
Hi Tim, The decision of which atoms you can and cannot see in your map is rather subjective. Also the way you generate your map can make a big (enough) difference. A new map after additional refinement, an NCS averaged map, or a feature-enhanced map might show you the position of (some of) the missing atoms. I prefer the 'high B-factor' model unless you have a very good reason to believe the compound is in any way chemically modified. Cheers, Robbie -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Friday, June 13, 2014 13:37 To: Robbie Joosten; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Robbie, maybe it is good not to use coordinates for calculations if you cannot measure the coordinates? Cheers, Tim On 06/13/2014 12:35 PM, Robbie Joosten wrote: Hi Tim, The problem with missing atoms in ligands is that you cannot use the coordinates for any follow-up calculation that requires ligand topology (e.g. restraint generation). That forces you to rely on the annotation of the compound, for instance at the PDB. That can be quite messy and leaves extra room for errors and misunderstandings. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Friday, June 13, 2014 12:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands Hi Frank, if you can calculate their position, i.e. it is part of a rigid group, I would leave it. If it is flexible, I would remove it because the reader of my deposited structure may not be a crystallographer and misinterpret the result. If it is obvious that some atoms are missing, it is even better because it is more likely to make the reader think about the reasons why part of the ligand is not displayed in the model. Cheers, Tim On 06/13/2014 11:45 AM, Frank von Delft wrote: Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx - -- - -- 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/ iD8DBQFTmuJyUxlJ7aRr7hoRAjdqAJ95tqbDlWhqW01lAuVvLwsMIAkv1wCaA0 Bk O0z7t7Bl7O7amDF9CxM0CI0= =QSdy -END PGP SIGNATURE-
Re: [ccp4bb] Invisible atoms in ligands
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Robbie, Frank probably meant the status of the model when the author is ready for deposition, i.e., already after additional refinement. The B-factor assumes a harmonic oscillation of its atom on a linear trajectory (maybe the superposition of one trajectory in each of the three dimensions) - that's almost always a very poor assumption for an atom for which you don't see the density, and by using the B-value to mop up, you only adjust a parameter and may reduce the R-value, i.e. improve your model w.r.t. crystallographic data. As you remove the atoms you don't see, you improve your model with respect to its usability after deposition. Cheers, Tim On 06/13/2014 01:59 PM, Robbie Joosten wrote: Hi Tim, The decision of which atoms you can and cannot see in your map is rather subjective. Also the way you generate your map can make a big (enough) difference. A new map after additional refinement, an NCS averaged map, or a feature-enhanced map might show you the position of (some of) the missing atoms. I prefer the 'high B-factor' model unless you have a very good reason to believe the compound is in any way chemically modified. Cheers, Robbie -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Friday, June 13, 2014 13:37 To: Robbie Joosten; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands Hi Robbie, maybe it is good not to use coordinates for calculations if you cannot measure the coordinates? Cheers, Tim On 06/13/2014 12:35 PM, Robbie Joosten wrote: Hi Tim, The problem with missing atoms in ligands is that you cannot use the coordinates for any follow-up calculation that requires ligand topology (e.g. restraint generation). That forces you to rely on the annotation of the compound, for instance at the PDB. That can be quite messy and leaves extra room for errors and misunderstandings. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Friday, June 13, 2014 12:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands Hi Frank, if you can calculate their position, i.e. it is part of a rigid group, I would leave it. If it is flexible, I would remove it because the reader of my deposited structure may not be a crystallographer and misinterpret the result. If it is obvious that some atoms are missing, it is even better because it is more likely to make the reader think about the reasons why part of the ligand is not displayed in the model. Cheers, Tim On 06/13/2014 11:45 AM, Frank von Delft wrote: Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is implied in the residue name. * for whole residues, their presence is implied in the sequence numbering However: what about ligands? Nowhere else in the PDB file is their presence implied - or have I missed something? (Certainly disorder in a ligand is important information that needs to be captured!) Cheers phx - -- - -- 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/ iD8DBQFTmuzWUxlJ7aRr7hoRAsazAJ0bkmlFBRPNxDDOnvuzRp9y5FMYBwCg3yj0 XosHt98UyfOcUrW4OWizoow= =YDU4 -END PGP SIGNATURE-
