Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
Okay fair enough: my straw man is the *final* model, the one we deposit and then do things with, the one that needs to agree with all the data. Silly me, for wanting to beat that. :-) The original question sounded suspiciously like, I can't get this one last crappy loop in bad density to have good B factors, please, how can I make it behave? Struck me as requiring a rigorous reply. phx On 28/08/2010 06:48, Ethan Merritt wrote: On Friday 27 August 2010, Frank von Delft wrote: I'm sorry, I can't simply drop this thread, not when it keeps ignoring the physics of diffraction: In order to attempt any (rigorous) scientific conclusions from a structure, one needs the best model, the one that's converged against the data. I think you are arguing with a straw man that you set in place yourself. Either that or there's a mis-match of words being used. The rest of us [I think] are using the word refinement to mean something I do to improve the model, if only incrementally. I.e., it is one step on a long journey, not the journey in its entirety. When you run real-space refinement, you're refining against maps that come from a set of phases - but phases are *derived* data: derived from the starting model -- from ALL of the starting model. Which real-space refinement has now changed. So to achieve *convergence*, you have to recalculate the phases. From ALL of the starting model. So? That's what we have to do in non-linear least-squares refinement in reciprocal space also. Without an analytical solution to the phase problem, it's all we _can_ do, whether it be in real space or reciprocal space. Iterative improvement is our stock in trade. I'm mystified how this procedure can be considered local to a few atoms. (Even if it is intensely pleasing to watch RSR make a model snap into some bothersome density.) The procedure is local for precisely the reasons you already stated. That doesn't mean there are no global effects. And it certainly doesn't mean you are finished with your model. It just means you have refined (and hopefully improved but maybe not) the position of some set of atoms. Do you see this as different from, say, adjusting rotamers under the guidance of molprobity? That's a local change made to improve agreement with an external prior, rather than to improve agreement with either the map or with current |mFo-Fc|. Whether it actually improves your R factors or not won't be known until the next round of refinement. phx. P.S. The availability of spectacular experimental phases *should* allow convergence purely through real-space refinement, of course. But I've seen a lot of phasing, and I've never encountered this situation. If you want to pursue this as a new topic, I'm game. But can we first agree on definitions for refinement and convergence? In the usage that I am familiar with, any well-behaved refinement algorithm will converge, if only asymptoticly. You may not like the place it converged to, but that's a different issue. Converged is not the same as found the true global minimum. So yes, I agree that real-space refinement often converges to a non-optimal state. That's why we need an accept/reject button in the Coot interface :-) But converge it does, nonetheless. Ethan On 28/08/2010 00:19, Gerard Bricogne wrote: Dear Pavel, Yes, I may indeed have been focussed too much attention on your subversive-looking last paragraph, without fully seeing it in the context of the whole thread. I am also sorry that I was so strident in my criticism: I should not be writing e-mails on this topic late on a Friday night :-)) . Have a nice weekend. Gerard. -- On Fri, Aug 27, 2010 at 03:48:03PM -0700, Pavel Afonine wrote: Dear Gerard, I guess you simply did not understand my email, at all. It's in the archive, you may read it again -:) All the best! Pavel. P.S. Are you saying people producing (nearly manually) first macromolecular structures BEFORE the era of cool refinement packages were all doing 2hr0s ? I would stay away from such a strong statements. On 8/27/10 3:35 PM, Gerard Bricogne wrote: Dear Pavel, I must say that I find some of the statements in your message rather glib and shallow, especially on the part of a developer. Where is all the Bayesian wisdom that Phenix is advertised to have absorbed? Your last paragraph is shocking in this respect. The whole idea of Bayesian inference is precisely that it isn't good enough to pull out of a hat, by means of a trick/blackbox, a model that corresponds to the data, but that one needs to see how many models would do fare more or less as well and to give some rough probability distribution over them; and if your are going to finally deliver a single model, it had better be as representative as possible of that weighted ensemble of possible ones, rather than just a model that happens to have been
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
The requirement sounds extremely suspect: every atom in the structure contributes to every reflection, so refining only some atoms makes as little mathematical sense as refining against only a subset of reflections. Especially not Bfactors, which are after all where errors get pushed into. So if you refine Bfactors for only some atoms, all you're doing is making the refinement program shove all the errors in the *whole* structure into the Bfactors of a few atoms. You'd have to explain extremely carefully why those atoms deserve that -- and even then I doubt anybody would believe you. phx. On 26/08/2010 22:19, Hailiang Zhang wrote: Thanks a lot Ethan, I will give it a try. Best Regards, Hailiang On Thursday 26 August 2010 11:56:39 am Hailiang Zhang wrote: Hi, I want to refine B factors for several residues only (all the other B factors and all coordinates fixed, I know it sounds weird but there is a reason to try that). Maybe you could tell us what this reason is? Is there anyway CCP4 can do this? Thanks for any suggestions! Suggestion 1) Calculate structure factors for the entire rest of the model. Include these as F_partial contributing to the refinement of a model containing only your residues of interest. In this refinement, refine only the B terms. Caveat: I think you will encounter problems with how to handle the bulk solvent correction. Perhaps that must be included in F_partial also, and omitted from the subsequence mini-refinement. Suggestion 2) - Place your residues of interest in a single TLS group. - Do not assign any other atoms or residues to a TLS group. - Refine the entire model using refmac in TLS refinement mode. Choose 5 or 10 cycles of TLS refinement, but 0 cycles of coordinate/Biso refinement. Disregard all output other than the refined TLS description for the B factors in your residues of interest. - Use TLSANL to expand the TLS parameters back to individual Biso if you like. Best Regards, Hailiang -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
On Friday 27 August 2010, Frank von Delft wrote: The requirement sounds extremely suspect: every atom in the structure contributes to every reflection, so refining only some atoms makes as little mathematical sense as refining against only a subset of reflections. I agree with you that the requirement sounds dubious. But the specific argument you make is not quite right. Two common counter-examples are real-space refinement and rigid-body placement of a known fragment relative to an existing partial model. Especially not Bfactors, which are after all where errors get pushed into. So if you refine Bfactors for only some atoms, all you're doing is making the refinement program shove all the errors in the *whole* structure into the Bfactors of a few atoms. You'd have to explain extremely carefully why those atoms deserve that -- and even then I doubt anybody would believe you. Indeed. Ethan phx. On 26/08/2010 22:19, Hailiang Zhang wrote: Thanks a lot Ethan, I will give it a try. Best Regards, Hailiang On Thursday 26 August 2010 11:56:39 am Hailiang Zhang wrote: Hi, I want to refine B factors for several residues only (all the other B factors and all coordinates fixed, I know it sounds weird but there is a reason to try that). Maybe you could tell us what this reason is? Is there anyway CCP4 can do this? Thanks for any suggestions! Suggestion 1) Calculate structure factors for the entire rest of the model. Include these as F_partial contributing to the refinement of a model containing only your residues of interest. In this refinement, refine only the B terms. Caveat: I think you will encounter problems with how to handle the bulk solvent correction. Perhaps that must be included in F_partial also, and omitted from the subsequence mini-refinement. Suggestion 2) - Place your residues of interest in a single TLS group. - Do not assign any other atoms or residues to a TLS group. - Refine the entire model using refmac in TLS refinement mode. Choose 5 or 10 cycles of TLS refinement, but 0 cycles of coordinate/Biso refinement. Disregard all output other than the refined TLS description for the B factors in your residues of interest. - Use TLSANL to expand the TLS parameters back to individual Biso if you like. Best Regards, Hailiang -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
The requirement sounds extremely suspect: every atom in the structure contributes to every reflection, so refining only some atoms makes as little mathematical sense as refining against only a subset of reflections. I agree with you that the requirement sounds dubious. But the specific argument you make is not quite right. Two common counter-examples are real-space refinement and rigid-body placement of a known fragment relative to an existing partial model. Not so: they're tricks to get out of local minima and maybe improve phases, but they're /not/ useful for generating the model that best fits the data, and would be useful for interpretation. Or would one deposit a model for which real-space refinement has been the final step? phx
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
Hello, The requirement sounds extremely suspect: every atom in the structure contributes to every reflection, so refining only some atoms makes as little mathematical sense as refining against only a subset of reflections. I agree with you that the requirement sounds dubious. But the specific argument you make is not quite right. Two common counter-examples are real-space refinement and rigid-body placement of a known fragment relative to an existing partial model. Not so: they're tricks to get out of local minima and maybe improve phases, but they're /not/ useful for generating the model that best fits the data, I completely agree with Ethan. Although the overall goal of refining B-factors only for a subset of atoms is not clear (there are at least three example where I do it in phenix.refine - I won't go into technicalities here, it's hidden under the hood and no-one knows -:) ), doing so makes perfect sense in general. Or would one deposit a model for which real-space refinement has been the final step? Of course you would. Refinement - in whatever space - is just a trick/blackbox to get your model to correspond to the data, and how you do it: in real, reciprocal or both spaces, manually moving atoms or letting minimizer or grid search do that - it does not matter. Pavel.
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
Dear Pavel, I must say that I find some of the statements in your message rather glib and shallow, especially on the part of a developer. Where is all the Bayesian wisdom that Phenix is advertised to have absorbed? Your last paragraph is shocking in this respect. The whole idea of Bayesian inference is precisely that it isn't good enough to pull out of a hat, by means of a trick/blackbox, a model that corresponds to the data, but that one needs to see how many models would do fare more or less as well and to give some rough probability distribution over them; and if your are going to finally deliver a single model, it had better be as representative as possible of that weighted ensemble of possible ones, rather than just a model that happens to have been persuaded to fit the data by hook or by crook. Closer to practicalities, the procedure by which a model that ends up being deposited should be reproducible by third parties as the endpoint of a refinement calculation from the deposited coordinates and X-ray data, conducted according to the author's description of their own refinement procedure. That procedure, however, should always end with a justifiable purely computational step. It seems very dangerous to state that a model in which some manual moving around of atoms was given the last word is as good as anything else. If you start encouraging such casual attitudes, you may end up with 2hr0. With best wishes, Gerard. -- On Fri, Aug 27, 2010 at 02:02:48PM -0700, Pavel Afonine wrote: Hello, The requirement sounds extremely suspect: every atom in the structure contributes to every reflection, so refining only some atoms makes as little mathematical sense as refining against only a subset of reflections. I agree with you that the requirement sounds dubious. But the specific argument you make is not quite right. Two common counter-examples are real-space refinement and rigid-body placement of a known fragment relative to an existing partial model. Not so: they're tricks to get out of local minima and maybe improve phases, but they're /not/ useful for generating the model that best fits the data, I completely agree with Ethan. Although the overall goal of refining B-factors only for a subset of atoms is not clear (there are at least three example where I do it in phenix.refine - I won't go into technicalities here, it's hidden under the hood and no-one knows -:) ), doing so makes perfect sense in general. Or would one deposit a model for which real-space refinement has been the final step? Of course you would. Refinement - in whatever space - is just a trick/blackbox to get your model to correspond to the data, and how you do it: in real, reciprocal or both spaces, manually moving atoms or letting minimizer or grid search do that - it does not matter. Pavel. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
Dear Gerard, I guess you simply did not understand my email, at all. It's in the archive, you may read it again -:) All the best! Pavel. P.S. Are you saying people producing (nearly manually) first macromolecular structures BEFORE the era of cool refinement packages were all doing 2hr0s ? I would stay away from such a strong statements. On 8/27/10 3:35 PM, Gerard Bricogne wrote: Dear Pavel, I must say that I find some of the statements in your message rather glib and shallow, especially on the part of a developer. Where is all the Bayesian wisdom that Phenix is advertised to have absorbed? Your last paragraph is shocking in this respect. The whole idea of Bayesian inference is precisely that it isn't good enough to pull out of a hat, by means of a trick/blackbox, a model that corresponds to the data, but that one needs to see how many models would do fare more or less as well and to give some rough probability distribution over them; and if your are going to finally deliver a single model, it had better be as representative as possible of that weighted ensemble of possible ones, rather than just a model that happens to have been persuaded to fit the data by hook or by crook. Closer to practicalities, the procedure by which a model that ends up being deposited should be reproducible by third parties as the endpoint of a refinement calculation from the deposited coordinates and X-ray data, conducted according to the author's description of their own refinement procedure. That procedure, however, should always end with a justifiable purely computational step. It seems very dangerous to state that a model in which some manual moving around of atoms was given the last word is as good as anything else. If you start encouraging such casual attitudes, you may end up with 2hr0. With best wishes, Gerard. -- On Fri, Aug 27, 2010 at 02:02:48PM -0700, Pavel Afonine wrote: Hello, The requirement sounds extremely suspect: every atom in the structure contributes to every reflection, so refining only some atoms makes as little mathematical sense as refining against only a subset of reflections. I agree with you that the requirement sounds dubious. But the specific argument you make is not quite right. Two common counter-examples are real-space refinement and rigid-body placement of a known fragment relative to an existing partial model. Not so: they're tricks to get out of local minima and maybe improve phases, but they're /not/ useful for generating the model that best fits the data, I completely agree with Ethan. Although the overall goal of refining B-factors only for a subset of atoms is not clear (there are at least three example where I do it in phenix.refine - I won't go into technicalities here, it's hidden under the hood and no-one knows -:) ), doing so makes perfect sense in general. Or would one deposit a model for which real-space refinement has been the final step? Of course you would. Refinement - in whatever space - is just a trick/blackbox to get your model to correspond to the data, and how you do it: in real, reciprocal or both spaces, manually moving atoms or letting minimizer or grid search do that - it does not matter. Pavel.
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
Dear Pavel, Yes, I may indeed have been focussed too much attention on your subversive-looking last paragraph, without fully seeing it in the context of the whole thread. I am also sorry that I was so strident in my criticism: I should not be writing e-mails on this topic late on a Friday night :-)) . Have a nice weekend. Gerard. -- On Fri, Aug 27, 2010 at 03:48:03PM -0700, Pavel Afonine wrote: Dear Gerard, I guess you simply did not understand my email, at all. It's in the archive, you may read it again -:) All the best! Pavel. P.S. Are you saying people producing (nearly manually) first macromolecular structures BEFORE the era of cool refinement packages were all doing 2hr0s ? I would stay away from such a strong statements. On 8/27/10 3:35 PM, Gerard Bricogne wrote: Dear Pavel, I must say that I find some of the statements in your message rather glib and shallow, especially on the part of a developer. Where is all the Bayesian wisdom that Phenix is advertised to have absorbed? Your last paragraph is shocking in this respect. The whole idea of Bayesian inference is precisely that it isn't good enough to pull out of a hat, by means of a trick/blackbox, a model that corresponds to the data, but that one needs to see how many models would do fare more or less as well and to give some rough probability distribution over them; and if your are going to finally deliver a single model, it had better be as representative as possible of that weighted ensemble of possible ones, rather than just a model that happens to have been persuaded to fit the data by hook or by crook. Closer to practicalities, the procedure by which a model that ends up being deposited should be reproducible by third parties as the endpoint of a refinement calculation from the deposited coordinates and X-ray data, conducted according to the author's description of their own refinement procedure. That procedure, however, should always end with a justifiable purely computational step. It seems very dangerous to state that a model in which some manual moving around of atoms was given the last word is as good as anything else. If you start encouraging such casual attitudes, you may end up with 2hr0. With best wishes, Gerard. -- On Fri, Aug 27, 2010 at 02:02:48PM -0700, Pavel Afonine wrote: Hello, The requirement sounds extremely suspect: every atom in the structure contributes to every reflection, so refining only some atoms makes as little mathematical sense as refining against only a subset of reflections. I agree with you that the requirement sounds dubious. But the specific argument you make is not quite right. Two common counter-examples are real-space refinement and rigid-body placement of a known fragment relative to an existing partial model. Not so: they're tricks to get out of local minima and maybe improve phases, but they're /not/ useful for generating the model that best fits the data, I completely agree with Ethan. Although the overall goal of refining B-factors only for a subset of atoms is not clear (there are at least three example where I do it in phenix.refine - I won't go into technicalities here, it's hidden under the hood and no-one knows -:) ), doing so makes perfect sense in general. Or would one deposit a model for which real-space refinement has been the final step? Of course you would. Refinement - in whatever space - is just a trick/blackbox to get your model to correspond to the data, and how you do it: in real, reciprocal or both spaces, manually moving atoms or letting minimizer or grid search do that - it does not matter. Pavel. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
I'm sorry, I can't simply drop this thread, not when it keeps ignoring the physics of diffraction: In order to attempt any (rigorous) scientific conclusions from a structure, one needs the best model, the one that's converged against the data. When you run real-space refinement, you're refining against maps that come from a set of phases - but phases are *derived* data: derived from the starting model -- from ALL of the starting model. Which real-space refinement has now changed. So to achieve *convergence*, you have to recalculate the phases. From ALL of the starting model. I'm mystified how this procedure can be considered local to a few atoms. (Even if it is intensely pleasing to watch RSR make a model snap into some bothersome density.) phx. P.S. The availability of spectacular experimental phases *should* allow convergence purely through real-space refinement, of course. But I've seen a lot of phasing, and I've never encountered this situation. On 28/08/2010 00:19, Gerard Bricogne wrote: Dear Pavel, Yes, I may indeed have been focussed too much attention on your subversive-looking last paragraph, without fully seeing it in the context of the whole thread. I am also sorry that I was so strident in my criticism: I should not be writing e-mails on this topic late on a Friday night :-)) . Have a nice weekend. Gerard. -- On Fri, Aug 27, 2010 at 03:48:03PM -0700, Pavel Afonine wrote: Dear Gerard, I guess you simply did not understand my email, at all. It's in the archive, you may read it again -:) All the best! Pavel. P.S. Are you saying people producing (nearly manually) first macromolecular structures BEFORE the era of cool refinement packages were all doing 2hr0s ? I would stay away from such a strong statements. On 8/27/10 3:35 PM, Gerard Bricogne wrote: Dear Pavel, I must say that I find some of the statements in your message rather glib and shallow, especially on the part of a developer. Where is all the Bayesian wisdom that Phenix is advertised to have absorbed? Your last paragraph is shocking in this respect. The whole idea of Bayesian inference is precisely that it isn't good enough to pull out of a hat, by means of a trick/blackbox, a model that corresponds to the data, but that one needs to see how many models would do fare more or less as well and to give some rough probability distribution over them; and if your are going to finally deliver a single model, it had better be as representative as possible of that weighted ensemble of possible ones, rather than just a model that happens to have been persuaded to fit the data by hook or by crook. Closer to practicalities, the procedure by which a model that ends up being deposited should be reproducible by third parties as the endpoint of a refinement calculation from the deposited coordinates and X-ray data, conducted according to the author's description of their own refinement procedure. That procedure, however, should always end with a justifiable purely computational step. It seems very dangerous to state that a model in which some manual moving around of atoms was given the last word is as good as anything else. If you start encouraging such casual attitudes, you may end up with 2hr0. With best wishes, Gerard. -- On Fri, Aug 27, 2010 at 02:02:48PM -0700, Pavel Afonine wrote: Hello, The requirement sounds extremely suspect: every atom in the structure contributes to every reflection, so refining only some atoms makes as little mathematical sense as refining against only a subset of reflections. I agree with you that the requirement sounds dubious. But the specific argument you make is not quite right. Two common counter-examples are real-space refinement and rigid-body placement of a known fragment relative to an existing partial model. Not so: they're tricks to get out of local minima and maybe improve phases, but they're /not/ useful for generating the model that best fits the data, I completely agree with Ethan. Although the overall goal of refining B-factors only for a subset of atoms is not clear (there are at least three example where I do it in phenix.refine - I won't go into technicalities here, it's hidden under the hood and no-one knows -:) ), doing so makes perfect sense in general. Or would one deposit a model for which real-space refinement has been the final step? Of course you would. Refinement - in whatever space - is just a trick/blackbox to get your model to correspond to the data, and how you do it: in real, reciprocal or both spaces, manually moving atoms or letting minimizer or grid search do that - it does not matter. Pavel.
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
On Friday 27 August 2010, Frank von Delft wrote: I'm sorry, I can't simply drop this thread, not when it keeps ignoring the physics of diffraction: In order to attempt any (rigorous) scientific conclusions from a structure, one needs the best model, the one that's converged against the data. I think you are arguing with a straw man that you set in place yourself. Either that or there's a mis-match of words being used. The rest of us [I think] are using the word refinement to mean something I do to improve the model, if only incrementally. I.e., it is one step on a long journey, not the journey in its entirety. When you run real-space refinement, you're refining against maps that come from a set of phases - but phases are *derived* data: derived from the starting model -- from ALL of the starting model. Which real-space refinement has now changed. So to achieve *convergence*, you have to recalculate the phases. From ALL of the starting model. So? That's what we have to do in non-linear least-squares refinement in reciprocal space also. Without an analytical solution to the phase problem, it's all we _can_ do, whether it be in real space or reciprocal space. Iterative improvement is our stock in trade. I'm mystified how this procedure can be considered local to a few atoms. (Even if it is intensely pleasing to watch RSR make a model snap into some bothersome density.) The procedure is local for precisely the reasons you already stated. That doesn't mean there are no global effects. And it certainly doesn't mean you are finished with your model. It just means you have refined (and hopefully improved but maybe not) the position of some set of atoms. Do you see this as different from, say, adjusting rotamers under the guidance of molprobity? That's a local change made to improve agreement with an external prior, rather than to improve agreement with either the map or with current |mFo-Fc|. Whether it actually improves your R factors or not won't be known until the next round of refinement. phx. P.S. The availability of spectacular experimental phases *should* allow convergence purely through real-space refinement, of course. But I've seen a lot of phasing, and I've never encountered this situation. If you want to pursue this as a new topic, I'm game. But can we first agree on definitions for refinement and convergence? In the usage that I am familiar with, any well-behaved refinement algorithm will converge, if only asymptoticly. You may not like the place it converged to, but that's a different issue. Converged is not the same as found the true global minimum. So yes, I agree that real-space refinement often converges to a non-optimal state. That's why we need an accept/reject button in the Coot interface :-) But converge it does, nonetheless. Ethan On 28/08/2010 00:19, Gerard Bricogne wrote: Dear Pavel, Yes, I may indeed have been focussed too much attention on your subversive-looking last paragraph, without fully seeing it in the context of the whole thread. I am also sorry that I was so strident in my criticism: I should not be writing e-mails on this topic late on a Friday night :-)) . Have a nice weekend. Gerard. -- On Fri, Aug 27, 2010 at 03:48:03PM -0700, Pavel Afonine wrote: Dear Gerard, I guess you simply did not understand my email, at all. It's in the archive, you may read it again -:) All the best! Pavel. P.S. Are you saying people producing (nearly manually) first macromolecular structures BEFORE the era of cool refinement packages were all doing 2hr0s ? I would stay away from such a strong statements. On 8/27/10 3:35 PM, Gerard Bricogne wrote: Dear Pavel, I must say that I find some of the statements in your message rather glib and shallow, especially on the part of a developer. Where is all the Bayesian wisdom that Phenix is advertised to have absorbed? Your last paragraph is shocking in this respect. The whole idea of Bayesian inference is precisely that it isn't good enough to pull out of a hat, by means of a trick/blackbox, a model that corresponds to the data, but that one needs to see how many models would do fare more or less as well and to give some rough probability distribution over them; and if your are going to finally deliver a single model, it had better be as representative as possible of that weighted ensemble of possible ones, rather than just a model that happens to have been persuaded to fit the data by hook or by crook. Closer to practicalities, the procedure by which a model that ends up being deposited should be reproducible by third parties as the endpoint of a refinement calculation from the deposited coordinates and X-ray data, conducted according to the author's description of their own refinement procedure. That procedure, however, should
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
On Thursday 26 August 2010 11:56:39 am Hailiang Zhang wrote: Hi, I want to refine B factors for several residues only (all the other B factors and all coordinates fixed, I know it sounds weird but there is a reason to try that). Maybe you could tell us what this reason is? Is there anyway CCP4 can do this? Thanks for any suggestions! Suggestion 1) Calculate structure factors for the entire rest of the model. Include these as F_partial contributing to the refinement of a model containing only your residues of interest. In this refinement, refine only the B terms. Caveat: I think you will encounter problems with how to handle the bulk solvent correction. Perhaps that must be included in F_partial also, and omitted from the subsequence mini-refinement. Suggestion 2) - Place your residues of interest in a single TLS group. - Do not assign any other atoms or residues to a TLS group. - Refine the entire model using refmac in TLS refinement mode. Choose 5 or 10 cycles of TLS refinement, but 0 cycles of coordinate/Biso refinement. Disregard all output other than the refined TLS description for the B factors in your residues of interest. - Use TLSANL to expand the TLS parameters back to individual Biso if you like. Best Regards, Hailiang -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
Thanks a lot Ethan, I will give it a try. Best Regards, Hailiang On Thursday 26 August 2010 11:56:39 am Hailiang Zhang wrote: Hi, I want to refine B factors for several residues only (all the other B factors and all coordinates fixed, I know it sounds weird but there is a reason to try that). Maybe you could tell us what this reason is? Is there anyway CCP4 can do this? Thanks for any suggestions! Suggestion 1) Calculate structure factors for the entire rest of the model. Include these as F_partial contributing to the refinement of a model containing only your residues of interest. In this refinement, refine only the B terms. Caveat: I think you will encounter problems with how to handle the bulk solvent correction. Perhaps that must be included in F_partial also, and omitted from the subsequence mini-refinement. Suggestion 2) - Place your residues of interest in a single TLS group. - Do not assign any other atoms or residues to a TLS group. - Refine the entire model using refmac in TLS refinement mode. Choose 5 or 10 cycles of TLS refinement, but 0 cycles of coordinate/Biso refinement. Disregard all output other than the refined TLS description for the B factors in your residues of interest. - Use TLSANL to expand the TLS parameters back to individual Biso if you like. Best Regards, Hailiang -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Can CCP4 refine B factors for several residues only?
One more additional way is to apply harmonic restraint on all coordinates and all B values apart from those you want to refine. If harmonic restraints are strong enough then B values will not move much. But I do not like this option. Regards Garib On 26 Aug 2010, at 19:56, Hailiang Zhang wrote: Hi, I want to refine B factors for several residues only (all the other B factors and all coordinates fixed, I know it sounds weird but there is a reason to try that). Is there anyway CCP4 can do this? Thanks for any suggestions! Best Regards, Hailiang
