Re: [ccp4bb] EDSTATS for an extracted fragment
Is n't the danger here that you are just fitting to noise generated by the rest of the Unit Cell that you are ignoring. So it is easy to do a 'good bit' of modelling in a specific region. Just like some tennis players have very good serves but do not win matches. From: George Devaniranjan devaniran...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, 11 June 2014, 19:22 Subject: Re: [ccp4bb] EDSTATS for an extracted fragment Thank you Gerard for your suggestion. I will look into the paper you suggested and MAPMAN too. I am idealizing fragments of PDB and while this would not agree when compared with the well refined structure, my goal really is seeing if these ideal fragments can still be identifiable when I look at the electron density and how to quantify that. (Ideal here refers to a small number of Phi and Psi values I picked as representative of different regions in the Ramachandran map). Isn't the danger here that you are can't tell how much improvement is just fitting to noise from improvements that should be made in the rest of the model? Unless you go on and do a final full refinement you can't know if your modelling is warranted by a global improvement in fit. It could be the case that you are improving globally but I don't know how you can tell that by fitting to just a bit of the map. We have all had that experience of rebuilding a residue so it looks 'right' to us locally but then the refinement program knows better after making a global assessment and puts it back. If some way to give local density 'error bars' that might be helpful so that a maximum likelihood approach could be used during real space fitting. Is that similar to what those useful LLG maps give in heavy atom model refinement? regards Martyn Cambridge I picked on EDSTATS to explore since it gave individual residue information but realize now that since I am dealing with a small sub-set of residues an alternative is required. On Wed, Jun 11, 2014 at 2:01 PM, Gerard DVD Kleywegt ger...@xray.bmc.uu.se wrote: What you want is a test for how well each model agrees with its own map. It is fair to argue that the model that is more self-consistent (agrees better with its own map) is the better model. But you won't learn that by comparing model A to map B. However, conversely, if your modified model fits the original map better than the model that was used to calculate the map itself, you've done a good bit of model building. If you want to do this calculation (with all the warnings and caveats), you can also use MAPMAN - http://xray.bmc.uu.se/usf/mapman_man.html#S41 . The method you propose is essentially the same as this one: http://www.ncbi.nlm.nih.gov/pubmed/18598022 but for a fragment of your macromolecule instead of for a ligand (if you don't have access to the journal, you can request a reprint here: http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=87 ) --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] EDSTATS for an extracted fragment
Hi George Yes you do. It's important to understand that you are not comparing the MTZ file (the data) with the PDB file (the model): that's not possible, at least not directly. So you can't simply change the PDB file, redo the comparison and hope to get sensible results. EDSTATS is _not_ fitting the PDB file into the density. Rather, what you are doing is comparing 2 density maps both calculated using the _same_ MTZ file (since it contains multiple columns), specifically the observed (2mFo-DFc) exp(i phic) density with the calculated DFc exp(i phic) density. The function of the PDB file is first to calculate Fc phic and the map coefficients: you have to do that yourself using Refmac, and then in EDSTATS to define the regions of density where the comparisons are to take place (using the atomic co-ordinates calculated radii). So the PDB file supplied to EDSTATS must be _exactly_ the same one that was used to calculate SFs in Refmac (i.e. the one output by Refmac). The Fc and phic values needed to calculate both maps require the whole model, otherwise the results will be meaningless. When you talk about the model of a structure, you mean the entire structure (as far as it is known), not selected bits of it. HTH Cheers -- Ian On 11 June 2014 01:24, George Devaniranjan devaniran...@gmail.com wrote: Thank you Ethan. Supposing I want to compare with the experimental map, a small fragment of the model (let's say residues 15-30 in a protein of 100 residues). Supposing I start with one model but now extract from that model residues 15-30 (let's call it model 1) , modify it and now want to check if the modified model (model 2) is better than model1? Of course residues 1-14 and 30-100 (in a 100 residue protein) are the same. How can I measure which fragment (model 1 or model 2) is better. Do I have to insert model2 where model 1 was and use EDStats for the whole protein? On Tue, Jun 10, 2014 at 8:04 PM, Ethan A Merritt merr...@u.washington.edu wrote: On Tuesday, 10 June, 2014 19:13:57 George Devaniranjan wrote: Thank you Ian. To clarify, I actually want to compare the new PDB file to the old MTZ file to see how well the residues fit. This is why I mentioned that I have the old MTZ file I generated from SF's which I got from the PDB. I am not trying to improve the deposited structure, I am trying to get a metric of how bad the residues become if I change certain residue phi and psi values when I fit into the original electron density. That is not a valid test. The old map resulted from refinement of the old model, and it corresponds to phases that are only correct for that same old model. If you perturb the model you will of course get a different map, but different != bad. The old model won't agree with your new map and the new model won't agree with the old map. That doesn't prove that either the old model or the new model is better or worse. What you want is a test for how well each model agrees with its own map. It is fair to argue that the model that is more self-consistent (agrees better with its own map) is the better model. But you won't learn that by comparing model A to map B. Caveat: This all assumes that the map phases are generated entirely from the model. If you have a map generated from experimental phases, then it certainly makes sense to ask which of several models is in better agreement with the experimental map. cheers, Ethan On Tue, Jun 10, 2014 at 5:55 PM, Ian Tickle ianj...@gmail.com wrote: Hi, sorry small clarification. The complete PDB file that you used to run the refinement job (i.e. the input PDB file) will obviously only be suitable in the case that you did 0 cycles of refinement. If you did some refinement of the model then the co-ordinates will have changed, and then you need the _output_ PDB file from that refinement as input to EDSTATS (clearly if you did 0 cycles the input and output PDB files from the refinement will be the same it doesn't matter which one you use). Cheers -- Ian On 10 June 2014 21:46, Ian Tickle ianj...@gmail.com wrote: Hi, I'm puzzled by what you are trying to do. You say you have the original MTZ/MAP files. What have the original files got to do with it? EDSTATS requires the MTZ/MAP file calculated for the supplied model. The documentation states: ... the PDB file and the maps should all be from the same refinement job.. The refinement job referred to could be 0 cycles but the MTZ file must have been calculated from the PDB file supplied. If you have changed the PDB file then the original MTZ/MAP files will no longer be suitable. This means you have to supply exactly the same complete PDB file that you used to run the refinement job. Cheers -- Ian On 10 June 2014 19:52, George Devaniranjan devaniran...@gmail.com
Re: [ccp4bb] EDSTATS for an extracted fragment
What you want is a test for how well each model agrees with its own map. It is fair to argue that the model that is more self-consistent (agrees better with its own map) is the better model. But you won't learn that by comparing model A to map B. However, conversely, if your modified model fits the original map better than the model that was used to calculate the map itself, you've done a good bit of model building. If you want to do this calculation (with all the warnings and caveats), you can also use MAPMAN - http://xray.bmc.uu.se/usf/mapman_man.html#S41 . The method you propose is essentially the same as this one: http://www.ncbi.nlm.nih.gov/pubmed/18598022 but for a fragment of your macromolecule instead of for a ligand (if you don't have access to the journal, you can request a reprint here: http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=87 ) --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] EDSTATS for an extracted fragment
On Wednesday, 11 June, 2014 20:01:45 Gerard DVD Kleywegt wrote: What you want is a test for how well each model agrees with its own map. It is fair to argue that the model that is more self-consistent (agrees better with its own map) is the better model. But you won't learn that by comparing model A to map B. However, conversely, if your modified model fits the original map better than the model that was used to calculate the map itself, you've done a good bit of model building. But the current context is a question about using EDSTATS, which asks for a difference map as part of evaluating the fit. If the fit of the original model is bad, its difference map is going to be polluted by both positive and negative peaks. Any nearby residues will get a bad score. Now suppose you somehow have a new model that is perfect. If you try to score the new model using that same map, those same difference peaks are still present (obviously) and the nearby residues in the new model will also get a bad score even though they are blameless in that they wouldn't have generated any difference peaks themselves, being perfect. So far as I can see, it never makes sense to score model A based on a difference map generated from model B. Ethan If you want to do this calculation (with all the warnings and caveats), you can also use MAPMAN - http://xray.bmc.uu.se/usf/mapman_man.html#S41 . The method you propose is essentially the same as this one: http://www.ncbi.nlm.nih.gov/pubmed/18598022 but for a fragment of your macromolecule instead of for a ligand (if you don't have access to the journal, you can request a reprint here: http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=87 ) --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! ** -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] EDSTATS for an extracted fragment
Thank you Gerard for your suggestion. I will look into the paper you suggested and MAPMAN too. I am idealizing fragments of PDB and while this would not agree when compared with the well refined structure, my goal really is seeing if these ideal fragments can still be identifiable when I look at the electron density and how to quantify that. (Ideal here refers to a small number of Phi and Psi values I picked as representative of different regions in the Ramachandran map). I picked on EDSTATS to explore since it gave individual residue information but realize now that since I am dealing with a small sub-set of residues an alternative is required. On Wed, Jun 11, 2014 at 2:01 PM, Gerard DVD Kleywegt ger...@xray.bmc.uu.se wrote: What you want is a test for how well each model agrees with its own map. It is fair to argue that the model that is more self-consistent (agrees better with its own map) is the better model. But you won't learn that by comparing model A to map B. However, conversely, if your modified model fits the original map better than the model that was used to calculate the map itself, you've done a good bit of model building. If you want to do this calculation (with all the warnings and caveats), you can also use MAPMAN - http://xray.bmc.uu.se/usf/mapman_man.html#S41 . The method you propose is essentially the same as this one: http://www.ncbi.nlm.nih.gov/ pubmed/18598022 but for a fragment of your macromolecule instead of for a ligand (if you don't have access to the journal, you can request a reprint here: http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=87 ) --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
[ccp4bb] EDSTATS for an extracted fragment
HI, I want to calculate real-space R factor/RSCC and such parameters using EDSTATS in CCP4 but only for a selected fragment that has been extracted and then modified (changed the Phi and Psi) from the native. I have the original MTZ and MAP. Is it even possible to calculate these values without inserting the extracted fragment back into the rest of the PDB (the unmodified part)? I am reluctant to do that since I have many such fragments I have extracted and modified and wish to compare with the native. Thank you, George
Re: [ccp4bb] EDSTATS for an extracted fragment
Hi, I'm puzzled by what you are trying to do. You say you have the original MTZ/MAP files. What have the original files got to do with it? EDSTATS requires the MTZ/MAP file calculated for the supplied model. The documentation states: ... the PDB file and the maps should all be from the same refinement job.. The refinement job referred to could be 0 cycles but the MTZ file must have been calculated from the PDB file supplied. If you have changed the PDB file then the original MTZ/MAP files will no longer be suitable. This means you have to supply exactly the same complete PDB file that you used to run the refinement job. Cheers -- Ian On 10 June 2014 19:52, George Devaniranjan devaniran...@gmail.com wrote: HI, I want to calculate real-space R factor/RSCC and such parameters using EDSTATS in CCP4 but only for a selected fragment that has been extracted and then modified (changed the Phi and Psi) from the native. I have the original MTZ and MAP. Is it even possible to calculate these values without inserting the extracted fragment back into the rest of the PDB (the unmodified part)? I am reluctant to do that since I have many such fragments I have extracted and modified and wish to compare with the native. Thank you, George
Re: [ccp4bb] EDSTATS for an extracted fragment
Hi, sorry small clarification. The complete PDB file that you used to run the refinement job (i.e. the input PDB file) will obviously only be suitable in the case that you did 0 cycles of refinement. If you did some refinement of the model then the co-ordinates will have changed, and then you need the _output_ PDB file from that refinement as input to EDSTATS (clearly if you did 0 cycles the input and output PDB files from the refinement will be the same it doesn't matter which one you use). Cheers -- Ian On 10 June 2014 21:46, Ian Tickle ianj...@gmail.com wrote: Hi, I'm puzzled by what you are trying to do. You say you have the original MTZ/MAP files. What have the original files got to do with it? EDSTATS requires the MTZ/MAP file calculated for the supplied model. The documentation states: ... the PDB file and the maps should all be from the same refinement job.. The refinement job referred to could be 0 cycles but the MTZ file must have been calculated from the PDB file supplied. If you have changed the PDB file then the original MTZ/MAP files will no longer be suitable. This means you have to supply exactly the same complete PDB file that you used to run the refinement job. Cheers -- Ian On 10 June 2014 19:52, George Devaniranjan devaniran...@gmail.com wrote: HI, I want to calculate real-space R factor/RSCC and such parameters using EDSTATS in CCP4 but only for a selected fragment that has been extracted and then modified (changed the Phi and Psi) from the native. I have the original MTZ and MAP. Is it even possible to calculate these values without inserting the extracted fragment back into the rest of the PDB (the unmodified part)? I am reluctant to do that since I have many such fragments I have extracted and modified and wish to compare with the native. Thank you, George
Re: [ccp4bb] EDSTATS for an extracted fragment
Thank you Ian. To clarify, I actually want to compare the new PDB file to the old MTZ file to see how well the residues fit. This is why I mentioned that I have the old MTZ file I generated from SF's which I got from the PDB. I am not trying to improve the deposited structure, I am trying to get a metric of how bad the residues become if I change certain residue phi and psi values when I fit into the original electron density. On Tue, Jun 10, 2014 at 5:55 PM, Ian Tickle ianj...@gmail.com wrote: Hi, sorry small clarification. The complete PDB file that you used to run the refinement job (i.e. the input PDB file) will obviously only be suitable in the case that you did 0 cycles of refinement. If you did some refinement of the model then the co-ordinates will have changed, and then you need the _output_ PDB file from that refinement as input to EDSTATS (clearly if you did 0 cycles the input and output PDB files from the refinement will be the same it doesn't matter which one you use). Cheers -- Ian On 10 June 2014 21:46, Ian Tickle ianj...@gmail.com wrote: Hi, I'm puzzled by what you are trying to do. You say you have the original MTZ/MAP files. What have the original files got to do with it? EDSTATS requires the MTZ/MAP file calculated for the supplied model. The documentation states: ... the PDB file and the maps should all be from the same refinement job.. The refinement job referred to could be 0 cycles but the MTZ file must have been calculated from the PDB file supplied. If you have changed the PDB file then the original MTZ/MAP files will no longer be suitable. This means you have to supply exactly the same complete PDB file that you used to run the refinement job. Cheers -- Ian On 10 June 2014 19:52, George Devaniranjan devaniran...@gmail.com wrote: HI, I want to calculate real-space R factor/RSCC and such parameters using EDSTATS in CCP4 but only for a selected fragment that has been extracted and then modified (changed the Phi and Psi) from the native. I have the original MTZ and MAP. Is it even possible to calculate these values without inserting the extracted fragment back into the rest of the PDB (the unmodified part)? I am reluctant to do that since I have many such fragments I have extracted and modified and wish to compare with the native. Thank you, George
Re: [ccp4bb] EDSTATS for an extracted fragment
On Tuesday, 10 June, 2014 19:13:57 George Devaniranjan wrote: Thank you Ian. To clarify, I actually want to compare the new PDB file to the old MTZ file to see how well the residues fit. This is why I mentioned that I have the old MTZ file I generated from SF's which I got from the PDB. I am not trying to improve the deposited structure, I am trying to get a metric of how bad the residues become if I change certain residue phi and psi values when I fit into the original electron density. That is not a valid test. The old map resulted from refinement of the old model, and it corresponds to phases that are only correct for that same old model. If you perturb the model you will of course get a different map, but different != bad. The old model won't agree with your new map and the new model won't agree with the old map. That doesn't prove that either the old model or the new model is better or worse. What you want is a test for how well each model agrees with its own map. It is fair to argue that the model that is more self-consistent (agrees better with its own map) is the better model. But you won't learn that by comparing model A to map B. Caveat: This all assumes that the map phases are generated entirely from the model. If you have a map generated from experimental phases, then it certainly makes sense to ask which of several models is in better agreement with the experimental map. cheers, Ethan On Tue, Jun 10, 2014 at 5:55 PM, Ian Tickle ianj...@gmail.com wrote: Hi, sorry small clarification. The complete PDB file that you used to run the refinement job (i.e. the input PDB file) will obviously only be suitable in the case that you did 0 cycles of refinement. If you did some refinement of the model then the co-ordinates will have changed, and then you need the _output_ PDB file from that refinement as input to EDSTATS (clearly if you did 0 cycles the input and output PDB files from the refinement will be the same it doesn't matter which one you use). Cheers -- Ian On 10 June 2014 21:46, Ian Tickle ianj...@gmail.com wrote: Hi, I'm puzzled by what you are trying to do. You say you have the original MTZ/MAP files. What have the original files got to do with it? EDSTATS requires the MTZ/MAP file calculated for the supplied model. The documentation states: ... the PDB file and the maps should all be from the same refinement job.. The refinement job referred to could be 0 cycles but the MTZ file must have been calculated from the PDB file supplied. If you have changed the PDB file then the original MTZ/MAP files will no longer be suitable. This means you have to supply exactly the same complete PDB file that you used to run the refinement job. Cheers -- Ian On 10 June 2014 19:52, George Devaniranjan devaniran...@gmail.com wrote: HI, I want to calculate real-space R factor/RSCC and such parameters using EDSTATS in CCP4 but only for a selected fragment that has been extracted and then modified (changed the Phi and Psi) from the native. I have the original MTZ and MAP. Is it even possible to calculate these values without inserting the extracted fragment back into the rest of the PDB (the unmodified part)? I am reluctant to do that since I have many such fragments I have extracted and modified and wish to compare with the native. Thank you, George -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] EDSTATS for an extracted fragment
Thank you Ethan. Supposing I want to compare with the experimental map, a small fragment of the model (let's say residues 15-30 in a protein of 100 residues). Supposing I start with one model but now extract from that model residues 15-30 (let's call it model 1) , modify it and now want to check if the modified model (model 2) is better than model1? Of course residues 1-14 and 30-100 (in a 100 residue protein) are the same. How can I measure which fragment (model 1 or model 2) is better. Do I have to insert model2 where model 1 was and use EDStats for the whole protein? On Tue, Jun 10, 2014 at 8:04 PM, Ethan A Merritt merr...@u.washington.edu wrote: On Tuesday, 10 June, 2014 19:13:57 George Devaniranjan wrote: Thank you Ian. To clarify, I actually want to compare the new PDB file to the old MTZ file to see how well the residues fit. This is why I mentioned that I have the old MTZ file I generated from SF's which I got from the PDB. I am not trying to improve the deposited structure, I am trying to get a metric of how bad the residues become if I change certain residue phi and psi values when I fit into the original electron density. That is not a valid test. The old map resulted from refinement of the old model, and it corresponds to phases that are only correct for that same old model. If you perturb the model you will of course get a different map, but different != bad. The old model won't agree with your new map and the new model won't agree with the old map. That doesn't prove that either the old model or the new model is better or worse. What you want is a test for how well each model agrees with its own map. It is fair to argue that the model that is more self-consistent (agrees better with its own map) is the better model. But you won't learn that by comparing model A to map B. Caveat: This all assumes that the map phases are generated entirely from the model. If you have a map generated from experimental phases, then it certainly makes sense to ask which of several models is in better agreement with the experimental map. cheers, Ethan On Tue, Jun 10, 2014 at 5:55 PM, Ian Tickle ianj...@gmail.com wrote: Hi, sorry small clarification. The complete PDB file that you used to run the refinement job (i.e. the input PDB file) will obviously only be suitable in the case that you did 0 cycles of refinement. If you did some refinement of the model then the co-ordinates will have changed, and then you need the _output_ PDB file from that refinement as input to EDSTATS (clearly if you did 0 cycles the input and output PDB files from the refinement will be the same it doesn't matter which one you use). Cheers -- Ian On 10 June 2014 21:46, Ian Tickle ianj...@gmail.com wrote: Hi, I'm puzzled by what you are trying to do. You say you have the original MTZ/MAP files. What have the original files got to do with it? EDSTATS requires the MTZ/MAP file calculated for the supplied model. The documentation states: ... the PDB file and the maps should all be from the same refinement job.. The refinement job referred to could be 0 cycles but the MTZ file must have been calculated from the PDB file supplied. If you have changed the PDB file then the original MTZ/MAP files will no longer be suitable. This means you have to supply exactly the same complete PDB file that you used to run the refinement job. Cheers -- Ian On 10 June 2014 19:52, George Devaniranjan devaniran...@gmail.com wrote: HI, I want to calculate real-space R factor/RSCC and such parameters using EDSTATS in CCP4 but only for a selected fragment that has been extracted and then modified (changed the Phi and Psi) from the native. I have the original MTZ and MAP. Is it even possible to calculate these values without inserting the extracted fragment back into the rest of the PDB (the unmodified part)? I am reluctant to do that since I have many such fragments I have extracted and modified and wish to compare with the native. Thank you, George -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
