Re: [ccp4bb] a challenge
Dear James, your challenge in its current form ignores an important source of information for model building that is available for your simulated data - namely, it does not allow to use anomalous phase information in the model building. In difficult cases on the edge of success such as this one, this typically makes the difference between building and not building. If you can make the F+/F- and Se substructure available, we can test whether this is the case indeed. However, while I expect this would push the challenge further significantly, most likely you would be able to decrease the Se incorporation of your simulated data further to such levels that the anomalous signal is again no longer sufficient to build the structure. And most likely, there would again exist an edge where a small decrease in the Se incorporation would lead from a model built to no model built. Best regards, -- Pavol Skubak Biophysical Structural Chemistry Gorleaus Laboratories Einsteinweg 55 Leiden University LEIDEN 2333CC the Netherlands tel: 0031715274414 web: http://bsc.lic.leidenuniv.nl/people/skubak-0
Re: [ccp4bb] a challenge
Dear James, I agree with Pavel that your example is not very realistic. In practice one would start from the heavy atom positions. As well as providing starting phases, they are useful in other ways. For example. shelxe (and probably most other tracing programs) adds them to a 'no-go' map so it knows where NOT to trace the main-chain. Best wishes, George Dear James, your challenge in its current form ignores an important source of information for model building that is available for your simulated data - namely, it does not allow to use anomalous phase information in the model building. In difficult cases on the edge of success such as this one, this typically makes the difference between building and not building. If you can make the F+/F- and Se substructure available, we can test whether this is the case indeed. However, while I expect this would push the challenge further significantly, most likely you would be able to decrease the Se incorporation of your simulated data further to such levels that the anomalous signal is again no longer sufficient to build the structure. And most likely, there would again exist an edge where a small decrease in the Se incorporation would lead from a model built to no model built. Best regards, -- Pavol Skubak Biophysical Structural Chemistry Gorleaus Laboratories Einsteinweg 55 Leiden University LEIDEN 2333CC the Netherlands tel: 0031715274414 tel:0031715274414 web: http://bsc.lic.leidenuniv.nl/people/skubak-0 -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] a challenge
Fair enough! I have just now added DANO and I(+)/I(-) to the files. I'll be very interested to see what you can come up with! For the record, the phases therein came from running mlphare with default parameters but exactly the correct heavy-atom constellation (all the sulfur atoms in 3dko), and then running dm with default parameters. Yes, there are other ways to run mlphare and dm that give better phases, but I was only able to determine those parameters by cheating (comparing the resulting map to the right answer), so I don't think it is fair to use those maps. I have had a few questions about what is cheating and what is not cheating. I don't have a problem with the use of sequence information because that actually is something that you realistically would know about your protein when you sat down to collect data. The sequence of this molecule is that of 3dko: http://bl831.als.lbl.gov/~jamesh/challenge/seq.pir I also don't have a problem with anyone actually using an automation program to _help_ them solve the impossible dataset as long as they can explain what they did. Simply putting the above sequence into BALBES would, of course, be cheating! I suppose one could try eliminating 3dko and its homologs from the BALBES search, but that, in and of itself, is perhaps relevant to the challenge: what is the most distance homolog that still allows you to solve the structure?. That, I think, is also a stringent test of model-building skill. I have already tried ARP/wARP, phenix.autobuild and buccaneer/refmac. With default parameters, all of these programs fail on both the possible and impossible datasets. It was only with some substantial tweaking that I found a way to get phenix.autobuild to crack the possible dataset (using 20 models in parallel). I have not yet found a way to get any automation program to build its way out of the impossible dataset. Personally, I think that the breakthrough might be something like what Tom Terwilliger mentioned. If you build a good enough starting set of atoms, then I think an automation program should be able to take you the rest of the way. If that is the case, then it means people like Tom who develop such programs for us might be able to use that insight to improve the software, and that is something that will benefit all of us. Or, it is entirely possible that I'm just not running the current software properly! If so, I'd love it if someone who knows better (such as their developers) could enlighten me. -James Holton MAD Scientist On 1/12/2013 3:07 AM, Pavol Skubak wrote: Dear James, your challenge in its current form ignores an important source of information for model building that is available for your simulated data - namely, it does not allow to use anomalous phase information in the model building. In difficult cases on the edge of success such as this one, this typically makes the difference between building and not building. If you can make the F+/F- and Se substructure available, we can test whether this is the case indeed. However, while I expect this would push the challenge further significantly, most likely you would be able to decrease the Se incorporation of your simulated data further to such levels that the anomalous signal is again no longer sufficient to build the structure. And most likely, there would again exist an edge where a small decrease in the Se incorporation would lead from a model built to no model built. Best regards, -- Pavol Skubak Biophysical Structural Chemistry Gorleaus Laboratories Einsteinweg 55 Leiden University LEIDEN 2333CC the Netherlands tel: 0031715274414 tel:0031715274414 web: http://bsc.lic.leidenuniv.nl/people/skubak-0
Re: [ccp4bb] a challenge
Fair enough! The heavy atom positions are simply the S atoms in 3dko. There are 22 of them. Also, in this case the Met side chains (12 of those) are 32% occupied with Se. The other 68% is sulfur. I think it is realistic that one could know the extent of Se incorporation ahead of time from something like mass spec (especially if you knew it could make-or-break your structure determination). However, I don't think it is realistic that you would know where they are before running shelx. -James Holton MAD Scientist On 1/12/2013 7:46 AM, George Sheldrick wrote: Dear James, I agree with Pavel that your example is not very realistic. In practice one would start from the heavy atom positions. As well as providing starting phases, they are useful in other ways. For example. shelxe (and probably most other tracing programs) adds them to a 'no-go' map so it knows where NOT to trace the main-chain. Best wishes, George Dear James, your challenge in its current form ignores an important source of information for model building that is available for your simulated data - namely, it does not allow to use anomalous phase information in the model building. In difficult cases on the edge of success such as this one, this typically makes the difference between building and not building. If you can make the F+/F- and Se substructure available, we can test whether this is the case indeed. However, while I expect this would push the challenge further significantly, most likely you would be able to decrease the Se incorporation of your simulated data further to such levels that the anomalous signal is again no longer sufficient to build the structure. And most likely, there would again exist an edge where a small decrease in the Se incorporation would lead from a model built to no model built. Best regards, -- Pavol Skubak Biophysical Structural Chemistry Gorleaus Laboratories Einsteinweg 55 Leiden University LEIDEN 2333CC the Netherlands tel: 0031715274414 tel:0031715274414 web: http://bsc.lic.leidenuniv.nl/people/skubak-0 -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] a challenge
Woops! sorry folks. I made a mistake with the I(+)/I(-) entry. They had the wrong axis convention relative to 3dko and the F in the same file. Sorry about that. The files on the website now should be right. http://bl831.als.lbl.gov/~jamesh/challenge/possible.mtz http://bl831.als.lbl.gov/~jamesh/challenge/impossible.mtz md5 sums: c4bdb32a08c884884229e8080228d166 impossible.mtz caf05437132841b595be1c0dc1151123 possible.mtz -James Holton MAD Scientist On 1/12/2013 8:25 AM, James Holton wrote: Fair enough! I have just now added DANO and I(+)/I(-) to the files. I'll be very interested to see what you can come up with! For the record, the phases therein came from running mlphare with default parameters but exactly the correct heavy-atom constellation (all the sulfur atoms in 3dko), and then running dm with default parameters. Yes, there are other ways to run mlphare and dm that give better phases, but I was only able to determine those parameters by cheating (comparing the resulting map to the right answer), so I don't think it is fair to use those maps. I have had a few questions about what is cheating and what is not cheating. I don't have a problem with the use of sequence information because that actually is something that you realistically would know about your protein when you sat down to collect data. The sequence of this molecule is that of 3dko: http://bl831.als.lbl.gov/~jamesh/challenge/seq.pir I also don't have a problem with anyone actually using an automation program to _help_ them solve the impossible dataset as long as they can explain what they did. Simply putting the above sequence into BALBES would, of course, be cheating! I suppose one could try eliminating 3dko and its homologs from the BALBES search, but that, in and of itself, is perhaps relevant to the challenge: what is the most distance homolog that still allows you to solve the structure?. That, I think, is also a stringent test of model-building skill. I have already tried ARP/wARP, phenix.autobuild and buccaneer/refmac. With default parameters, all of these programs fail on both the possible and impossible datasets. It was only with some substantial tweaking that I found a way to get phenix.autobuild to crack the possible dataset (using 20 models in parallel). I have not yet found a way to get any automation program to build its way out of the impossible dataset. Personally, I think that the breakthrough might be something like what Tom Terwilliger mentioned. If you build a good enough starting set of atoms, then I think an automation program should be able to take you the rest of the way. If that is the case, then it means people like Tom who develop such programs for us might be able to use that insight to improve the software, and that is something that will benefit all of us. Or, it is entirely possible that I'm just not running the current software properly! If so, I'd love it if someone who knows better (such as their developers) could enlighten me. -James Holton MAD Scientist On 1/12/2013 3:07 AM, Pavol Skubak wrote: Dear James, your challenge in its current form ignores an important source of information for model building that is available for your simulated data - namely, it does not allow to use anomalous phase information in the model building. In difficult cases on the edge of success such as this one, this typically makes the difference between building and not building. If you can make the F+/F- and Se substructure available, we can test whether this is the case indeed. However, while I expect this would push the challenge further significantly, most likely you would be able to decrease the Se incorporation of your simulated data further to such levels that the anomalous signal is again no longer sufficient to build the structure. And most likely, there would again exist an edge where a small decrease in the Se incorporation would lead from a model built to no model built. Best regards, -- Pavol Skubak Biophysical Structural Chemistry Gorleaus Laboratories Einsteinweg 55 Leiden University LEIDEN 2333CC the Netherlands tel: 0031715274414 tel:0031715274414 web: http://bsc.lic.leidenuniv.nl/people/skubak-0
Re: [ccp4bb] a challenge
James, I had in fact just come to the conclusion that the indexing was consistent with 3dko for 'possible' but not for 'impossible', which I suppose was logical. George Woops! sorry folks. I made a mistake with the I(+)/I(-) entry. They had the wrong axis convention relative to 3dko and the F in the same file. Sorry about that. The files on the website now should be right. http://bl831.als.lbl.gov/~jamesh/challenge/possible.mtz http://bl831.als.lbl.gov/~jamesh/challenge/impossible.mtz md5 sums: c4bdb32a08c884884229e8080228d166 impossible.mtz caf05437132841b595be1c0dc1151123 possible.mtz -James Holton MAD Scientist On 1/12/2013 8:25 AM, James Holton wrote: Fair enough! I have just now added DANO and I(+)/I(-) to the files. I'll be very interested to see what you can come up with! For the record, the phases therein came from running mlphare with default parameters but exactly the correct heavy-atom constellation (all the sulfur atoms in 3dko), and then running dm with default parameters. Yes, there are other ways to run mlphare and dm that give better phases, but I was only able to determine those parameters by cheating (comparing the resulting map to the right answer), so I don't think it is fair to use those maps. I have had a few questions about what is cheating and what is not cheating. I don't have a problem with the use of sequence information because that actually is something that you realistically would know about your protein when you sat down to collect data. The sequence of this molecule is that of 3dko: http://bl831.als.lbl.gov/~jamesh/challenge/seq.pir I also don't have a problem with anyone actually using an automation program to _help_ them solve the impossible dataset as long as they can explain what they did. Simply putting the above sequence into BALBES would, of course, be cheating! I suppose one could try eliminating 3dko and its homologs from the BALBES search, but that, in and of itself, is perhaps relevant to the challenge: what is the most distance homolog that still allows you to solve the structure?. That, I think, is also a stringent test of model-building skill. I have already tried ARP/wARP, phenix.autobuild and buccaneer/refmac. With default parameters, all of these programs fail on both the possible and impossible datasets. It was only with some substantial tweaking that I found a way to get phenix.autobuild to crack the possible dataset (using 20 models in parallel). I have not yet found a way to get any automation program to build its way out of the impossible dataset. Personally, I think that the breakthrough might be something like what Tom Terwilliger mentioned. If you build a good enough starting set of atoms, then I think an automation program should be able to take you the rest of the way. If that is the case, then it means people like Tom who develop such programs for us might be able to use that insight to improve the software, and that is something that will benefit all of us. Or, it is entirely possible that I'm just not running the current software properly! If so, I'd love it if someone who knows better (such as their developers) could enlighten me. -James Holton MAD Scientist On 1/12/2013 3:07 AM, Pavol Skubak wrote: Dear James, your challenge in its current form ignores an important source of information for model building that is available for your simulated data - namely, it does not allow to use anomalous phase information in the model building. In difficult cases on the edge of success such as this one, this typically makes the difference between building and not building. If you can make the F+/F- and Se substructure available, we can test whether this is the case indeed. However, while I expect this would push the challenge further significantly, most likely you would be able to decrease the Se incorporation of your simulated data further to such levels that the anomalous signal is again no longer sufficient to build the structure. And most likely, there would again exist an edge where a small decrease in the Se incorporation would lead from a model built to no model built. Best regards, -- Pavol Skubak Biophysical Structural Chemistry Gorleaus Laboratories Einsteinweg 55 Leiden University LEIDEN 2333CC the Netherlands tel: 0031715274414 tel:0031715274414 web: http://bsc.lic.leidenuniv.nl/people/skubak-0 -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] a challenge
I admit that made impossible more difficult to solve than possible, but not in the way I had intended! Again, sorry about that. It is corrected now. The change in indexing arises because I am processing the simulated images with a default run of XDS and as you know the autoindexing picks an indexing convention at random. I flipped it back at the time, but when I just now went back to get the I(+)/I(-) I went just one step too far. Once again, sorry. It was not my intention to waste anyone's time! -James Holton MAD Scientist On 1/12/2013 2:09 PM, George Sheldrick wrote: James, I had in fact just come to the conclusion that the indexing was consistent with 3dko for 'possible' but not for 'impossible', which I suppose was logical. George Woops! sorry folks. I made a mistake with the I(+)/I(-) entry. They had the wrong axis convention relative to 3dko and the F in the same file. Sorry about that. The files on the website now should be right. http://bl831.als.lbl.gov/~jamesh/challenge/possible.mtz http://bl831.als.lbl.gov/~jamesh/challenge/impossible.mtz md5 sums: c4bdb32a08c884884229e8080228d166 impossible.mtz caf05437132841b595be1c0dc1151123 possible.mtz -James Holton MAD Scientist On 1/12/2013 8:25 AM, James Holton wrote: Fair enough! I have just now added DANO and I(+)/I(-) to the files. I'll be very interested to see what you can come up with! For the record, the phases therein came from running mlphare with default parameters but exactly the correct heavy-atom constellation (all the sulfur atoms in 3dko), and then running dm with default parameters. Yes, there are other ways to run mlphare and dm that give better phases, but I was only able to determine those parameters by cheating (comparing the resulting map to the right answer), so I don't think it is fair to use those maps. I have had a few questions about what is cheating and what is not cheating. I don't have a problem with the use of sequence information because that actually is something that you realistically would know about your protein when you sat down to collect data. The sequence of this molecule is that of 3dko: http://bl831.als.lbl.gov/~jamesh/challenge/seq.pir I also don't have a problem with anyone actually using an automation program to _help_ them solve the impossible dataset as long as they can explain what they did. Simply putting the above sequence into BALBES would, of course, be cheating! I suppose one could try eliminating 3dko and its homologs from the BALBES search, but that, in and of itself, is perhaps relevant to the challenge: what is the most distance homolog that still allows you to solve the structure?. That, I think, is also a stringent test of model-building skill. I have already tried ARP/wARP, phenix.autobuild and buccaneer/refmac. With default parameters, all of these programs fail on both the possible and impossible datasets. It was only with some substantial tweaking that I found a way to get phenix.autobuild to crack the possible dataset (using 20 models in parallel). I have not yet found a way to get any automation program to build its way out of the impossible dataset. Personally, I think that the breakthrough might be something like what Tom Terwilliger mentioned. If you build a good enough starting set of atoms, then I think an automation program should be able to take you the rest of the way. If that is the case, then it means people like Tom who develop such programs for us might be able to use that insight to improve the software, and that is something that will benefit all of us. Or, it is entirely possible that I'm just not running the current software properly! If so, I'd love it if someone who knows better (such as their developers) could enlighten me. -James Holton MAD Scientist On 1/12/2013 3:07 AM, Pavol Skubak wrote: Dear James, your challenge in its current form ignores an important source of information for model building that is available for your simulated data - namely, it does not allow to use anomalous phase information in the model building. In difficult cases on the edge of success such as this one, this typically makes the difference between building and not building. If you can make the F+/F- and Se substructure available, we can test whether this is the case indeed. However, while I expect this would push the challenge further significantly, most likely you would be able to decrease the Se incorporation of your simulated data further to such levels that the anomalous signal is again no longer sufficient to build the structure. And most likely, there would again exist an edge where a small decrease in the Se incorporation would lead from a model built to no model built. Best regards, -- Pavol Skubak Biophysical Structural Chemistry Gorleaus Laboratories Einsteinweg 55 Leiden University LEIDEN 2333CC the Netherlands tel: 0031715274414 tel:0031715274414 web:
Re: [ccp4bb] a challenge
I can build from the impossible.mtz data in the following two steps: 1. getting the SE substructure from anomalous difference map constructed from impossible.mtz 2. running combined model building using the substructure from step 1 and starting from the impossible.mtz map Only impossible.mtz and the sequence (which is probably not really necessary) is used in this solution. It is not a fully automatic solution - step 2 (model building combined with density modif. and phasing via a recently developed multivariate SAD function) was performed automatically using CRANK (which calls Buccaneer, REFMAC and Parrot), step 1 manually - using CCP4 tools (cfft and peakmax). Comparing to the deposited model, 96% of the mainchain is (correctly) built and 92% is (correctly) docked and R factor is 21% - clearly, the (relatively) weak anomalous signal is the only limitation in this case. However, the model building procedure did not struggle too much - I expect it would still work if the Se incorporation is decreased somewhat further (as long as the substructure can be obtained in some way). Of course, this is not a pure solution in the sense that I started from impossible.mtz rather than from scratch, ie from the data only. Obtaining the substructure from scratch might be more difficult. Pavol On Sat, Jan 12, 2013 at 10:50 PM, James Holton jmhol...@lbl.gov wrote: Woops! sorry folks. I made a mistake with the I(+)/I(-) entry. They had the wrong axis convention relative to 3dko and the F in the same file. Sorry about that. The files on the website now should be right. http://bl831.als.lbl.gov/~jamesh/challenge/possible.mtz http://bl831.als.lbl.gov/~jamesh/challenge/impossible.mtz md5 sums: c4bdb32a08c884884229e8080228d166 impossible.mtz caf05437132841b595be1c0dc1151123 possible.mtz -James Holton MAD Scientist On 1/12/2013 8:25 AM, James Holton wrote: Fair enough! I have just now added DANO and I(+)/I(-) to the files. I'll be very interested to see what you can come up with! For the record, the phases therein came from running mlphare with default parameters but exactly the correct heavy-atom constellation (all the sulfur atoms in 3dko), and then running dm with default parameters. Yes, there are other ways to run mlphare and dm that give better phases, but I was only able to determine those parameters by cheating (comparing the resulting map to the right answer), so I don't think it is fair to use those maps. I have had a few questions about what is cheating and what is not cheating. I don't have a problem with the use of sequence information because that actually is something that you realistically would know about your protein when you sat down to collect data. The sequence of this molecule is that of 3dko: http://bl831.als.lbl.gov/~jamesh/challenge/seq.pir I also don't have a problem with anyone actually using an automation program to _help_ them solve the impossible dataset as long as they can explain what they did. Simply putting the above sequence into BALBES would, of course, be cheating! I suppose one could try eliminating 3dko and its homologs from the BALBES search, but that, in and of itself, is perhaps relevant to the challenge: what is the most distance homolog that still allows you to solve the structure?. That, I think, is also a stringent test of model-building skill. I have already tried ARP/wARP, phenix.autobuild and buccaneer/refmac. With default parameters, all of these programs fail on both the possible and impossible datasets. It was only with some substantial tweaking that I found a way to get phenix.autobuild to crack the possible dataset (using 20 models in parallel). I have not yet found a way to get any automation program to build its way out of the impossible dataset. Personally, I think that the breakthrough might be something like what Tom Terwilliger mentioned. If you build a good enough starting set of atoms, then I think an automation program should be able to take you the rest of the way. If that is the case, then it means people like Tom who develop such programs for us might be able to use that insight to improve the software, and that is something that will benefit all of us. Or, it is entirely possible that I'm just not running the current software properly! If so, I'd love it if someone who knows better (such as their developers) could enlighten me. -James Holton MAD Scientist On 1/12/2013 3:07 AM, Pavol Skubak wrote: Dear James, your challenge in its current form ignores an important source of information for model building that is available for your simulated data - namely, it does not allow to use anomalous phase information in the model building. In difficult cases on the edge of success such as this one, this typically makes the difference between building and not building. If you can make the F+/F- and Se substructure available, we can test whether this is the
