[ccp4bb] phenix.refine and refmac
Dear All, I have post a similar question about CNS and refmac before, now in another structure I met a similar problem. I have an almost finished structure, the Rfree of which is about 0.28 by refmac. Then I used phenix to refine it, below is the result: REMARK REFINEMENT SUMMARY: QUICK FACTS *** REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213 REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374 REMARK Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file. But I found that at the first several cycle of refmac the Rfree decreased, then both the R and Rfree values continued increasing and FOM decreasing. The best R/Rfree/FOM during the refinement is - Overall R factor = 0.1932 Free R factor= 0.2513 Overall figure of merit = 0.8168 - And after 40 cycles the final result is: - Overall R factor = 0.2008 Free R factor= 0.2772 Overall figure of merit = 0.7902 - The values looks like keep going up if increase the cycles. Then which value should I take as the final result? The phenix or the best Refmac result or I have to take a converged value from refmac?
Re: [ccp4bb] phenix.refine and refmac
phenix.refine also produces an mtz file by default, and that can be auto-opened with coot, along with the coordinates. On Mar 4, 2008, at 7:27 AM, yang li wrote: Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file.
Re: [ccp4bb] phenix.refine and refmac
Yes, I got the mtz file which can be oopened by coot, so can I take the phenix result? I am customed to use refmac before, but now is confused when several choices come out. On 3/4/08, William Scott [EMAIL PROTECTED] wrote: phenix.refine also produces an mtz file by default, and that can be auto-opened with coot, along with the coordinates. On Mar 4, 2008, at 7:27 AM, yang li wrote: Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file.
Re: [ccp4bb] phenix.refine and refmac
Dear Yang, it would be better if you could provide more details about your refinement strategies. As I can see from your results you might have used the default values in phenix giving you finally very low rmsd values. Refmac by default is not using so tight restraints and even if you used tight restraints in refmac the difference between R and Rfree might be much lower than the 7% in Phenix. I am guessing that the values that you are reporting have to do also with the weight values each program uses and how you are define them. Also have you used TLS in any of the two programs? regards Nikos - Dr. Nikos Pinotsis Section of Structural Biology Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London SW3 6JB, UK Tel: +44 20 7153 5453 / 5447 - yang li wrote: Dear All, I have post a similar question about CNS and refmac before, now in another structure I met a similar problem. I have an almost finished structure, the Rfree of which is about 0.28 by refmac. Then I used phenix to refine it, below is the result: REMARK REFINEMENT SUMMARY: QUICK FACTS *** REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213 REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374 REMARK Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file. But I found that at the first several cycle of refmac the Rfree decreased, then both the R and Rfree values continued increasing and FOM decreasing. The best R/Rfree/FOM during the refinement is - Overall R factor = 0.1932 Free R factor= 0.2513 Overall figure of merit = 0.8168 - And after 40 cycles the final result is: - Overall R factor = 0.2008 Free R factor= 0.2772 Overall figure of merit = 0.7902 - The values looks like keep going up if increase the cycles. Then which value should I take as the final result? The phenix or the best Refmac result or I have to take a converged value from refmac? The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] phenix.refine and refmac
Hi Yang how many reflections do you have in your test-set for calculating R-free? Too few reflections, typically less than 500, may not constitute a statistically robust cross-validation data set, and thus may lead to fluctuations in R-free plus a tendency for R-free to increase as a function of refinement cycle. Some of the early publications from Axel Brunger on crystallographic cross-validation address the need for enough reflections (500) in the test-set. In addition, the presence of even a handful of strong but inaccurately measured/integrated low-resolution reflections in a limited test-set can aggravate abnormal behavior in R-free. Best wishes Savvas toQuoting yang li [EMAIL PROTECTED]: Dear All, I have post a similar question about CNS and refmac before, now in another structure I met a similar problem. I have an almost finished structure, the Rfree of which is about 0.28 by refmac. Then I used phenix to refine it, below is the result: REMARK REFINEMENT SUMMARY: QUICK FACTS *** REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213 REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374 REMARK Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file. But I found that at the first several cycle of refmac the Rfree decreased, then both the R and Rfree values continued increasing and FOM decreasing. The best R/Rfree/FOM during the refinement is - Overall R factor = 0.1932 Free R factor= 0.2513 Overall figure of merit = 0.8168 - And after 40 cycles the final result is: - Overall R factor = 0.2008 Free R factor= 0.2772 Overall figure of merit = 0.7902 - The values looks like keep going up if increase the cycles. Then which value should I take as the final result? The phenix or the best Refmac result or I have to take a converged value from refmac?
Re: [ccp4bb] phenix.refine and refmac
One point which I don't understand is how can someone compare the two different programs when they don't use the same numbers for xray:geometry terms? Taking the default settings for a given resolution might not be enough.. ! On Tue, Mar 4, 2008 at 7:58 PM, Savvas Savvides [EMAIL PROTECTED] wrote: Hi Yang how many reflections do you have in your test-set for calculating R-free? Too few reflections, typically less than 500, may not constitute a statistically robust cross-validation data set, and thus may lead to fluctuations in R-free plus a tendency for R-free to increase as a function of refinement cycle. Some of the early publications from Axel Brunger on crystallographic cross-validation address the need for enough reflections (500) in the test-set. In addition, the presence of even a handful of strong but inaccurately measured/integrated low-resolution reflections in a limited test-set can aggravate abnormal behavior in R-free. Best wishes Savvas toQuoting yang li [EMAIL PROTECTED]: Dear All, I have post a similar question about CNS and refmac before, now in another structure I met a similar problem. I have an almost finished structure, the Rfree of which is about 0.28 by refmac. Then I used phenix to refine it, below is the result: REMARK REFINEMENT SUMMARY: QUICK FACTS *** REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213 REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374 REMARK Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file. But I found that at the first several cycle of refmac the Rfree decreased, then both the R and Rfree values continued increasing and FOM decreasing. The best R/Rfree/FOM during the refinement is - Overall R factor = 0.1932 Free R factor= 0.2513 Overall figure of merit = 0.8168 - And after 40 cycles the final result is: - Overall R factor = 0.2008 Free R factor= 0.2772 Overall figure of merit = 0.7902 - The values looks like keep going up if increase the cycles. Then which value should I take as the final result? The phenix or the best Refmac result or I have to take a converged value from refmac? -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] phenix.refine and refmac
Thanks for your replies. I did use default settings in phenix refine, included TLS in it. This is an about 2.3A data, and the number Rfree used to refine is big enough. I also kept the same Rfree in two programs. In refmac I also tried diffenrent weighting sets--from defaut 0.3 to 0.02, TLS included--maybe there are some other ways to define the restrains. The R and Rfree will increase as the weighting is set too low, and the gap didnot improve much. I donnot know in this case if the phenix refine has converged, but the not stable Rfree in refmac made me nervous. Simply, in this case, which one should I choose? Certainly to my private opinion I would prefer to Scott's answer, Rfree is the most obvious parameter than something esle like geometry, eg. Just looks good. :) On 3/5/08, Partha Chakrabarti [EMAIL PROTECTED] wrote: One point which I don't understand is how can someone compare the two different programs when they don't use the same numbers for xray:geometry terms? Taking the default settings for a given resolution might not be enough.. ! On Tue, Mar 4, 2008 at 7:58 PM, Savvas Savvides [EMAIL PROTECTED] wrote: Hi Yang how many reflections do you have in your test-set for calculating R-free? Too few reflections, typically less than 500, may not constitute a statistically robust cross-validation data set, and thus may lead to fluctuations in R-free plus a tendency for R-free to increase as a function of refinement cycle. Some of the early publications from Axel Brunger on crystallographic cross-validation address the need for enough reflections (500) in the test-set. In addition, the presence of even a handful of strong but inaccurately measured/integrated low-resolution reflections in a limited test-set can aggravate abnormal behavior in R-free. Best wishes Savvas toQuoting yang li [EMAIL PROTECTED]: Dear All, I have post a similar question about CNS and refmac before, now in another structure I met a similar problem. I have an almost finished structure, the Rfree of which is about 0.28 by refmac. Then I used phenix to refine it, below is the result: REMARK REFINEMENT SUMMARY: QUICK FACTS *** REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213 REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374 REMARK Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file. But I found that at the first several cycle of refmac the Rfree decreased, then both the R and Rfree values continued increasing and FOM decreasing. The best R/Rfree/FOM during the refinement is - Overall R factor = 0.1932 Free R factor= 0.2513 Overall figure of merit = 0.8168 - And after 40 cycles the final result is: - Overall R factor = 0.2008 Free R factor= 0.2772 Overall figure of merit = 0.7902 - The values looks like keep going up if increase the cycles. Then which value should I take as the final result? The phenix or the best Refmac result or I have to take a converged value from refmac? -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
