Re: [ccp4bb] R-free flag problem
Dear Ed, It turns out that the format of the structure file I sent to the PDB guys is not right. I found out this when running phenix.model_vs_data. After I resent the structrue file, sfcheck gives something OK, which is, High_Res Low_Res Compl Num_Ref R_obs R_work R_free Corr(Fo-Fc) Reported PHENIX 1.695 36.657 95.51 46167 0.1488 0.1474 0.1742 N/A SFCHECK without TLS 1.69 39.42 95.9 45158 0.1604 0.162 0.183 0.9546 REFMAC without TLS 1.694 39.426 95.428 46172 0.148 0.1464 0.1736 0.964 PHENIX 1.69 36.66 96.0 46167 N/A 0.1475 0.1741 N/A Thank you all for your suggestions, Best wishes, Vinson 发件人： Ed Pozharski 收件人： CCP4BB@JISCMAIL.AC.UK 发送日期： 2010/10/23 (周六) 12:07:48 上午 主 题： Re: [ccp4bb] R-free flag problem I must note that it is also interesting to know why the sfcheck produced the R-factor that is twice as high. Of course, the R/Rfree are not supposed to match precisely (as I recall, sfcheck uses Babinet bulk solvent correction which is presumably inferior to the mask-based approach), but 28.6 versus 14.7? Something may be seriously wrong. On Fri, 2010-10-22 at 09:37 +0200, Tim Gruene wrote: > Dear Vinson, > > I would still be interested about what was the cause of the missing R-free >flags > and how you resolved it (I hope I did not miss an email). > > Kind regards, Tim > > On Fri, Oct 22, 2010 at 02:33:03PM +0800, Vinson LIANG wrote: > > > > > > Dear all, > > > > > > > > > > Thank you very much for your suggestions. > > > > I try Pavel's easy method. Hopefully, the result from phenix.model_vs_data >would be enough for PDB. > > > > > > Best wishes, > > > > Vinson > > > > > > > > > > > > > > > > > > 发件人： Pavel Afonine > > 收件人： PHENIX user mailing list > > 抄 送： Vinson LIANG > > 发送日期： 2010/10/22 (周五) 12:44:58 上午 > > 主 题： Re: [phenixbb] R-free problem with phenix.refine > > > > Hi, > > > > > > > > > > Recently I deposited a structure to PDB. However, I was told > > >> The R value of SF check are different from your reported value. > > >> > > >> R work in SF check = 0.2859 > > >> your reported R work = 0.1474 > > >> Also there are no R free flags in your sending files, but you reported R > > >> free value in your all deposition. > > well, SF check is not the best tool to check things - it's not just my only >vision, see lots of conversations on this topic on bb. > > > > Just run > > > > phenix.model_vs_data model.pdb data.hkl > > > > and if output statistics matches the one you deposited to PDB, then you are >100% good. If it doesn't match then there is something to worry about. > > > > > > > > So, I rerun my deposited file with phenix.refine, and it gave a >R-work=0.1475, R-free=0.1742. > > > > > Sounds good. > > > > > > > > However, when I tried to run the same file with refmac5, error came with >"Free R label has not been set". I guess phenix.refine gives Rree-R label that >other program could not recognize. > > > > > No surprises. Jumping between programs is tricky. You have to account for a >lot of things to match things that different programs expect differently. > > > > > > > > Could anyone please help me to solve this problem? > > Step-by-step: > > > > 1) Run > > phenix.model_vs_data model.pdb data.hkl > > > > 2) if output statistics matches the one you deposited to PDB, then you are >100% good. Come back to PDB and say this. > > > > > 3) If it doesn't match then there is something that you need to fix. If you >can't fix or have no idea what's wrong, you can send me the data and model and >I >will have a look. > > > > Pavel. > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] R-free flag problem
I must note that it is also interesting to know why the sfcheck produced the R-factor that is twice as high. Of course, the R/Rfree are not supposed to match precisely (as I recall, sfcheck uses Babinet bulk solvent correction which is presumably inferior to the mask-based approach), but 28.6 versus 14.7? Something may be seriously wrong. On Fri, 2010-10-22 at 09:37 +0200, Tim Gruene wrote: > Dear Vinson, > > I would still be interested about what was the cause of the missing R-free > flags > and how you resolved it (I hope I did not miss an email). > > Kind regards, Tim > > On Fri, Oct 22, 2010 at 02:33:03PM +0800, Vinson LIANG wrote: > > > > > > Dear all, > > > > > > > > > > Thank you very much for your suggestions. > > > > I try Pavel's easy method. Hopefully, the result from phenix.model_vs_data > > would be enough for PDB. > > > > > > Best wishes, > > > > Vinson > > > > > > > > > > > > > > > > > > 发件人： Pavel Afonine > > 收件人： PHENIX user mailing list > > 抄 送： Vinson LIANG > > 发送日期： 2010/10/22 (周五) 12:44:58 上午 > > 主 题： Re: [phenixbb] R-free problem with phenix.refine > > > > Hi, > > > > > > > > > > Recently I deposited a structure to PDB. However, I was told > > >> The R value of SF check are different from your reported value. > > >> > > >> R work in SF check = 0.2859 > > >> your reported R work = 0.1474 > > >> Also there are no R free flags in your sending files, but you reported R > > >> free value in your all deposition. > > well, SF check is not the best tool to check things - it's not just my only > > vision, see lots of conversations on this topic on bb. > > > > Just run > > > > phenix.model_vs_data model.pdb data.hkl > > > > and if output statistics matches the one you deposited to PDB, then you are > > 100% good. If it doesn't match then there is something to worry about. > > > > > > > > So, I rerun my deposited file with phenix.refine, and it gave a > > R-work=0.1475, R-free=0.1742. > > > > Sounds good. > > > > > > > > However, when I tried to run the same file with refmac5, error came with > > "Free R label has not been set". I guess phenix.refine gives Rree-R label > > that other program could not recognize. > > > > No surprises. Jumping between programs is tricky. You have to account for a > > lot of things to match things that different programs expect differently. > > > > > > > > Could anyone please help me to solve this problem? > > Step-by-step: > > > > 1) Run > > phenix.model_vs_data model.pdb data.hkl > > > > 2) if output statistics matches the one you deposited to PDB, then you are > > 100% good. Come back to PDB and say this. > > > > 3) If it doesn't match then there is something that you need to fix. If you > > can't fix or have no idea what's wrong, you can send me the data and model > > and I will have a look. > > > > Pavel. > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] R-free flag problem
Dear Vinson, I would still be interested about what was the cause of the missing R-free flags and how you resolved it (I hope I did not miss an email). Kind regards, Tim On Fri, Oct 22, 2010 at 02:33:03PM +0800, Vinson LIANG wrote: > > > Dear all, > > > > > Thank you very much for your suggestions. > > I try Pavel's easy method. Hopefully, the result from phenix.model_vs_data > would be enough for PDB. > > > Best wishes, > > Vinson > > > > > > > > > 发件人： Pavel Afonine > 收件人： PHENIX user mailing list > 抄 送： Vinson LIANG > 发送日期： 2010/10/22 (周五) 12:44:58 上午 > 主 题： Re: [phenixbb] R-free problem with phenix.refine > > Hi, > > > > > Recently I deposited a structure to PDB. However, I was told > >> The R value of SF check are different from your reported value. > >> > >> R work in SF check = 0.2859 > >> your reported R work = 0.1474 > >> Also there are no R free flags in your sending files, but you reported R > >> free value in your all deposition. > well, SF check is not the best tool to check things - it's not just my only > vision, see lots of conversations on this topic on bb. > > Just run > > phenix.model_vs_data model.pdb data.hkl > > and if output statistics matches the one you deposited to PDB, then you are > 100% good. If it doesn't match then there is something to worry about. > > > > So, I rerun my deposited file with phenix.refine, and it gave a > R-work=0.1475, R-free=0.1742. > > Sounds good. > > > > However, when I tried to run the same file with refmac5, error came with > "Free R label has not been set". I guess phenix.refine gives Rree-R label > that other program could not recognize. > > No surprises. Jumping between programs is tricky. You have to account for a > lot of things to match things that different programs expect differently. > > > > Could anyone please help me to solve this problem? > Step-by-step: > > 1) Run > phenix.model_vs_data model.pdb data.hkl > > 2) if output statistics matches the one you deposited to PDB, then you are > 100% good. Come back to PDB and say this. > > 3) If it doesn't match then there is something that you need to fix. If you > can't fix or have no idea what's wrong, you can send me the data and model > and I will have a look. > > Pavel. > > > > > > > > > > > > > > -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] R-free flag problem
Dear all, Thank you very much for your suggestions. I try Pavel's easy method. Hopefully, the result from phenix.model_vs_data would be enough for PDB. Best wishes, Vinson 发件人： Pavel Afonine 收件人： PHENIX user mailing list 抄 送： Vinson LIANG 发送日期： 2010/10/22 (周五) 12:44:58 上午 主 题： Re: [phenixbb] R-free problem with phenix.refine Hi, Recently I deposited a structure to PDB. However, I was told >> The R value of SF check are different from your reported value. >> >> R work in SF check = 0.2859 >> your reported R work = 0.1474 >> Also there are no R free flags in your sending files, but you reported R >> free value in your all deposition. well, SF check is not the best tool to check things - it's not just my only vision, see lots of conversations on this topic on bb. Just run phenix.model_vs_data model.pdb data.hkl and if output statistics matches the one you deposited to PDB, then you are 100% good. If it doesn't match then there is something to worry about. So, I rerun my deposited file with phenix.refine, and it gave a R-work=0.1475, R-free=0.1742. Sounds good. However, when I tried to run the same file with refmac5, error came with "Free R label has not been set". I guess phenix.refine gives Rree-R label that other program could not recognize. No surprises. Jumping between programs is tricky. You have to account for a lot of things to match things that different programs expect differently. Could anyone please help me to solve this problem? Step-by-step: 1) Run phenix.model_vs_data model.pdb data.hkl 2) if output statistics matches the one you deposited to PDB, then you are 100% good. Come back to PDB and say this. 3) If it doesn't match then there is something that you need to fix. If you can't fix or have no idea what's wrong, you can send me the data and model and I will have a look. Pavel.
Re: [ccp4bb] R-free flag problem.
Dear Vinson, Liang have a look at the penultimate table from mtzdmp your_mtz_file.mtz where your_mtz_file.mtz is the mtz-file you are using to deposit/ for refinement. That second last table lists the columns which are present in your mtz-file, their types and names and should give a clue what phenix uses as Rfree-flag and why refmac and sfcheck do not recognise it. You can send us that table if you are not sure how to interpret the data it presents. Tim On Thu, Oct 21, 2010 at 01:50:04PM +0800, Vinson LIANG wrote: > Dear all, > > Recently I deposited a structure to PDB. However, I was told > >> The R value of SF check are different from your reported value. > >> > >> R work in SF check = 0.2859 > >> your reported R work = 0.1474 > >> Also there are no R free flags in your sending files, but you reported R > >> free value in your all deposition. > > > > So, I rerun my deposited file with phenix.refine, and it gave a > R-work=0.1475, R-free=0.1742. > > However, when I tried to run the same file with refmac5, error came with > "Free R label has not been set". I guess phenix.refine gives Rree-R label > that other program could not recognize. > > Could anyone please help me to solve this problem? > > Thank you very much in advance, > > Best, > > Vinson, Liang > > > > > > > -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] R-free flag problem.
Dear all, Recently I deposited a structure to PDB. However, I was told >> The R value of SF check are different from your reported value. >> >> R work in SF check = 0.2859 >> your reported R work = 0.1474 >> Also there are no R free flags in your sending files, but you reported R >> free value in your all deposition. So, I rerun my deposited file with phenix.refine, and it gave a R-work=0.1475, R-free=0.1742. However, when I tried to run the same file with refmac5, error came with "Free R label has not been set". I guess phenix.refine gives Rree-R label that other program could not recognize. Could anyone please help me to solve this problem? Thank you very much in advance, Best, Vinson, Liang
