Re: [ccp4bb] Rsym problems...maybe???
No - no - no! Probably you should have integrated to a higher resolution! Eleanor Daniel Bonsor wrote: Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying?
Re: [ccp4bb] Rsym problems...maybe???
Am 20:59, schrieb Poul Nissen: I very much agree - refinement will tell you if the high-res data make sense. Another very good test is the Wilson plot - it should look straight and reasonable. Inflated I/sigI values will not escape a strange appearance such as the WIlson plot flattening out at higher resolution. I normally find a very good consistency between the resolution cut-offs indicated by the wilson plot and the refinement statistics. good advice Poul On 22/04/2010, at 19.59, Edward A. Berry wrote: There are plenty of structures in the database with R-sym=0.99. But something is odd here. If I understand R-pim, it should always be bigger than Rsym, because this factor of sqrt(N/(N-1)) is always >1 Are you saying Rpim is .30 and Rsym is 1.00? a correction: the factor of sqrt(N/(N-1)) that you quote is for R-rim (same as R_meas), not for R-pim. R-pim (more or less same as R_mrgd-I) has a factor of sqrt(1/(N-1)) so a value of 30% is believable. As this is on intensities, the equivalent quantity calculated on amplitudes should be even less. That means that refinement should be happy with those data! see the wiki: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/R-factors HTH, Kay Last time I deposited a structure, Rsym and Rmerge in the last shell are optional. I would leave it out and rely on the excellent I/sigI in the last shell, and use all the data (provided after refinement R-free in the last shell is < .4). Ed Daniel Bonsor wrote: Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying? smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] Rsym problems...maybe???
I'd worry a bit. If the data are strong and the R factor is that bad you may have got your space group wrong (pseudo, not crystallographic 4 fold?) Pete Artymiuk On 22 Apr 2010, at 18:22, Frank von Delft wrote: > Yeah, stop worrying! Your I/sdI is all that matters. > phx > > > On 22/04/2010 18:06, Daniel Bonsor wrote: >> Hello again. >> >> At first I was not worry but maybe now I am. I have completed a structure >> and submitted to the PDB. They queried my Rsym value in the highest >> resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the >> time as I had: >> >> 99.4% completeness >> Mean(I/sdI) of 2.5 >> and a redundancy of 11 (which would explain the high Rsym) >> Space group I422 >> >> My Rpim in this shell is 30%. >> >> Should I reduce the resolution and start from scratch again or is everything >> fine and dandy and I should stop worrying? >>
Re: [ccp4bb] Rsym problems...maybe???
I very much agree - refinement will tell you if the high-res data make sense. Another very good test is the Wilson plot - it should look straight and reasonable. Inflated I/sigI values will not escape a strange appearance such as the WIlson plot flattening out at higher resolution. I normally find a very good consistency between the resolution cut-offs indicated by the wilson plot and the refinement statistics. Poul On 22/04/2010, at 19.59, Edward A. Berry wrote: There are plenty of structures in the database with R-sym=0.99. But something is odd here. If I understand R-pim, it should always be bigger than Rsym, because this factor of sqrt(N/(N-1)) is always >1 Are you saying Rpim is .30 and Rsym is 1.00? Last time I deposited a structure, Rsym and Rmerge in the last shell are optional. I would leave it out and rely on the excellent I/sigI in the last shell, and use all the data (provided after refinement R-free in the last shell is < .4). Ed Daniel Bonsor wrote: Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying?
Re: [ccp4bb] Rsym problems...maybe???
There are Rpim and Rrim, Rpim is sqrt(1/(N-1)) and is usually small and Rrim (or Rmeas)=sqrt(N/(N-1)) and is large. I usually go with I/sigma cutoff. Maia - Original Message - From: "Edward A. Berry" To: Sent: Thursday, April 22, 2010 11:59 AM Subject: Re: [ccp4bb] Rsym problems...maybe??? There are plenty of structures in the database with R-sym=0.99. But something is odd here. If I understand R-pim, it should always be bigger than Rsym, because this factor of sqrt(N/(N-1)) is always >1 Are you saying Rpim is .30 and Rsym is 1.00? Last time I deposited a structure, Rsym and Rmerge in the last shell are optional. I would leave it out and rely on the excellent I/sigI in the last shell, and use all the data (provided after refinement R-free in the last shell is < .4). Ed Daniel Bonsor wrote: Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying?
Re: [ccp4bb] Rsym problems...maybe???
There are plenty of structures in the database with R-sym=0.99. But something is odd here. If I understand R-pim, it should always be bigger than Rsym, because this factor of sqrt(N/(N-1)) is always >1 Are you saying Rpim is .30 and Rsym is 1.00? Last time I deposited a structure, Rsym and Rmerge in the last shell are optional. I would leave it out and rely on the excellent I/sigI in the last shell, and use all the data (provided after refinement R-free in the last shell is < .4). Ed Daniel Bonsor wrote: Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying?
Re: [ccp4bb] Rsym problems...maybe???
Yeah, but how was I/sdI determined? Most programs allow you to multiply your sdI by any number you want which in turns means that you can create any I/sdI that you want. A multiplicity of 11 does not explain a high Rsym to me. Jim On Thu, 22 Apr 2010, Frank von Delft wrote: Yeah, stop worrying! Your I/sdI is all that matters. phx On 22/04/2010 18:06, Daniel Bonsor wrote: Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying?
Re: [ccp4bb] Rsym problems...maybe???
Yeah, stop worrying! Your I/sdI is all that matters. phx On 22/04/2010 18:06, Daniel Bonsor wrote: Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying?
Re: [ccp4bb] Rsym problems...maybe???
R-statistics are unstable for weak data (such as systematic absences). Ignore R-sym for your highest-angle bin. I/sdI is more informative, and from the look of yours I would say you can "reduce" your resolution in the sense that you probably have useful data (I/sdI > 1) to better than 2.5 A. Some people may wish to cut their resolution for refinement, which is fine by me as long as you note this and deposit all your data. Also, I'm told that British journals don't like the word "redundancy" since it has a negative connotation in their language. Try using "multiplicity" whenever possible. Although I admit I am still not sure how to re-phrase "highly redundant data set" without using more ink. -James Holton MAD Scientist Daniel Bonsor wrote: Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying?
[ccp4bb] Rsym problems...maybe???
Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying?
