[ccp4bb] high R factor calculated by sfcheck
Dear all, I have solved a 3.5ang structure with R/Rfree = 0.23/0.32 (refmac5.6 result). But when I used sfcheck to validate the coordinates and structure factors, I got a high R factor > 0.38 ! Could anybody tell me the reason? Is that possible to deposit the coordinate to PDB? Thank you very much!
Re: [ccp4bb] high temp factor in coot!
Dear Ed, Why the variance is the square of standard deviation? thank you very much! 在 2012年4月23日，20:53，Ed Pozharski 写道： > On Sun, 2012-04-22 at 12:47 +0530, Arka Chakraborty wrote: >> baverage program in ccp4 gave average bfactor of 25.0 for the residue >> but coot is showing 150! > > Variance is the square of standard deviation, thus var=150 means > sigmaB~12 in that particular residue. High, but not impossible. > > -- > I don't know why the sacrifice thing didn't work. > Science behind it seemed so solid. >Julian, King of Lemurs
Re: [ccp4bb] high temp factor in coot!
Dear Johan, "the standard deviation is defined as the square root of the variance." while "The standard deviation has the same unit as the values you're measuring." So we can say what's the unit of deviation? Is it the square of the unit of standard deviation? I always think that the unit of deviation is the same to the values we're measuring. Maybe I make a mistake... Thank you very much! On 04/24/2012 10:30 AM, Johan Hattne wrote: Hi Qixu; This is by definition--the standard deviation is defined as the square root of the variance. http://mathworld.wolfram.com/StandardDeviation.html The standard deviation has the same unit as the values you're measuring, which makes its interpretation a tad easier. // Best wishes; Johan On 23 Apr 2012, at 18:13, Qixu Cai wrote: Dear Ed, Why the variance is the square of standard deviation? thank you very much! 在 2012年4月23日，20:53，Ed Pozharski 写道： On Sun, 2012-04-22 at 12:47 +0530, Arka Chakraborty wrote: baverage program in ccp4 gave average bfactor of 25.0 for the residue but coot is showing 150! Variance is the square of standard deviation, thus var=150 means sigmaB~12 in that particular residue. High, but not impossible. -- I don't know why the sacrifice thing didn't work. Science behind it seemed so solid. Julian, King of Lemurs Postdoctoral Fellow @ Physical Biosciences Division __ Lawrence Berkeley National Laboratory * 1 Cyclotron Rd. Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055
Re: [ccp4bb] high temp factor in coot!
Dear Tim, Sorry about my typo. I just want to know what is the unit of variance when the standard deviation has the same unit as the values? What's the definition of variance actually? Thank you very much! 在 2012年4月24日 下午4:01，Tim Gruene 写道： > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Qixu, > > there is no contradiction in your quotes and what you are thinking: > * "The standard deviation has the same unit as the values you're > measuring." > * I always think that the unit of deviation is the same to the values > we're measuring. > > this fits, don't you see? > > Cheers, > Tim > > On 04/24/12 05:21, Qixu Cai wrote: > > Dear Johan, > > > > "the standard deviation is defined as the square root of the > > variance." while "The standard deviation has the same unit as the > > values you're measuring." > > > > So we can say what's the unit of deviation? Is it the square of the > > unit of standard deviation? > > > > I always think that the unit of deviation is the same to the > > values we're measuring. Maybe I make a mistake... > > > > Thank you very much! > > > > > > > > On 04/24/2012 10:30 AM, Johan Hattne wrote: > >> Hi Qixu; > >> > >> This is by definition--the standard deviation is defined as the > >> square root of the variance. > >> > >> http://mathworld.wolfram.com/StandardDeviation.html > >> > >> The standard deviation has the same unit as the values you're > >> measuring, which makes its interpretation a tad easier. > >> > >> // Best wishes; Johan > >> > >> > >> On 23 Apr 2012, at 18:13, Qixu Cai wrote: > >> > >>> Dear Ed, > >>> > >>> Why the variance is the square of standard deviation? > >>> > >>> thank you very much! > >>> > >>> > >>> 在 2012年4月23日，20:53，Ed Pozharski 写道： > >>> > >>>> On Sun, 2012-04-22 at 12:47 +0530, Arka Chakraborty wrote: > >>>>> baverage program in ccp4 gave average bfactor of 25.0 for > >>>>> the residue but coot is showing 150! > >>>> Variance is the square of standard deviation, thus var=150 > >>>> means sigmaB~12 in that particular residue. High, but not > >>>> impossible. > >>>> > >>>> -- I don't know why the sacrifice thing didn't work. Science > >>>> behind it seemed so solid. Julian, King of Lemurs > >> Postdoctoral Fellow @ Physical Biosciences Division > >> __ > >> > >> > Lawrence Berkeley National Laboratory * 1 Cyclotron Rd. > >> Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055 > >> > >> > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFPll3YUxlJ7aRr7hoRAoOfAJ4kh9s7MryWp9u53dFudMLzbCkT9wCfZ+gV > kTkvc8sma3Z8Ym/9n5JkuOw= > =d+ug > -END PGP SIGNATURE- >
[ccp4bb] P321 space group reindex problem
Dear all, I have a dataset at P321 space group. And I want to reindex from (h,k,l) to (k,h,l) or (h,k,-l), because I want to merge this dataset to the native dataset. At first, I used the "reindex" program in CCP4i, and got an error: (either for (k,h,l) or (h,k,-l)) Data line--- reindex HKL h, k, -l Data line--- end $TEXT:Warning: $$ comment $$ WARNING: Reindexing matrix INVERTS hand $$ REINDEX: You are NOT allowed to do this - Changing all signs in reindexing matrix Times: User: 0.0s System:0.0s Elapsed: 0:00 = Could you please tell me the reason? At last, I converted the mtz file to CNS format, and write a script to exchange the h and k, and converted to mtz file. When I tried to use "cad" to merge this dataset to the native dataset, if I chose "Automatically check and enforce consistent indexing between different files", the index would be changed back to the original index. Why? Thank you very much for your attention. Best wishes, Qixu Cai
[ccp4bb] MAD data process problem
Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai
Re: [ccp4bb] P321 space group reindex problem
Thanks for your help. How to use CAD to invert the hand? 2012/5/29 Ian Tickle > In principle there's no reason why you can't invert the hand of the > indices, as long as the program which does it also takes care to > convert any hand-dependent columns such as anomalous differences, > F+/F- etc in the appropriate manner at the same time. The program > will also need to convert any phase or phase-coefficient columns, but > it will have to do this anyway, even if the hand is not inverted, in > those cases where the space group contains screw axes (since then you > will get phase shifts on reindexing for certain subsets of > reflections). > > So if the data consist only of I's or F's without anomalous data or > phases then inverting the hand will have absolutely no effect (it's > called "Friedel's Law"). > > I note from the documentation that reindex will invert the hand if the > keyword 'LEFT' is supplied, though whether it then treats the > anomalous data and phases correctly is anyone's guess! > > The question is really whether it's likely ever to be _necessary_ to > invert the hand; this will depend on the reciprocal space asymmetric > unit chosen by the processing program. One could imagine a situation > where the a.u. chosen by one processing program was on a different > hand from the a.u. required by another. In such a situation you would > have no choice but to invert the hand of the indices, though I suspect > you would be better off doing it with CAD which will do it reliably, > rather than reindex which may not (judging by the comments in the > reindex code!). Whether such a situation ever occurs in practice, I > don't know, maybe not. > > Cheers > > -- Ian > > On 29 May 2012 09:57, Graeme Winter wrote: > > Hello Qixu Cai, > > > > What you want is a reindexing operator which permutes the axes rather > > than one which changes the sign of an axis. The easiest way to do this > > is with pointless: > > > > pointless hklin input.mtz hklref reference.mtz hklout output.mtz > > > > and let pointless figure out the right operation to use. You may find > > the following helpful: > > > > http://www.ccp4.ac.uk/html/reindexing.html > > > > Best wishes, > > > > Graeme > > > > On 29 May 2012 09:48, Qixu Cai wrote: > >> Dear all, > >> > >> I have a dataset at P321 space group. And I want to reindex from > (h,k,l) to > >> (k,h,l) or (h,k,-l), because I want to merge this dataset to the native > >> dataset. > >> At first, I used the "reindex" program in CCP4i, and got an error: > (either > >> for (k,h,l) or (h,k,-l)) > >> > >> > >> Data line--- reindex HKL h, k, -l > >> Data line--- end > >> > >> $TEXT:Warning: $$ comment $$ > >> WARNING: Reindexing matrix INVERTS hand > >> $$ > >> REINDEX: You are NOT allowed to do this - Changing all signs in > >> reindexing matrix > >> Times: User: 0.0s System:0.0s Elapsed: 0:00 > >> = > >> > >> Could you please tell me the reason? > >> > >> At last, I converted the mtz file to CNS format, and write a script to > >> exchange the h and k, and converted to mtz file. > >> When I tried to use "cad" to merge this dataset to the native dataset, > if I > >> chose "Automatically check and enforce consistent indexing between > different > >> files", > >> the index would be changed back to the original index. Why? > >> > >> Thank you very much for your attention. > >> > >> Best wishes, > >> > >> Qixu Cai >
Re: [ccp4bb] P321 space group reindex problem
Thanks for your help. How to override the warning? 2012/5/29 Mark J van Raaij > In different datasets of P321 crystals, when you index them separately, > the hand may be different and you may need to invert it for some. They > "prohibition" in reindex is really a warning, and can be overridden. > > Mark J van Raaij > Laboratorio M-4 > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > c/Darwin 3 > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 > http://www.cnb.csic.es/~mjvanraaij > > > > On 29 May 2012, at 13:52, Ian Tickle wrote: > > > In principle there's no reason why you can't invert the hand of the > > indices, as long as the program which does it also takes care to > > convert any hand-dependent columns such as anomalous differences, > > F+/F- etc in the appropriate manner at the same time. The program > > will also need to convert any phase or phase-coefficient columns, but > > it will have to do this anyway, even if the hand is not inverted, in > > those cases where the space group contains screw axes (since then you > > will get phase shifts on reindexing for certain subsets of > > reflections). > > > > So if the data consist only of I's or F's without anomalous data or > > phases then inverting the hand will have absolutely no effect (it's > > called "Friedel's Law"). > > > > I note from the documentation that reindex will invert the hand if the > > keyword 'LEFT' is supplied, though whether it then treats the > > anomalous data and phases correctly is anyone's guess! > > > > The question is really whether it's likely ever to be _necessary_ to > > invert the hand; this will depend on the reciprocal space asymmetric > > unit chosen by the processing program. One could imagine a situation > > where the a.u. chosen by one processing program was on a different > > hand from the a.u. required by another. In such a situation you would > > have no choice but to invert the hand of the indices, though I suspect > > you would be better off doing it with CAD which will do it reliably, > > rather than reindex which may not (judging by the comments in the > > reindex code!). Whether such a situation ever occurs in practice, I > > don't know, maybe not. > > > > Cheers > > > > -- Ian > > > > On 29 May 2012 09:57, Graeme Winter wrote: > >> Hello Qixu Cai, > >> > >> What you want is a reindexing operator which permutes the axes rather > >> than one which changes the sign of an axis. The easiest way to do this > >> is with pointless: > >> > >> pointless hklin input.mtz hklref reference.mtz hklout output.mtz > >> > >> and let pointless figure out the right operation to use. You may find > >> the following helpful: > >> > >> http://www.ccp4.ac.uk/html/reindexing.html > >> > >> Best wishes, > >> > >> Graeme > >> > >> On 29 May 2012 09:48, Qixu Cai wrote: > >>> Dear all, > >>> > >>> I have a dataset at P321 space group. And I want to reindex from > (h,k,l) to > >>> (k,h,l) or (h,k,-l), because I want to merge this dataset to the native > >>> dataset. > >>> At first, I used the "reindex" program in CCP4i, and got an error: > (either > >>> for (k,h,l) or (h,k,-l)) > >>> > >>> > >>> Data line--- reindex HKL h, k, -l > >>> Data line--- end > >>> > >>> $TEXT:Warning: $$ comment $$ > >>> WARNING: Reindexing matrix INVERTS hand > >>> $$ > >>> REINDEX: You are NOT allowed to do this - Changing all signs > in > >>> reindexing matrix > >>> Times: User: 0.0s System:0.0s Elapsed: 0:00 > >>> = > >>> > >>> Could you please tell me the reason? > >>> > >>> At last, I converted the mtz file to CNS format, and write a script to > >>> exchange the h and k, and converted to mtz file. > >>> When I tried to use "cad" to merge this dataset to the native dataset, > if I > >>> chose "Automatically check and enforce consistent indexing between > different > >>> files", > >>> the index would be changed back to the original index. Why? > >>> > >>> Thank you very much for your attention. > >>> > >>> Best wishes, > >>> > >>> Qixu Cai >
Re: [ccp4bb] P321 space group reindex problem
P3 is another possible alternate indexing? is that correct? 2012/5/29 Ian Tickle > Mark, thanks for pointing that out, I see it now: > > In P321 the only possible alternate indexing is (-h, -k, l): this is a > 2-fold || c which is an operator of the hexagonal lattice but is not > an equivalent reflection. > > The standard CCP4 a.u. is h = k, l >= 0 or h > k, k >= 0, so for > example (3,2,1) would be in the standard a.u. (3 > 2 and 2 >= 0). In > the alternate indexing this would be (-3, -2, 1); however it's > impossible to transform this to the a.u. with any non-inverting > equivalent. The only possibility is to invert the hand, i.e. to (3, > 2, -1) which is again in the a.u.. > > So the required re-indexing operator to match (3, 2, -1) with (3, 2, > 1) is (h, k, -l) which reindex won't allow without the LEFT keyword > (and you would be well-advised to avoid doing it with phase columns!). > > Cheers > > -- Ian > > On 29 May 2012 12:55, Mark J van Raaij wrote: > > In different datasets of P321 crystals, when you index them separately, > the hand may be different and you may need to invert it for some. They > "prohibition" in reindex is really a warning, and can be overridden. > > > > Mark J van Raaij > > Laboratorio M-4 > > Dpto de Estructura de Macromoleculas > > Centro Nacional de Biotecnologia - CSIC > > c/Darwin 3 > > E-28049 Madrid, Spain > > tel. (+34) 91 585 4616 > > http://www.cnb.csic.es/~mjvanraaij > > > > > > > > On 29 May 2012, at 13:52, Ian Tickle wrote: > > > >> In principle there's no reason why you can't invert the hand of the > >> indices, as long as the program which does it also takes care to > >> convert any hand-dependent columns such as anomalous differences, > >> F+/F- etc in the appropriate manner at the same time. The program > >> will also need to convert any phase or phase-coefficient columns, but > >> it will have to do this anyway, even if the hand is not inverted, in > >> those cases where the space group contains screw axes (since then you > >> will get phase shifts on reindexing for certain subsets of > >> reflections). > >> > >> So if the data consist only of I's or F's without anomalous data or > >> phases then inverting the hand will have absolutely no effect (it's > >> called "Friedel's Law"). > >> > >> I note from the documentation that reindex will invert the hand if the > >> keyword 'LEFT' is supplied, though whether it then treats the > >> anomalous data and phases correctly is anyone's guess! > >> > >> The question is really whether it's likely ever to be _necessary_ to > >> invert the hand; this will depend on the reciprocal space asymmetric > >> unit chosen by the processing program. One could imagine a situation > >> where the a.u. chosen by one processing program was on a different > >> hand from the a.u. required by another. In such a situation you would > >> have no choice but to invert the hand of the indices, though I suspect > >> you would be better off doing it with CAD which will do it reliably, > >> rather than reindex which may not (judging by the comments in the > >> reindex code!). Whether such a situation ever occurs in practice, I > >> don't know, maybe not. > >> > >> Cheers > >> > >> -- Ian > >> > >> On 29 May 2012 09:57, Graeme Winter wrote: > >>> Hello Qixu Cai, > >>> > >>> What you want is a reindexing operator which permutes the axes rather > >>> than one which changes the sign of an axis. The easiest way to do this > >>> is with pointless: > >>> > >>> pointless hklin input.mtz hklref reference.mtz hklout output.mtz > >>> > >>> and let pointless figure out the right operation to use. You may find > >>> the following helpful: > >>> > >>> http://www.ccp4.ac.uk/html/reindexing.html > >>> > >>> Best wishes, > >>> > >>> Graeme > >>> > >>> On 29 May 2012 09:48, Qixu Cai wrote: > >>>> Dear all, > >>>> > >>>> I have a dataset at P321 space group. And I want to reindex from > (h,k,l) to > >>>> (k,h,l) or (h,k,-l), because I want to merge this dataset to the > native > >>>> dataset. > >>>> At first, I used the "reindex" program in CCP4i, and got an error: &g
Re: [ccp4bb] P321 space group reindex problem
Dear all, thank you for your help. I think I must describe my case in detail. I collected a native dataset and two heavy atom derivant datasets （in fact, i don not know whether these two kind of heavy atom have soked into the crystal, i just collect the data to check it）. i processed all of three datasets with automar, and merged them by CAD. I used scaleit to get the Rfactor between datasets and got a strange result. the R factor between derivant1 and native is 26% and the R factor between derivant2 and native is 59%! so I think it may be the problem of index （space group is P321）. so i exchange the h and k of derivant2 by the some awk script and merged to native data by CAD. After scaleit analysis, I got the R factor 29% between derivant2 and native. Here is my questions, 1, at my case, is that right to invert the hand? is that the special problem of the P3 or p321 space group? 2, I have carryed out some suggestion of yours, such as use pointless （use native data as reference for derivant2 reindex）, or reindex the derivant2 dataset by （k, h, -l）, and I always got the high R factor 59% between derivant2 and native. Any suggestion? thanks a lot! Qixu Cai 在 2012-5-29，下午10:36，Laurent Maveyraud 写道： > Hi... and apologies ! > > I was a little quick in my answer... in P321, h k l and -h -k l are valid > indexing schemes... > It is in P3 that you can have h k l and k h -l > as Ian and Phil agreed on the BB ! > > sorry, > laurent > > Hi, > > you might have several possible spacegroups possible when processing your > data (at the indexation step). These will be based on the metrics of your > cell (vector length and angles). If you happen to have something like a = b, > and alpha=beta90° and gamma=120°, then it is likely that your crystal is > trigonal or hexagonal. > > You will have to wait until the scaling step (or pointless after integration) > in order to decide which spacegroup is the right one, based on the symmetry > operations in your dataset and on systematic absences. There you have to > choose between P3, P31, P32, P312, P321 in trigonal. > > When comparing two datasets from trigonal crystals, even for identical > crystals and hence identical spacegroups, you have different ways to index > your dataset... > In P321, one dataset might be indexed one way (eg. h k l), the other might be > index the other way (k h -l). When you compared this two dataset, they will > appear to be different, because both indexing schemes, although valid, are > not equivalent. > > Take one reflection; e.g. 3 2 1 from your crystal A. The very same reflection > will be indexed 2 3 -1 for your crystal B, and the one indexed 3 2 1 for > crytal B will not be equivalent to the 3 2 1 reflection from crystal A. > If you try to merge your two datasets, you will have huge Rmerge, because you > are trying to average non equivalent reflections. > > You will have to ensure that the same indexing scheme is used for both > datasets, eg reindex B using the reindex k h -l command in reindex, before > being able to merge A and B. > > hope this helps... please feel free to as if I am not clear... > > best regards > > laurent > > Le 29/05/2012 16:03, Qixu Cai a écrit : >> P3 is another possible alternate indexing? is that correct? >> >> >> 2012/5/29 Ian Tickle mailto:ianj...@gmail.com>> >> >>Mark, thanks for pointing that out, I see it now: >> >>In P321 the only possible alternate indexing is (-h, -k, l): this is a >>2-fold || c which is an operator of the hexagonal lattice but is not >>an equivalent reflection. >> >>The standard CCP4 a.u. is h = k, l >= 0 or h > k, k >= 0, so for >>example (3,2,1) would be in the standard a.u. (3 > 2 and 2 >= 0). In >>the alternate indexing this would be (-3, -2, 1); however it's >>impossible to transform this to the a.u. with any non-inverting >>equivalent. The only possibility is to invert the hand, i.e. to (3, >>2, -1) which is again in the a.u.. >> >>So the required re-indexing operator to match (3, 2, -1) with (3, 2, >>1) is (h, k, -l) which reindex won't allow without the LEFT keyword >>(and you would be well-advised to avoid doing it with phase columns!). >> >>Cheers >> >>-- Ian >> >>On 29 May 2012 12:55, Mark J van Raaij ><mailto:mjvanra...@cnb.csic.es>> wrote: >> > In different datasets of P321 crystals, when you index them >>separately, the hand may be different and you may need to invert it >>for some. They "prohibition" in reindex is really a warning, and can >>be overrid
[ccp4bb] PyMol APBS Tools ERRORS
Dear all, When I use APBS Tools2 plugin for PyMol, there are some errors. --- Error: 6 CmdException Exception in Tk callback Function: at 0x4080140> (type: ) Args: () Traceback (innermost last): File "/usr/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", line 153, in command=lambda self=self, name=name: self._doCommand(name)) File "/usr/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwDialog.py", line 132, in _doCommand return command(name) File "/usr/lib64/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line 974, in execute good = self.generatePymolPqrFile() File "/usr/lib64/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line 1596, in generatePymolPqrFile assign.missing_c_termini(sel) File "/usr/lib64/python2.7/site-packages/chempy/champ/assign.py", line 39, in missing_c_termini while cmd.pop(tmp_sele2,tmp_sele1)>0: # complete the carboxy terminus File "/usr/lib64/python2.7/site-packages/pymol/selecting.py", line 162, in pop if _self._raising(r,_self): raise pymol.CmdException CmdException: --- Can anybody tell me how to solve these problems? Thank you very much! -- Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China **from thunderbird**
[ccp4bb] low resolution refinement
Dear all, Recently, I refine two low resolution structures in refmac 5.5. Their resolutions are 3A and 3.5A respectively. For 3A structure, after MR by phaser and rigidbody refinement&restraint refinement by refmac5.5, I got R factor 25% and R free 35%. And then each time, after my model building in coot and restraint refinement by refmac 5.5, the R factor stays 25%, but R free increases to 38%, even 39%. For 3.5A structure, the R factor stays 27%, but R free increases from 37% to 42% after my slightly model building in coot. Could you help me to find the reason? Maybe the reason is the overfit of the structure? I found that new version of refmac 5.6 has many new features for low resolution refinement, such as jelly boy, secondary structure restraints. But I don't know how to use these new features in old version ccp4i (6.1.13)? I also used phenix.refine with the "reference model" ( I have high resolution model for one domain of the low resolution protein) and "secondary structure restraints", but it seams the same. Any suggestion? BTW, is that simulator annealing not suitable for low resolution structure? I used the simulator annealing method of CNS and phenix.refine, but the geometry of the structure is always destroyed seriously. Could you help me? Thank you very much!
Re: [ccp4bb] / or
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Calculate_average_I/sigma_from_.sca_file Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China **from thunderbird** On 02/13/2014 12:20 AM, Ronald E Stenkamp wrote: How did people get when using HKL2000? Ron On Wed, 12 Feb 2014, Phil Evans wrote: On 12 Feb 2014, at 11:43, Cai Qixu wrote: Dear all, Does the I/sigmaI in “Table 1” mean for / or ? Thanks for your answer. Best wishes, Qixu Cai
[ccp4bb] difference between polar angle and eulerian angle
Dear all, From the definition of CCP4 (http://www.ccp4.ac.uk/html/rotationmatrices.html), the polar angle (ϕ, ω, κ) can be visualised as rotation ϕ about Z, rotation ω about the new Y, rotation κ about the new Z. It seems the same as the ZXZ convention of eulerian angle definition. What's the difference between the CCP4 polar angle definition and eulerian angle ZXZ definition? And what's the definition of polar angle XYK convention in GLRF program? Thank you very much! Best wishes, -- Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China **from thunderbird**
Re: [ccp4bb] P321 space group reindex problem
At first, I processed the data at P3 space group. But after phenix.xtriage analysis, the Xtriage told me the space group must be P321, so I used P321 to process my data, and got an acceptable Rmerge. Qixu Cai 2012/5/29 Phil Evans > How do you know the point group is 321? What does Pointless tell you if > you put in the unmerged data? > > Despite some of the things said earlier (by me!), the possible indexing > schemes in 321 are h,k,l and -h,-k,l > If that doesn't work, it suggests that the point group is a lower symmetry > eg P3 > > Phil > > > On 29 May 2012, at 16:29, Qixu Cai wrote: > > > Dear all, > > > > thank you for your help. > > > > I think I must describe my case in detail. I collected a native dataset > and two heavy atom derivant datasets （in fact, i don not know whether these > two kind of heavy atom have soked into the crystal, i just collect the data > to check it）. > > > > i processed all of three datasets with automar, and merged them by CAD. > I used scaleit to get the Rfactor between datasets and got a strange > result. the R factor between derivant1 and native is 26% and the R factor > between derivant2 and native is 59%! > > > > so I think it may be the problem of index （space group is P321）. so i > exchange the h and k of derivant2 by the some awk script and merged to > native data by CAD. After scaleit analysis, I got the R factor 29% between > derivant2 and native. > > > > Here is my questions, > > > > 1, at my case, is that right to invert the hand? is that the special > problem of the P3 or p321 space group? > > > > 2, I have carryed out some suggestion of yours, such as use pointless > （use native data as reference for derivant2 reindex）, or reindex the > derivant2 dataset by （k, h, -l）, and I always got the high R factor 59% > between derivant2 and native. > > > > Any suggestion? > > > > thanks a lot! > > > > Qixu Cai > > > > > > 在 2012-5-29，下午10:36，Laurent Maveyraud 写道： > > > >> Hi... and apologies ! > >> > >> I was a little quick in my answer... in P321, h k l and -h -k l are > valid indexing schemes... > >> It is in P3 that you can have h k l and k h -l > >> as Ian and Phil agreed on the BB ! > >> > >> sorry, > >> laurent > >> > >> Hi, > >> > >> you might have several possible spacegroups possible when processing > your data (at the indexation step). These will be based on the metrics of > your cell (vector length and angles). If you happen to have something like > a = b, and alpha=beta90° and gamma=120°, then it is likely that your > crystal is trigonal or hexagonal. > >> > >> You will have to wait until the scaling step (or pointless after > integration) in order to decide which spacegroup is the right one, based on > the symmetry operations in your dataset and on systematic absences. There > you have to choose between P3, P31, P32, P312, P321 in trigonal. > >> > >> When comparing two datasets from trigonal crystals, even for identical > crystals and hence identical spacegroups, you have different ways to index > your dataset... > >> In P321, one dataset might be indexed one way (eg. h k l), the other > might be index the other way (k h -l). When you compared this two dataset, > they will appear to be different, because both indexing schemes, although > valid, are not equivalent. > >> > >> Take one reflection; e.g. 3 2 1 from your crystal A. The very same > reflection will be indexed 2 3 -1 for your crystal B, and the one indexed 3 > 2 1 for crytal B will not be equivalent to the 3 2 1 reflection from > crystal A. > >> If you try to merge your two datasets, you will have huge Rmerge, > because you are trying to average non equivalent reflections. > >> > >> You will have to ensure that the same indexing scheme is used for both > datasets, eg reindex B using the reindex k h -l command in reindex, before > being able to merge A and B. > >> > >> hope this helps... please feel free to as if I am not clear... > >> > >> best regards > >> > >> laurent > >> > >> Le 29/05/2012 16:03, Qixu Cai a écrit : > >>> P3 is another possible alternate indexing? is that correct? > >>> > >>> > >>> 2012/5/29 Ian Tickle mailto:ianj...@gmail.com>> > >>> > >>> Mark, thanks for pointing that out, I see it now: > >>> > >>> In P321 the only possible alternate indexing is (-h, -k, l): this is > a > >>> 2-fold || c which is
Re: [ccp4bb] MAD data process problem
Thank you very much for your reply. In my own understanding, We collect the peak dataset, because of the large F'', and we can get strong anomalous signal. We collect the edge dataset, because of the large F', and combined with the remote dataset, we can use the method just like SIR to get some information about the phase. so I think for peak dataset, anomalous processing is necessary, and for edge and remote dataset, anomalous processing is not necessary. Is my understanding correct? Thank you very much for your help. Best wish, Qixu Cai 2012/5/29 Tim Gruene > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Qixu Cai, > > MAD phasing is based on the comparison of Bijvoet-pairs, i.e. I(hkl) > with I(-h-k-l), both within one data set and between data sets. > Therefore you might get better results if your integration program does > not assume Friedel-pairs to have identical intensities, even though > the difference is probably only marginal (integration programs do not > merge data). > So it is safest click on 'anomalous' for all data sets involved . > > Tim > > On 05/29/12 11:11, Qixu Cai wrote: > > Dear all, > > > > Sorry for the question from MAD beginner. > > > > When we process the MAD datasets, including the peak-data, > > edge-data and remote-data, which datasets need to be process with > > anomalous? > > > > I know peak-data obviously need data processing with anomalous, but > > what about edge-data and remote-data when we want to use MAD > > method? > > > > Thank you very much! > > > > Best wishes, > > > > Qixu Cai > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFPxJfaUxlJ7aRr7hoRAm3EAKCKkyvT8z0wg6MFjflkHkiq8RR5GQCgyvF3 > lOIOLypSzCcN3N6OR/3NcC8= > =m6ax > -END PGP SIGNATURE- >
Re: [ccp4bb] P321 space group reindex problem
Why the 29% Rfactor indicate the derivatives are not isomorphous to native dataset? Native dataset cell constant: 181.39 181.39 110.217 90 90 120 derivative1 cell constant: 181.909 181.909 109.62 90 90 120Rfactor to native: 26% derivative2 cell constant: 181.527 181.527 109.32 90 90 120Rfactor to native: 29% The Rfactor at low resolution is larger than in high resolution. Could you please to help me figure out where the heavy atoms had been soaked into the crystal? Thank you very much. Best wishe, Qixu Cai 2012/5/30 Laurent Maveyraud > Hi, > > it is therefore likely that your spacegroup is really P321... hopefully, > your data set is not twinned, did you check that ? > > You are left with 2 possible indexing schemes, as already mentionned. Chek > scaling derivative / native scaling for each indexation of the derivative : > the lowest Rfactor will likely indicate the right one. > It appears that you end up with Rfactor of about 29 %, which suggest that > your derivatives are not isomorphous to your native dataset. How do cell > parameters compare for each data set ? > Check also how the Rfactor varies with resolution, you might still have > usefull phasing info at low resolution. > > hope this helps > > laurent > > > > Le 30/05/2012 07:50, Qixu Cai a écrit : > >> At first, I processed the data at P3 space group. But after >> phenix.xtriage analysis, the Xtriage told me the space group must be >> P321, so I used P321 to process my data, and got an acceptable Rmerge. >> >> Qixu Cai >> >> >> >> 2012/5/29 Phil Evans mailto:p...@mrc-lmb.cam.ac.uk >> >**> >> >> >>How do you know the point group is 321? What does Pointless tell you >>if you put in the unmerged data? >> >>Despite some of the things said earlier (by me!), the possible >>indexing schemes in 321 are h,k,l and -h,-k,l >>If that doesn't work, it suggests that the point group is a lower >>symmetry eg P3 >> >>Phil >> >> >>On 29 May 2012, at 16:29, Qixu Cai wrote: >> >> > Dear all, >> > >> > thank you for your help. >> > >> > I think I must describe my case in detail. I collected a native >>dataset and two heavy atom derivant datasets （in fact, i don not >>know whether these two kind of heavy atom have soked into the >>crystal, i just collect the data to check it）. >> > >> > i processed all of three datasets with automar, and merged them >>by CAD. I used scaleit to get the Rfactor between datasets and got a >>strange result. the R factor between derivant1 and native is 26% and >>the R factor between derivant2 and native is 59%! >> > >> > so I think it may be the problem of index （space group is >>P321）. so i exchange the h and k of derivant2 by the some awk >>script and merged to native data by CAD. After scaleit analysis, I >>got the R factor 29% between derivant2 and native. >> > >> > Here is my questions, >> > >> > 1, at my case, is that right to invert the hand? is that the >>special problem of the P3 or p321 space group? >> > >> > 2, I have carryed out some suggestion of yours, such as use >>pointless （use native data as reference for derivant2 reindex）, or >>reindex the derivant2 dataset by （k, h, -l）, and I always got the >>high R factor 59% between derivant2 and native. >> > >> > Any suggestion? >> > >> > thanks a lot! >> > >> > Qixu Cai >> > >> > >> > 在 2012-5-29，下午10:36，Laurent Maveyraud >>> <mailto:laurent.maveyraud@**ipbs.fr>> >> 写道： >> >> > >> >> Hi... and apologies ! >> >> >> >> I was a little quick in my answer... in P321, h k l and -h -k l >>are valid indexing schemes... >> >> It is in P3 that you can have h k l and k h -l >> >> as Ian and Phil agreed on the BB ! >> >> >> >> sorry, >> >> laurent >> >> >> >> Hi, >> >> >> >> you might have several possible spacegroups possible when >>processing your data (at the indexation step). These will be based >>on the metrics of your cell (vector length and angles). If you >>happen to have something like a = b, and alpha=beta90° and >>gamma=120°, then it is likely that your
Re: [ccp4bb] P321 space group reindex problem
Thank you for your remind of the twin problem. I checked all of the datasets by Xtriage, and found that the native is not twinned, but the derivant1 and derivant2 are both twinned. So is the Rfactor between derivants and native useful for the judgement of the success of the heavy atom soaking? Thanks. Best wishes, Qixu Cai 2012/5/30 Laurent Maveyraud > Hi, > > it is therefore likely that your spacegroup is really P321... hopefully, > your data set is not twinned, did you check that ? > > You are left with 2 possible indexing schemes, as already mentionned. Chek > scaling derivative / native scaling for each indexation of the derivative : > the lowest Rfactor will likely indicate the right one. > It appears that you end up with Rfactor of about 29 %, which suggest that > your derivatives are not isomorphous to your native dataset. How do cell > parameters compare for each data set ? > Check also how the Rfactor varies with resolution, you might still have > usefull phasing info at low resolution. > > hope this helps > > laurent > > > > Le 30/05/2012 07:50, Qixu Cai a écrit : > >> At first, I processed the data at P3 space group. But after >> phenix.xtriage analysis, the Xtriage told me the space group must be >> P321, so I used P321 to process my data, and got an acceptable Rmerge. >> >> Qixu Cai >> >> >> >> 2012/5/29 Phil Evans mailto:p...@mrc-lmb.cam.ac.uk >> >**> >> >> >>How do you know the point group is 321? What does Pointless tell you >>if you put in the unmerged data? >> >>Despite some of the things said earlier (by me!), the possible >>indexing schemes in 321 are h,k,l and -h,-k,l >>If that doesn't work, it suggests that the point group is a lower >>symmetry eg P3 >> >>Phil >> >> >>On 29 May 2012, at 16:29, Qixu Cai wrote: >> >> > Dear all, >> > >> > thank you for your help. >> > >> > I think I must describe my case in detail. I collected a native >>dataset and two heavy atom derivant datasets （in fact, i don not >>know whether these two kind of heavy atom have soked into the >>crystal, i just collect the data to check it）. >> > >> > i processed all of three datasets with automar, and merged them >>by CAD. I used scaleit to get the Rfactor between datasets and got a >>strange result. the R factor between derivant1 and native is 26% and >>the R factor between derivant2 and native is 59%! >> > >> > so I think it may be the problem of index （space group is >>P321）. so i exchange the h and k of derivant2 by the some awk >>script and merged to native data by CAD. After scaleit analysis, I >>got the R factor 29% between derivant2 and native. >> > >> > Here is my questions, >> > >> > 1, at my case, is that right to invert the hand? is that the >>special problem of the P3 or p321 space group? >> > >> > 2, I have carryed out some suggestion of yours, such as use >>pointless （use native data as reference for derivant2 reindex）, or >>reindex the derivant2 dataset by （k, h, -l）, and I always got the >>high R factor 59% between derivant2 and native. >> > >> > Any suggestion? >> > >> > thanks a lot! >> > >> > Qixu Cai >> > >> > >> > 在 2012-5-29，下午10:36，Laurent Maveyraud >>> <mailto:laurent.maveyraud@**ipbs.fr>> >> 写道： >> >> > >> >> Hi... and apologies ! >> >> >> >> I was a little quick in my answer... in P321, h k l and -h -k l >>are valid indexing schemes... >> >> It is in P3 that you can have h k l and k h -l >> >> as Ian and Phil agreed on the BB ! >> >> >> >> sorry, >> >> laurent >> >> >> >> Hi, >> >> >> >> you might have several possible spacegroups possible when >>processing your data (at the indexation step). These will be based >>on the metrics of your cell (vector length and angles). If you >>happen to have something like a = b, and alpha=beta90° and >>gamma=120°, then it is likely that your crystal is trigonal or >>hexagonal. >> >> >> >> You will have to wait until the scaling step (or pointless after >>integration) in order to decide which spacegroup is the righ
[ccp4bb] PHENIX: sequence files input problem
Dear all, Sorry for the non-CCP4 question. My crystal is a complex of two proteins. I use Se-Met SAD method to solve the structure, and only one of the proteins is Se-Met protein. When I use phenix.autobuild to auto-build the model, how do I input the sequences? in a file or two files? And is that necessary to specify the location of MSE? Thanks a lot for your help. Qixu Cai
[ccp4bb] refmac5.7 refine pesudo-translational symmetry
Dear all, Can I use the "twin refinement" to refine the pesudo-translational symmetry dataset? Thanks a lot for your help. Best wishes, Qixu Cai
Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry
It's a P212121 dataset. I have used phaser to find four solution in ASU. This is the phaser log file: PEUDO-TRANSLATIONAL NCS VECTOR -- Space Group : P 21 21 21 Patterson Symmetry: P m m m Resolution of All Data (Number):2.45 49.00 (22968) Resolution of Patterson (Number): 5.00 9.99 (2364) There were 2 non-origin distinct peaks (i.e. more than 15 angstroms from the origin) 84.1% origin: FRAC 0.500 0.000 0.250 (ORTH 32.00.0 32.2) 72.2% origin: FRAC 0.000 0.000 0.500 (ORTH0.00.0 64.4) More than one pseudo-translational ncs vector found Correction factors will not be applied PS: I have used phenix.xtrige and found the p-value of pseudo-translational ncs is very little, which indicates the exist of the pseudo-translational ncs. And no twin found in this dataset. Now the problem is two in the four molecules of an ASU have worse electron density than the other two molecules. And after rigidbody and restraint refinement by refmac without "twin refinement", the R/Rfree is a little high (0.33/0.36). And if I turn on the "twin refinement" in refmac, the R/Rfree is 0.30/0.33. So, my question is, there is not twin in my data but pseudo-translational ncs, is it suitable to use "twin refinement" in refmac, which has a good R/Rfree result. Thanks a lot for your help. Best wishes, Qixu Cai 2012/7/31, Eleanor Dodson : > More details - what do you mean by pesudo-translational symmetry ? > Are there two molecules related by a translation vector? or its it > something more complicated? > Eleanor > > On 31 July 2012 10:47, Qixu Cai wrote: > >> Dear all, >> >> Can I use the "twin refinement" to refine the pesudo-translational >> symmetry dataset? >> >> Thanks a lot for your help. >> >> Best wishes, >> >> Qixu Cai >> > -- Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China
[ccp4bb] rigidbody group in refmac5
Dear all, When we are running the rigidbody refinement of refmac5, if we do not assign the rigidbody group in CCP4i GUI, what's the default rigidbody group in refmac5? Is it a rigidbody for each chain? Thanks a lot.
Re: [ccp4bb] rigidbody group in refmac5
Dear Lakshmanan Govindasamy, I cannot find the related information in refmac5 document. Could you please help me? Thanks. Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China **from thunderbird** On 08/01/2012 04:43 AM, Lakshmanan Govindasamy wrote: refer CCP4 Refmac5 manual for rigid body refinement instruction and clarification. Govinda On Tue, Jul 31, 2012 at 11:35 AM, Qixu Cai <mailto:caiq...@gmail.com>> wrote: Dear all, When we are running the rigidbody refinement of refmac5, if we do not assign the rigidbody group in CCP4i GUI, what's the default rigidbody group in refmac5? Is it a rigidbody for each chain? Thanks a lot.
Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry
Dear Randy, Thanks very much for your detailed explanation and helpful advice. I have run the phaser job just as you have said. This is the result. The resolution of this dataset is 2.45A. = I added the three commands to phaser job for all alternative space group of P212121: TNCS USE ON TNCS NMOL 4 TNCS PATT PERCENT 80.0 The phaser got a SINGLE solution for space group P22121, and Rval=88.2 SOLU SET RFZ=14.5 TFZ=22.3 PAK=0 +TNCS PAK=0 +TNCS PAK=0 +TNCS PAK=0 LLG=2565LLG=4322 SOLU SPAC P 2 21 21 SOLU 6DIM ENSE ensemble1 EULER 91.7 89.4 90.3 FRAC 0.49 0.51 0.99 BFAC 0.00 SOLU 6DIM ENSE ensemble1 EULER 269.3 89.4 90.2 FRAC -0.01 -0.00 0.74 BFAC 0.00 SOLU 6DIM ENSE ensemble1 EULER 269.0 89.1 90.0 FRAC 0.49 -0.00 1.00 BFAC 0.00 SOLU 6DIM ENSE ensemble1 EULER 91.5 89.3 90.2 FRAC 0.99 0.51 0.74 BFAC 0.00 After 50 cycles rigidbody refinement, R/Rfree=0.36/0.37 After 50 cycles restraint refinement (with jellybody refine and twin refine), R/Rfree=0.31/0.35 After several cycles of coot model building and restraint refinement, R/Rfree=0.27/0.31 After finding waters, R/Rfree=0.2478/0.2984 === If I run phaser job without those three added commands, the phaser got single solution at P21212 space group (Rval=0.3%): SOLU SET RFZ=17.0 TFZ=20.1 PAK=0 LLG=457 TFZ==16.2 RFZ=16.3 TFZ=62.1 PAK=0 LLG=2599 TFZ==19.8 (& TFZ=59.0 PAK=0 LLG=2403) LLG+=(2608 & 4349) LLG=4200 TFZ==22.2 PAK=0 RFZ=10.8 TFZ=56.4 PAK=0 LLG=5751 TFZ==22.5 LLG=9274 TFZ==27.5 SOLU SPAC P 21 21 2 SOLU 6DIM ENSE ensemble1 EULER 90.0 90.7 270.1 FRAC -0.00 0.26 0.13 BFAC -4.09 SOLU 6DIM ENSE ensemble1 EULER 271.2 89.4 90.3 FRAC 0.01 0.24 -0.38 BFAC -3.00 SOLU 6DIM ENSE ensemble1 EULER 270.3 90.8 270.1 FRAC 0.50 -0.25 -0.12 BFAC -1.25 SOLU 6DIM ENSE ensemble1 EULER 87.5 90.6 270.4 FRAC 0.02 0.26 -0.37 BFAC 11.58 And the electron density is worse than the P22121 solution. == Just as I have said last email, I can also get single solution at P212121 space group, and after 50 cycles rigidbody refinement and 50 cycles restraint refinement with jellybody and twin, I can get R/Rfree=0.30/0.33. But the electron density is worse than the P22121 solution, so I do not carry out the model building in coot. === My questiones: 1) Is the P22121 solution is my correct solution? These three solutions really confused me. 2) Why the R/Rfree is high even after I have good electron density and have found waters? (R/Rfree=0.478/0.2984 for 2.45A data) 3) What's the function of the command "TNCS USE ON"? Is it necessary? 4) I found if I used twin refinement in refmac5, the R/Rfree would decrease about 0.02 comparing to without twinn refinement. Is it reasonable? Is there any tNCS refinement options in refmac? Thanks for your help. Best wishes, Qixu Cai 2012/7/31 Randy Read > Hi, > > The second Patterson peak is twice the first (considering lattice > translations, where 1 is equivalent to 0 modulo 1), and then if you triple > the first vector you'll get minus the first vector (again considering > lattice translations, i.e. 3/4 is equal to 1 - 1/4 which is equivalent to > -1/4), which is equivalent by symmetry to the first vector so wouldn't > appear in the peak list. So the Patterson indicates 4 copies separated by > 0, 1, 2 and 3 times the top Patterson vector, in approximately the same > orientation. > > We've haven't fully dealt with the complications of multiple tNCS-related > copies in Phaser yet, but for this type of case there is a reasonable > treatment. You should add two commands to the Phaser job: > > TNCS NMOL 4 > TNCS PATT PERCENT 80 > > The first says that the Patterson translation is repeated 4 times, and the > second will cause the second Patterson peak to be ignored. > > I'd suggest repeating the Phaser run with these commands and making sure > that you end up with the same solution as you got when the tNCS was > ignored. When tNCS is ignored, it's possible to end up with a solution > that is only partially correct, which would be one explanation for having > some molecules that look better in density than others. > > Best wishes, > > Randy Read > > On 31 Jul 2012, at 13:11, Qixu Cai wrote: > > > It's a P212121 dataset. I have used phaser to find four solution in ASU. > > > > This is the phaser log file: > > > > PEUDO-TRANSLATIONAL NCS VECTOR > > -- > > > > Space Group : P 21 21 21 > > Patterso
Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry
Dear Eleanor, The cell dimensions of the dataset with tNCS are 63.995 75.459 128.860 90.00 90.00 90.00 in P 2 21 21 space group. But for the other dataset without tNCS of the same protein, the cell dimensions are 64.203 65.319 76.443 90.00 90.00 90.00 in C 2 2 21. So the cell volume of C2221 is 25% of the P22121. But I cannot index the data to C2221 space group. Thanks a lot. Best wishes, Qixu Cai 2012/8/1 Eleanor Dodson > Are your unit cell and SG correct? I think you maybe should reindex to get > a cell volume 25% of this one, and maybe SG P21 > That patterson peak is enormous.. > Eleanor > On 1 Aug 2012, at 08:45, Qixu Cai wrote: > > Dear Randy, > > Thanks very much for your detailed explanation and helpful advice. I have > run the phaser job just as you have said. This is the result. > > The resolution of this dataset is 2.45A. > > = > > I added the three commands to phaser job for all alternative space groupof > P212121: > > TNCS USE ON > TNCS NMOL 4 > TNCS PATT PERCENT 80.0 > > The phaser got a SINGLE solution for space group P22121, and Rval=88.2 > >SOLU SET RFZ=14.5 TFZ=22.3 PAK=0 +TNCS PAK=0 +TNCS PAK=0 +TNCS PAK=0 > LLG=2565LLG=4322 >SOLU SPAC P 2 21 21 >SOLU 6DIM ENSE ensemble1 EULER 91.7 89.4 90.3 FRAC 0.49 0.51 0.99 BFAC > 0.00 >SOLU 6DIM ENSE ensemble1 EULER 269.3 89.4 90.2 FRAC -0.01 -0.00 0.74 > BFAC 0.00 >SOLU 6DIM ENSE ensemble1 EULER 269.0 89.1 90.0 FRAC 0.49 -0.00 1.00 > BFAC 0.00 >SOLU 6DIM ENSE ensemble1 EULER 91.5 89.3 90.2 FRAC 0.99 0.51 0.74 BFAC > 0.00 > > After 50 cycles rigidbody refinement, R/Rfree=0.36/0.37 > After 50 cycles restraint refinement (with jellybody refine and twin > refine), R/Rfree=0.31/0.35 > After several cycles of coot model building and restraint refinement, > R/Rfree=0.27/0.31 > After finding waters, R/Rfree=0.2478/0.2984 > > === > If I run phaser job without those three added commands, the phaser got > single solution at P21212 space group (Rval=0.3%): > > >SOLU SET RFZ=17.0 TFZ=20.1 PAK=0 LLG=457 TFZ==16.2 RFZ=16.3 TFZ=62.1 > PAK=0 > LLG=2599 TFZ==19.8 (& TFZ=59.0 PAK=0 LLG=2403) LLG+=(2608 & 4349) > LLG=4200 > TFZ==22.2 PAK=0 RFZ=10.8 TFZ=56.4 PAK=0 LLG=5751 TFZ==22.5 LLG=9274 > TFZ==27.5 >SOLU SPAC P 21 21 2 >SOLU 6DIM ENSE ensemble1 EULER 90.0 90.7 270.1 FRAC -0.00 0.26 0.13 > BFAC -4.09 >SOLU 6DIM ENSE ensemble1 EULER 271.2 89.4 90.3 FRAC 0.01 0.24 -0.38 > BFAC -3.00 >SOLU 6DIM ENSE ensemble1 EULER 270.3 90.8 270.1 FRAC 0.50 -0.25 -0.12 > BFAC -1.25 >SOLU 6DIM ENSE ensemble1 EULER 87.5 90.6 270.4 FRAC 0.02 0.26 -0.37 > BFAC 11.58 > > And the electron density is worse than the P22121 solution. > > == > Just as I have said last email, I can also get single solution at P212121 > space group, > > and after 50 cycles rigidbody refinement and 50 cycles restraint > refinement with jellybody and twin, I can get R/Rfree=0.30/0.33. > > But the electron density is worse than the P22121 solution, so I do not > carry out the model building in coot. > > === > > My questiones: > > 1) Is the P22121 solution is my correct solution? These three solutions > really confused me. > > 2) Why the R/Rfree is high even after I have good electron density and > have found waters? (R/Rfree=0.478/0.2984 for 2.45A data) > > 3) What's the function of the command "TNCS USE ON"? Is it necessary? > > 4) I found if I used twin refinement in refmac5, the R/Rfree would > decrease about 0.02 comparing to without twinn refinement. Is it > reasonable? Is there any tNCS refinement options in refmac? > > Thanks for your help. > > Best wishes, > > Qixu Cai > > > > > 2012/7/31 Randy Read > >> Hi, >> >> The second Patterson peak is twice the first (considering lattice >> translations, where 1 is equivalent to 0 modulo 1), and then if you triple >> the first vector you'll get minus the first vector (again considering >> lattice translations, i.e. 3/4 is equal to 1 - 1/4 which is equivalent to >> -1/4), which is equivalent by symmetry to the first vector so wouldn't >> appear in the peak list. So the Patterson indicates 4 copies separated by >> 0, 1, 2 and 3 times the top Patterson vector, in approximately the same >> orientation. >> >> We've haven't fully dealt with the complications of multiple tNCS-related >> copies in Phaser y
Re: [ccp4bb] MR with Phaser
C222 means 2 possible space groups C222 and C2221. P222 means 8 possible space groups. ps: I don't understand the C2221A and C222A listed by phaser when I chose the "alternative space groups (listed)" option in C222 space group, because when I chose "all alternative space group", only C222 and C2221 were test, not C2221A and C222A. 2012/8/3 Roger Rowlett > A few thoughts: > >1. Search for all possible space groups (e.g., P2 and P21 in this >case). Be happy it isn't C222, which means 8 possible combinations of screw >axes to search! As mentioned already, P21 is far more common than P2. I >think P21 is one of the most common space groups in protein > crystallography. > 2. How are you determining how many copies of the search model go in >the ASU? It is not necessarily one biological unit, or an integral number >of biological units. Run a cell content analysis in Phaser (e.g. Matthews >probability calculator) and start there, but consider the results a >suggestion only. For larger ASUs, the predicted number is not very >accurate. "Six" might actually be 4 or 8 chains. > 3. Look at the crystal packing in Pymol, Coot, or in you favorite >tool. You can do this by enabling a large symmetry molecule radius. If you >see a regular lattice of proteins with nice solvent channels and >protein-protein contacts, things are looking up. (But you can be fooled >into a premature victory at times.) > 4. Partial Phaser solutions may provide a big hint about how many >molecules are in the ASU when packing is examined. Often the placement of >the missing molecules is quite obvious, as it completes a solvent channel >or fills in symmetrical protein-protein contacts. > 5. Finally, look at the maps. Crappy maps probably mean the wrong >space group, especially if chains don't pack well. Good maps with good >packing usually mean you are on the right track. > > Cheers and good luck, > > ___ > Roger S. Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 > fax: (315)-228-7935 > email: rrowl...@colgate.edu > > On 8/1/2012 2:27 PM, Uma Ratu wrote: > > Dear All: > > I try to use Phaser to solve the structure by Molecular Replacement. > > The data set is collected @180 degree. I process the data using HKL, and > have resonable good score: rejection (0.05), Linear R-factor (0.038), > completeness (98.3), resolution (50-1.5). > > I then use Phaser to do MR. The parameter setting are: > automated search > components in asymmetric unit;number of residue 1332; number in > asymmetric unit 1 > perform search search using "ensemble1" number of copies to search for 4 > > The protein is in tetramer form. I define this by using the residue number > (1332) which is 4 x monomer. > > After run, Phaser only gave 9 partial solutions, and no solution with all > components. The resulted PDB contains only dimer form of the protein, not > the tetramer. And the first TFZ score is around 2.5, which is too low for > MR. > > I have the report file of data processing and the summary of Phaser > attached. > > Could you please advice which part is wrong, why can I get the tetramer > form of the protein? > > Thank you > > Uma > > >
[ccp4bb] refmac5 problem
Dear all, What's the difference between "no prior phase information", "phase and FOM", Hendrickson-Lattman coefficients", and "SAD data directly" in the refmac5 GUI of CCP4i? I have a SAD dataset and solve the phase by phenix.autosol. Now I want to refine the structure by refmac5, which kind of input above I should choose? Another question is in the "Refinement Parameters" of refmac5. What's the meaning of "Use experimental sigmas to weight Xray terms"? If I use molecular replacement to solve the structure, shall I "uncheck" this item? Thanks very much for your help. Best wishes, Q. Cai
Re: [ccp4bb] refmac5 problem
Thank you very much for the help from all of you. I used "no prior phase information", and got R/Rfree = 0.2202/0.2544. I used "SAD data directly" and got R/Rfree = 0.2066/0.2302. I used "Hendrickson-Lattman coefficients" and got R/Rfree = 0.2255/0.2539. It seems that the "SAD data directly" gets a better result for my SAD data. Best wishes, Q. Cai Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2012/11/5 Navraj Pannu > > >> I am not sure how you would fare with SAD data directly.. >> >> > If you would like a comparison, check out the refmac paper. > > http://journals.iucr.org/d/issues/2011/04/00/ba5152/index.html > > See Figure 1 - this shows model building with ARP/wARP on over 100 data > sets using > the different Refmac functions that you asked about. > > The "MLHL" function is using "phase and fom" or "Hendrickson-Lattman" > coefficients > The "Rice" function is "no prior phase information" and the "SAD" function > is using "SAD > data directly". > > The figure shows fraction of the model built automatically. If you see > lot of red squares on the top left of the diagonal (which you do), this > just means the SAD function outperforms the 'Rice' function and you see > more Red squares then Blue circles, so SAD performs better than MLHL. You > can get more information on individual functions from references cited in > the Refmac paper. > > The top right shows data sets between 80-100% built by all functions: > thus, if your model/map is good enough, any function can build it. > > For SAD data sets that we have collected here, we always use the SAD > function even at the end of the refinement and found (unsurprisingly) a > lower difference between R-free and R then other functions. > > As Garib mentioned, Pavol Skubak and/or I are happy to answer any > questions. > > Best wishes, > Raj > > > >> But beware - do the HLs etc combine phases from the existing model and >> the anomalous signal - if so they may be biased towards the existing model, >> and make it harder to correct >> Eleanor >> >> On 5 Nov 2012, at 09:46, Qixu Cai wrote: >> >> > Dear all, >> > >> > What's the difference between "no prior phase information", "phase and >> FOM", Hendrickson-Lattman coefficients", and "SAD data directly" in the >> refmac5 GUI of CCP4i? >> > >> > I have a SAD dataset and solve the phase by phenix.autosol. Now I want >> to refine the structure by refmac5, which kind of input above I should >> choose? >> > >> > Another question is in the "Refinement Parameters" of refmac5. What's >> the meaning of "Use experimental sigmas to weight Xray terms"? If I use >> molecular replacement to solve the structure, shall I "uncheck" this item? >> > >> > Thanks very much for your help. >> > >> > Best wishes, >> > >> > Q. Cai >> > >> > >
[ccp4bb] about coot
Dear all, I have some problems about coot. 1, How to run the "Extensions --> All molecule --> Stepped refine" at "no-graphic" mode of coot? 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? 2, And is there any option to prevent coot auto-loading ~/.coot file? Thank you very much for your help! Q. Cai
Re: [ccp4bb] about coot
Dear Paul, Thanks for your reply. Because I have some code in ~/.coot related to the graphic, when I ran coot in "--no-graphic" mode, coot would crash. If I delete the ~/.coot file, coot will be ok at "no-graphic" mode. Another question: Many functions in coot, such as "refine-zone" or "refine-auto-range", have a parameter called "altconf", which is a string, but what's the meaning and function of "altconf"? Does it mean "alternative conformation"? And what kind of string will be used as correct argument in these functions? Thanks for your help. Best wishes, Q. Cai On 11/23/2012 07:32 PM, Paul Emsley wrote: On 23/11/12 08:54, Qixu Cai wrote: I have some problems about coot. 1, How to run the "Extensions --> All molecule --> Stepped refine" at "no-graphic" mode of coot? (let ((imol (read-pdb "coot-download/3rso.pdb")) (imol-map (make-and-draw-map "coot-download/r3rso-refmac.mtz" "FWT" "PHWT" "" 0 0))) (map (lambda (chain) (fit-chain imol chain)) (chain-ids imol))) 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? All and more, I think. They are in coot-top-dir/share/coot/python 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that?
Re: [ccp4bb] about coot
Dear Paul, Sorry to bother you again. In the scheme script you provided, it seems that the "imol-refinement-map" is not set. Is it necessary to add this code: "(set-imol-refinement-map imol-map)" to the script? Thanks for your reply. Best wishes, Q. Cai On 11/23/2012 07:32 PM, Paul Emsley wrote: On 23/11/12 08:54, Qixu Cai wrote: I have some problems about coot. 1, How to run the "Extensions --> All molecule --> Stepped refine" at "no-graphic" mode of coot? (let ((imol (read-pdb "coot-download/3rso.pdb")) (imol-map (make-and-draw-map "coot-download/r3rso-refmac.mtz" "FWT" "PHWT" "" 0 0))) (map (lambda (chain) (fit-chain imol chain)) (chain-ids imol))) 2, Are all of the extensions in coot the scheme/python scripts? If yes, where the script files store at? All and more, I think. They are in coot-top-dir/share/coot/python 2, And is there any option to prevent coot auto-loading ~/.coot file? No. Why would you want to do that?
Re: [ccp4bb] ccp4 update
Dear Andreas Förster, You can use "ccp4um" (ccp4 update manage) to update CCP4 from command line. Best wishes, Q. Cai Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/1/14 Andreas Förster > Dear CCP4 maintainers, > > I've come to appreciate the CCP4 update functionality, which, in our > multiuser network (RHEL 6.2), I used to invoke by calling $CCP4/bin/update. > > Update 012 removed that script with no immediately obvious replacement. > Was that on purpose? Is there a way of updating CCP4 from the command > line without calling CCP4i? > > Thanks > > > Andreas > > > (from update.log: > > [Thu Jan 3 2013 11:00:21] > Ready to make changes > > --- applying update 6.3.0-012 > --- update header read > --- creating restore package, please wait ... > --- done >... file '/csb/soft/Linux64/share/ccp4-**6.3.0/bin/update' removed >... file '/csb/soft/Linux64/share/ccp4-**6.3.0/lib_exec/update' removed >... file '/csb/soft/Linux64/share/ccp4-**6.3.0/lib_exec/_update' > removed >... directory '/csb/soft/Linux64/share/ccp4-**6.3.0/lib_exec' removed > > > some more blah blah) > > > -- > Andreas Förster, Research Associate > Paul Freemont & Xiaodong Zhang Labs > Department of Biochemistry, Imperial College London > http://www.msf.bio.ic.ac.uk >
[ccp4bb] relationship between resolution and B values
Dear all, Could you please teach me any method to present the relationship between resolution and B values of all the x-ray structures in Protein Data Bank. Can the PDB statistics in RCSB do it? Thank you very much! Q. Cai
Re: [ccp4bb] refmac5 vs phenix refine mixed up
Dear Tim Gruene, 2013/1/24 Tim Gruene > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Rajesh, > > first of all, a model is not "true" or "false", it can only be > "better" or "worse". > > The explanation of what you observe depends on what you did: > - - did you use the identical and very same mtz-file as input to all > three scenarios? Some people take the output mtz and use it as input > to the next refinement cycle, which is a very, very, bad thing to do. > Is the F/SIGF columns of the output mtz of refmac5 still the same as the F/SIGF columns of the input mtz? If they are the same, why cann't I use the F/SIGF columns of the output mtz as input to the next refinement? Thanks for your reply. > - - did you ensure always the same set of reflections was used for Rfree > when switching between programs? > If not, your R/Rfree are meaningless. > > It may also be that combining phenix and refmac5 indeed resulted in a > better mode - both programs have some substantial differences in how > they work. > > Best, > Tim > > On 01/24/2013 11:12 AM, rajesh harijan wrote: > > Dear All, > > > > I am working on a perfectly twinned data in space group P31. when > > I refine this data with phenix refine the R/Rfree is 26.6/29.4 and > > average B-factor is 38. > > > > I did one test now. I used phenix refined pdb and refine with > > refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. > > > > Now I used refmac5 refined pdb and refined with phenix again. Now > > R/Rfree is 22.1/24.8 and average B-factor is 56. > > > > > > My question is, why B-factor gone up now and R/Rfree reduced. In > > which refined model should I believe in. If last refined model is > > true then how should I reduce the B-factor? > > > > Thank you Rajesh > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFRAQ56UxlJ7aRr7hoRAsJmAJ9RcS1Bp7g53LwiTm1ZMAVAICHXAACfdWgD > FlLHo/1euT/BIeSW7EhrvHo= > =w9IY > -END PGP SIGNATURE- >
[ccp4bb] the matrix format
Dear all, The matrix formats in different program always confuse me. The matrix format of the "REMARK 290 SMTRY" section of pdb file is: r11r12r13tx r21r22r23ty r31r32r33tz What's the matrix format accepted by the "transform file" keywords of the pdbset program? is it "r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz"? And how to covert from the "pdb file format" to the "pdbset format"? What's the matrix format of "apply NCS operators" in phenix GUI? Thanks a lot! Qixu Cai
Re: [ccp4bb] the matrix format
Dear Jon, Thanks for your reply. The matrix format in the "REMARK 290" section of the pdb file (download from rcsb.org) is : r11r12r13tx r21r22r23ty r31r32r33tz And I want to extract the matrix information from the pdb file "REMARK 290" section and use the matrix in the pdbset. so I have to convert the matrix from r11r12r13tx r21r22r23ty r31r32r33tz to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz. How can I do it? Thanks. Qixu Cai Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/2/25 Jon Agirre > Dear Qixu, > > here's an excerpt from the pdbset manual: > > TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty > tz > > I'm not sure what you mean by "covert from the "pdb file format" to > the "pdbset format"". Please elaborate on this. > > Jon > > 2013/2/25 Qixu Cai : > > Dear all, > > > > The matrix formats in different program always confuse me. > > > > The matrix format of the "REMARK 290 SMTRY" section of pdb file is: > > > > r11r12r13tx > > r21r22r23ty > > r31r32r33tz > > > > What's the matrix format accepted by the "transform file" keywords of the > > pdbset program? > > is it "r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz"? > > And how to covert from the "pdb file format" to the "pdbset format"? > > > > What's the matrix format of "apply NCS operators" in phenix GUI? > > > > Thanks a lot! > > > > Qixu Cai > > > > -- > Jon Agirre, PhD > Unit of Biophysics (CSIC-UPV/EHU) > http://sourceforge.net/projects/projectrecon/ > +34656756888 >
Re: [ccp4bb] Measure Cell option in imosflm
Dear Harry, It's a useful function. Could you please added it? Thanks. Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/2/25 Harry Powell > Hi Richard > > I'm afraid it doesn't exist at the moment. It could be added if there's > sufficient demand for it. > > On 25 Feb 2013, at 12:57, Bayliss, Richard (Dr.) wrote: > > Does anyone know how to access the 'Measure Cell' function in iMosflm? > This function in ipmosflm allowed you to click on a pair of spots, then > input the number of diffraction orders, to output a rough measure of the > cell length. > > Any help appreciated! > Thanks > Richard > > = > Dr Richard Bayliss, Reader in Structural Biology > Department of Biochemistry > Henry Wellcome Building > University of Leicester > Lancaster Road, Leicester > LE1 9HN > > Tel: 0116 2297100 > Web: > http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research > > Elite Without Being Elitist > Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 > Follow us on Twitter http://twitter.com/uniofleicester > > >Harry > -- > Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick > Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH > Chairman of European Crystallographic Association SIG9 (Crystallographic > Computing) > > > > > > > >
Re: [ccp4bb] the matrix format
Thanks. That's what I need. Qixu Cai Email: caiq...@gmail.com 在 2013-2-25，下午9:38，Jon Agirre 写道： > If you just want to generate symm mates from MTRIX records, you may > want to give GK's 'xpand' a go: > http://xray.bmc.uu.se/usf/xpand_man.html > > Otherwise, I would follow Fred's advice. > > Jon > > 2013/2/25 vellieux : >> Hi, >> >> Emacs, vi, any (text file) editor ? I wouldn't advise a word processing >> program (Word and the likes). >> >> Unless you want to do this on many pdb files in which case writing a small >> program or shell script would be required. >> >> Fred. >> >> >> On 25/02/13 14:24, Qixu Cai wrote: >> >> Dear Jon, >> >> Thanks for your reply. >> >> The matrix format in the "REMARK 290" section of the pdb file (download from >> rcsb.org) is : >> r11r12r13tx >> r21r22r23ty >> r31r32r33tz >> >> And I want to extract the matrix information from the pdb file "REMARK 290" >> section and use the matrix in the pdbset. >> >> so I have to convert the matrix from >> r11r12r13tx >> r21r22r23ty >> r31r32r33tz >> >> to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz. >> >> How can I do it? >> >> Thanks. >> >> Qixu Cai >> >> >> Qixu Cai >> Email: caiq...@gmail.com >> School of Life Sciences, >> Xiamen University, Fujian, China >> >> >> 2013/2/25 Jon Agirre >>> >>> Dear Qixu, >>> >>> here's an excerpt from the pdbset manual: >>> >>> TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty >>> tz >>> >>> I'm not sure what you mean by "covert from the "pdb file format" to >>> the "pdbset format"". Please elaborate on this. >>> >>> Jon >>> >>> 2013/2/25 Qixu Cai : >>>> Dear all, >>>> >>>> The matrix formats in different program always confuse me. >>>> >>>> The matrix format of the "REMARK 290 SMTRY" section of pdb file is: >>>> >>>> r11r12r13tx >>>> r21r22r23ty >>>> r31r32r33tz >>>> >>>> What's the matrix format accepted by the "transform file" keywords of >>>> the >>>> pdbset program? >>>> is it "r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz"? >>>> And how to covert from the "pdb file format" to the "pdbset format"? >>>> >>>> What's the matrix format of "apply NCS operators" in phenix GUI? >>>> >>>> Thanks a lot! >>>> >>>> Qixu Cai >>> >>> >>> >>> -- >>> Jon Agirre, PhD >>> Unit of Biophysics (CSIC-UPV/EHU) >>> http://sourceforge.net/projects/projectrecon/ >>> +34656756888 >> >> >> >> >> -- >> Fred. Vellieux (B.Sc., Ph.D., hdr) >> IBS / ELMA >> 41 rue Jules Horowitz >> F-38027 Grenoble Cedex 01 >> Tel: +33 438789605 >> Fax: +33 438785494 > > > > -- > Jon Agirre, PhD > Unit of Biophysics (CSIC-UPV/EHU) > http://sourceforge.net/projects/projectrecon/ > +34656756888
Re: [ccp4bb] stereo monitor for DELL T7600
Dear Tim, Does the program of O support only the quad-buffered stereo mode, not the Zalman mode? Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China 2013/3/1 Tim Gruene > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Jl, > > the Zalmans are probably compatible with ANY graphics card you can buy > in a shop nowadays. The technique they use was invented in the 1920s... > > Best, > Tim > > On 03/01/2013 12:56 AM, jlliu liu wrote: > > Hi All, > > > > I am ordering a Dell workstation (Dell Precision,T7600n,MT,1300W) > > with 2GB nVIDIA Quadro 4000. Can anyone recommend to me which > > stereo monitor would be compatible with this model? > > > > I have some stereo models mentioned in previously ccp4bb email: > > > > > >> - Zalman ZM-M215W 21.5in - Zalman ZM-M240W 24in - Samsung > >> <http://proteincrystallography.org/ccp4bb/message29933.html>SyncMaster > >> S27A750D 27in - LG D2342P 23in / LG D2542P 25in > > > > > > > > Any advice will be highly appreciated. > > > > > > > > Thanks so much in advance! > > > > > > > > Jl > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFRMHhdUxlJ7aRr7hoRAjcLAKDNtG6SDyRpa+q34YDNV/KMFx90bQCdH/Ao > NMweR6el+xh57NaLl/8UtUc= > =NfXa > -END PGP SIGNATURE- >
[ccp4bb] PDB redo R free
Dear all, I'm using the PDB-REDO server to refine my structure. I found that PDB-REDO said that 5% R-free set is too small and it created a new R-free set. Is possible for the PDB-REDO server to keep the original R-free set to make final Rfree value comparable? Best regards, Qixu Cai Email: caiq...@gmail.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] PDB redo R free
Dear Robbie and Tim， Thanks a lot for your reply. I just do not understand that if we can change the R free set during different rounds of refinement, the gap between Rwork and Rfree would be small, and Rfree would be meaningless, as R-free set is not "free". Best regards, Qixu Cai Email: caiq...@gmail.com Robbie Joosten 于2023年4月28日周五 15:26写道： > Hi Qixu, > > PDB-REDO tries to have a minimum number test set reflections to reduce the > error margin in R-free. As Tim says this is not a problem but if you reach > out privately we can change your calculation to use your current testset. > That is not recommended though. > > Cheers, > Robbie > > On 28 Apr 2023 04:51, Qixu Cai wrote: > > Dear all, > > I'm using the PDB-REDO server to refine my structure. I found that > PDB-REDO said that 5% R-free set is too small and it created a new R-free > set. > > Is possible for the PDB-REDO server to keep the original R-free set to > make final Rfree value comparable? > > Best regards, > > Qixu Cai > Email: caiq...@gmail.com > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Mean B value in refmac5
Dear all, I found that the "Mean B value (OVERALL, A**2)" reported by refmac5 in the head region of pdb file is 62.76. However, I calculated the average B value of all B factors from all atoms and the result is 67.7. What makes the difference? The canonical restrained refinement mode was used in refmac5. When we prepare the Table 1 of manuscript, which one is correct for the "average B value"? Thanks and best regards, Qixu Cai Email: caiq...@gmail.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Mean B value in refmac5
Thanks for your reply. Does the refmac5 program weight the mean B value by the resolution? Qixu Cai Email: caiq...@gmail.com Ian Tickle 于2023年11月5日周日 19:34写道： > The arithmetic mean B value from the structure as quoted everywhere is > pretty meaningless anyway and 10 Ang.^2 either way is probably not > significant. Let's say some waters or LYS side-chains or whatever have B = > 1000 Ang.^2. That will bias the mean B upwards, but those atoms do not > contribute significantly to the total scattering except at very low > resolution and might as well not be there, so they should not be included > in the mean. A better method would be to weight the mean by the scattering > power at the resolution limit. That should more closely match the B value > from the Wilson plot. > > Cheers > > Ian > > > On Sun, 5 Nov 2023, 10:45 Qixu Cai, wrote: > >> Dear all, >> >> I found that the "Mean B value (OVERALL, A**2)" reported by refmac5 in >> the head region of pdb file is 62.76. However, I calculated the average B >> value of all B factors from all atoms and the result is 67.7. What makes >> the difference? The canonical restrained refinement mode was used in >> refmac5. When we prepare the Table 1 of manuscript, which one is correct >> for the "average B value"? >> >> Thanks and best regards, >> Qixu Cai >> Email: caiq...@gmail.com >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Mean B value in refmac5
I tried both and none of them is the same as reported by refmac5. Qixu Cai Email: caiq...@gmail.com James Holton 于2023年11月6日周一 01:11写道： > Are you averaging over all ATOM records? Or are you including HETATM as > well? > > On 11/5/2023 5:45 AM, Qixu Cai wrote: > > Dear all, > > I found that the "Mean B value (OVERALL, A**2)" reported by refmac5 in the > head region of pdb file is 62.76. However, I calculated the average B value > of all B factors from all atoms and the result is 67.7. What makes the > difference? The canonical restrained refinement mode was used in refmac5. > When we prepare the Table 1 of manuscript, which one is correct for the > "average B value"? > > Thanks and best regards, > Qixu Cai > Email: caiq...@gmail.com > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Mean B value in refmac5
Yes. I tried to weight those B values by occupancies, but the result is still not the same as the value reported by refmac5. Qixu Cai Email: caiq...@gmail.com Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> 于2023年11月6日周一 14:04写道： > Are there some atoms with occupancies < 1.0 ? > You would need to weight those Bs by occ > > On Sun, 5 Nov 2023 at 11:34, Ian Tickle wrote: > >> The arithmetic mean B value from the structure as quoted everywhere is >> pretty meaningless anyway and 10 Ang.^2 either way is probably not >> significant. Let's say some waters or LYS side-chains or whatever have B = >> 1000 Ang.^2. That will bias the mean B upwards, but those atoms do not >> contribute significantly to the total scattering except at very low >> resolution and might as well not be there, so they should not be included >> in the mean. A better method would be to weight the mean by the scattering >> power at the resolution limit. That should more closely match the B value >> from the Wilson plot. >> >> Cheers >> >> Ian >> >> >> On Sun, 5 Nov 2023, 10:45 Qixu Cai, wrote: >> >>> Dear all, >>> >>> I found that the "Mean B value (OVERALL, A**2)" reported by refmac5 in >>> the head region of pdb file is 62.76. However, I calculated the average B >>> value of all B factors from all atoms and the result is 67.7. What makes >>> the difference? The canonical restrained refinement mode was used in >>> refmac5. When we prepare the Table 1 of manuscript, which one is correct >>> for the "average B value"? >>> >>> Thanks and best regards, >>> Qixu Cai >>> Email: caiq...@gmail.com >>> >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] "LINK" and "REMARK 290" of pdb file
Dear all, I'm working on the refinement of a crystal structure. In the structure, one crystal packing interface is mediated by a compound with two coordinate covalent bonds to two macromolecules from different asymmetric units. Thus I need to specify two "LINK" records in the head of pdb file. The "LINK" record between the compound and macromolecule in the same asymmetric unit is generated by refmac automatically. However, refmac does not generate the other "LINK" between the compound and the symmetric macromolecule. Thus I want to add the LINK record myself. As the LINK is between different symmetric molecules, I need to specify the symmetry code, such as "1555", "2555" and so on. The symmetry code is dependent on the "REMARK 290" record. My question is: 1. How can I generate the "REMARK 290" information? 2. Any easier method to generate the "LINK" record between molecules from different asymmetric units? Thanks a lot for your help! Best regards, Qixu Cai Email: caiq...@gmail.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
