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
[ccp4bb] Phenix - Ligand search
Dear All Greetings I was searching for a ligand present in the active site of my protein using Ligand Search in PHENIX but i stuck in between with an error : A Python error was detected. This may be a problem with the program settings, an error in your data, or a bug; click OK to send a bug report to the PHENIX developers. AttributeError : ligand_identification instance has no attribute 'connections' Traceback: File /home/programs/linux/phenix-1.6.1-357/cctbx_project/libtbx/thread_utils.py, line 137, in run return_value = self._target(self._args, self._kwargs, self._c) File /home/programs/linux/phenix-1.6.1-357/cctbx_project/libtbx/runtime_utils.py, line 55, in __call__ result = self.target() File /home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py, line 1769, in __call__ identify_ligands = ligand_identification(args=list(self.args), quiet=False) File /home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py, line 308, in __init__ ligand_identification.Run(self, params) File /home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py, line 1454, in Run return self.connections['STOP '] I am not able to identify the problem? Please let me know if some one can identify the problem, i don't know whether it is a bug or problem in my files. Thanks for your suggestions in advance. Rajan -- Current Address: Rajan Vyas Research Scholar Deptt. of Biotechnology Panjab University Chandigarh, India 160014Mob. +919417374197 Fax: +91-172-2625254
Re: [ccp4bb] Phenix - Ligand search
Folks - the phenixbb is nice and lively. And you get answers asap. Use it for at least in cases like this were it's basically a bug report and not a scientific question. Sent from my iPhone On 24 Apr 2010, at 12:01, Rajan rajanv...@gmail.com wrote: Dear All Greetings I was searching for a ligand present in the active site of my protein using Ligand Search in PHENIX but i stuck in between with an error : A Python error was detected. This may be a problem with the program settings, an error in your data, or a bug; click OK to send a bug report to the PHENIX developers. AttributeError : ligand_identification instance has no attribute 'connections' Traceback: File /home/programs/linux/phenix-1.6.1-357/cctbx_project/libtbx/ thread_utils.py, line 137, in run return_value = self._target(self._args, self._kwargs, self._c) File /home/programs/linux/phenix-1.6.1-357/cctbx_project/libtbx/ runtime_utils.py, line 55, in __call__ result = self.target() File /home/programs/linux/phenix-1.6.1-357/phenix/phenix/ command_line/ligand_identification.py, line 1769, in __call__ identify_ligands = ligand_identification(args=list(self.args), quiet=False) File /home/programs/linux/phenix-1.6.1-357/phenix/phenix/ command_line/ligand_identification.py, line 308, in __init__ ligand_identification.Run(self, params) File /home/programs/linux/phenix-1.6.1-357/phenix/phenix/ command_line/ligand_identification.py, line 1454, in Run return self.connections['STOP '] I am not able to identify the problem? Please let me know if some one can identify the problem, i don't know whether it is a bug or problem in my files. Thanks for your suggestions in advance. Rajan -- Current Address: Rajan Vyas Research Scholar Deptt. of Biotechnology Panjab University Chandigarh, India 160014Mob. +919417374197 Fax: +91-172-2625254
Re: [ccp4bb] Shifting twin fraction with refinement - finally zero
Thank you, Frank, for pointing this out Here is the link to that presentation again: www.ysbl.york.ac.uk/refmac/Presentations/Refmac_February.ppt Garib On 24 Apr 2010, at 12:05, Frank von Delft wrote: Hi Garib, the link you sent doesn't work from here, phx. On 24/04/2010 00:17, Garib Murshudov wrote: I think your procedure is good with current technology. At early stages twin refinement may give misleading results. An intuitive resoning for low R factor would be: Twin is summation of intensities. As you sum intensities two things happen: 1) distribution of intensities become more symmetric (departs from wilson distribution or chisquared distribution with degrees of freedom 2 in case of acentric reflections) 2) distributions become narrower. As distribution becomes narrower probability that differences between randomly selected values from the population with this distribution is small will be higher. Hence R factors will be smaller. When errors in model becomes comparable with the errors in experiment then differences between observed structure and calculated structure factors become more independent and R factors become comparable. In practice it never happens (errors in model are always higher than errors in experimental data which is understandable). So twin R factor always going to be lower than corresponding non-twin R factor. As a general rule: One should be careful in comparing R factors from two different crystals. R factors are not only dependent on errors in coordinate model. But they are dependent on many statistical properties of crystal, twinning is just an example of such properties. There are some warnings about twin refinement for extreme cases on the presentation from www.ysbl.york.ac.uk:/y/people/garib/ Presentations/Refmac_February.ppt, slides number 17 and 18 (apologies if it sound like as self promotion) regards Garib On 23 Apr 2010, at 22:56, Jon Schuermann wrote: Hari, What twin tests have you run? Results? If your data really is P43212 and you drop to P212121 you will still have the additional two-fold operator in your data. An operator is a mathematical operator, which could be crystallographic or twin. I never refine a structure with twin refinement from the beginning (even if I suspect it is twinned). I do iterative rounds of model building and conventional refinement until I cannot get the R-factor any lower. Depending on many factors (resolution, twin fraction, etc.), I usually get stuck in the mid-30's. At this point I will investigate twin refinement or other possible SG's. If you start using twin refinement too early in the model building process, I have seen programs report much too low R-factors and exaggerated twin fractions. Probably, a programmer like Garib or Peter could comment on why. Jon On 04/23/2010 04:28 PM, hari jayaram wrote: I am refining a twinned dataset in possible spacegroup P212121 . Pointless thinks it is P43212 , but based on reading this posting (http://www.phenix-online.org/pipermail/phenixbb/2007-September/000501.html ) I think it is P212121. The starting R/Rfree after molecular replacement ( single site mutant) was 34/38 to 2.2 A After an initial round of restrained refinement ( without twin refinement) and minimal rebuilding I got the R/Rfree to 30/34 Then I did an amplitude based twin refinement - The twin fraction was 0.48 k,h,-l and 0.52 h,k,l and The r/rfree became 24/29 After a little more rebuilding ( a few residues out of 800 residues in ASU) and another twin refinement I got an r/rfree of 22/27 . Now the twin fraction was 0.87 (h,k,l) and 0.13 (k,h,-1) The maps looked a little better allowing me to fix a few more residues Finally the same twin refinement gives me no twin operators and the R/Rfree is 22/26 All the twinning tests indicate a serious twinning in my crystal. Any ideas why I am seeing this Hari -- Jonathan P. Schuermann, Ph. D. Beamline Scientist NE-CAT, Building 436E Advanced Photon Source (APS) Argonne National Laboratory 9700 South Cass Avenue Argonne, IL 60439 email: schue...@anl.gov Tel: (630) 252-0682 Fax: (630) 252-0687
[ccp4bb] SUMMARY: scala and xds data
as it turns out: the bad news (for me) 1. something went wrong in my data processing. point taken. yes. i was so hypnotized by the strange error message, that i did not realize this. the good news 2. pointless and scala run just fine (everybody can relax), and the strange messages are more an esthetic problem, that phil evans said he will fix in the next pointless release. had i looked at the pointless output i would have seen, of course, that my data are complete nonsense. embarassing ... thanks to phil for taking time to look over this, and thanks to the others who also replied and asked why i even scale xds data with scala rather than xscale. there are reasons for this, but the interesting news for me was, that it might be that xscale possibly delivers better data from xds than scala does, which, of course, now, i will have to look into ... time will tell ... greetings ingo
Re: [ccp4bb] SUMMARY: scala and xds data
Hi Ingo, Scala might be beneficial after xds when several datasets need to be scaled together. Scala will refine cell parameters to fit best all the datasets together where as xscale uses as cell parameters those of the first dataset. If you use xscale you have to be prudent in your choice of the first dataset. Peter. On Sat, Apr 24, 2010 at 7:31 PM, Ingo Korndoerfer korndoer...@crelux.comwrote: as it turns out: the bad news (for me) 1. something went wrong in my data processing. point taken. yes. i was so hypnotized by the strange error message, that i did not realize this. the good news 2. pointless and scala run just fine (everybody can relax), and the strange messages are more an esthetic problem, that phil evans said he will fix in the next pointless release. had i looked at the pointless output i would have seen, of course, that my data are complete nonsense. embarassing ... thanks to phil for taking time to look over this, and thanks to the others who also replied and asked why i even scale xds data with scala rather than xscale. there are reasons for this, but the interesting news for me was, that it might be that xscale possibly delivers better data from xds than scala does, which, of course, now, i will have to look into ... time will tell ... greetings ingo -- Peter
[ccp4bb] programmatic symmetry mate generation
Hello All, I want to programmatically generate the symmetry mates for a molecule and write out the files containing the symmetry related molecules. I'm resisting the urge to reinvent the wheel. What is the best way to do this? I'd prefer to do it within a python program using an open source library, but I'd settle for scripting an external program if that is the only option. James
Re: [ccp4bb] programmatic symmetry mate generation
On Sat, Apr 24, 2010 at 5:25 PM, James Stroud xtald...@gmail.com wrote: I want to programmatically generate the symmetry mates for a molecule and write out the files containing the symmetry related molecules. I'm resisting the urge to reinvent the wheel. What is the best way to do this? I'd prefer to do it within a python program using an open source library, but I'd settle for scripting an external program if that is the only option. Either PyMOL or CCTBX can do this, but it may take some experimenting and fine-tuning to get exactly what you want, which isn't entirely clear from your question. PyMOL just generates symmetry-related molecules within a specified radius of the original object, which is okay for interactive use (or if you just want to see crystal packing), but less useful if you want just the molecules related by the symmetry operators of the space group, or just the unit cell. (I'm assuming you can use PyMOL as a module to do this instead of running the full program, but I haven't tried this before.) Within CCTBX, it is very easy (although not at all intuitive) to apply the symmetry operators; a very rough example is appended below. However, these won't necessarily pack together or fill the unit cell. It is possible I am doing something completely wrong, because I never really understood symmetry very well, but the new chains all align perfectly with symmetry mates created by PyMOL, so I think the operators are being used correctly. An example in P212121 is shown here: http://cci.lbl.gov/~nat/img/symops.png I suspect there is an easy way to fill the unit cell instead, but I'm too tired to figure it out right now. If I can get my simple script working satisfactorily I'll add it to CCTBX. On the non-Python side, Gerard Kleywegt's program XPAND appears to be designed for this - haven't tried that either, but I suspect it will give you something closer to what you want. Not sure whether CCP4 exposes similar functionality anywhere. -Nat # usage: cctbx.python script_name pdb_file # the PDB file must contain a CRYST1 record. from iotbx.file_reader import any_file import scitbx.matrix from scitbx.array_family import flex import sys, os def run (args) : pdb_file = args[0] pdb_inp = any_file(pdb_file, force_type=pdb).file_object symm = pdb_inp.crystal_symmetry() sg = symm.space_group() uc = symm.unit_cell() symops = sg.all_ops() out = open(unit_cell.pdb, w) for symop in symops : r = symop.r() t = symop.t() rt = scitbx.matrix.rt((r.as_double(), t.as_double())) pdb_hierarchy = pdb_inp.construct_hierarchy().deep_copy() atoms = pdb_hierarchy.atoms() sites_frac = uc.fractionalize(sites_cart=atoms.extract_xyz()) new_sites = sites_frac * r.as_double() + t.as_double() atoms.set_xyz(uc.orthogonalize(sites_frac=new_sites)) out.write(pdb_hierarchy.as_pdb_string()) out.close() if __name__ == __main__ : run(sys.argv[1:])
Re: [ccp4bb] programmatic symmetry mate generation
James Stroud wrote: Hello All, I want to programmatically generate the symmetry mates for a molecule and write out the files containing the symmetry related molecules. I'm resisting the urge to reinvent the wheel. What is the best way to do this? I'd prefer to do it within a python program using an open source library, but I'd settle for scripting an external program if that is the only option. James If I could dare to mention a CCP4 program on this BB: PDBSET. The database is a text file called $SYMOP. To be able to control which other ASU get created, copy the symops from there into the script. You also need a CELL line if the .pdb lacks CRYST1 Depending what you're going to do, it may help to rename the new chains. For P212121: #!/bin/csh -f # # Make Cell contents # pdbset xyzin asu.pdb xyzout unitcell.pdb eof-1 symgen X,Y,Z symgen 1/2-X,-Y,1/2+Z symgen -X,1/2+Y,1/2-Z symgen 1/2+X,1/2-Y,-Z ! Rename chains in other ASU chain symmetry 2 A C chain symmetry 2 B D chain symmetry 3 A E chain symmetry 3 B F chain symmetry 4 A G chain symmetry 4 B H eof-1 then you have the problem Nat mentioned that the result probably will not be the best approximation to filling one unit cell (that is a hopeless goal anyway as molecules will always cross cell boundaries) But you can get a lot closer by adding unit cell translations to the symops and seeing where it puts the molecules. substitute Y with 1+y or -1+y (Y-1?) substitute 1/2+y with -1/2+y, 3/2+y etc and so on If you want the results in different files, one for each asu, include only one of the symops each time you run.
