Re: [ccp4bb] relationship between resolution and B values
Dear Qixu The RCSB has a webpage to show the statistics (the data populations and the correlation with the resolution) for all the annotated pdb data items. The current page is http://rcsb-auto-check.rutgers.edu/dev/pdbitem/index.html The graph that you need may be the one http://rcsb-auto-check.rutgers.edu/dev/pdbitem/DAT_STORE//refine_B_iso_mean_res.data.png Best, Huanwang On Sat, 19 Jan 2013 20:14:47 +0800, Qixu Cai caiq...@gmail.com wrote: 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] relationship between resolution and B values
Dear Qixu I am so sorry that I made a mistake. The webpage http://rcsb-auto-check.rutgers.edu/dev/pdbitem/index.html is under development and not available yet. The graph for B factor vs resolution is available http://rcsb-auto-check.rutgers.edu/dev/pdbitem/DAT_STORE//refine_B_iso_mean_res.data.png Regard, Huanwang On Sat, 19 Jan 2013 11:18:19 -0500, Huanwang Yang hy...@rcsb.rutgers.edu wrote: Dear Qixu The RCSB has a webpage to show the statistics (the data populations and the correlation with the resolution) for all the annotated pdb data items. The current page is http://rcsb-auto-check.rutgers.edu/dev/pdbitem/index.html The graph that you need may be the one http://rcsb-auto-check.rutgers.edu/dev/pdbitem/DAT_STORE//refine_B_iso_mean_res.data.png Best, Huanwang On Sat, 19 Jan 2013 20:14:47 +0800, Qixu Cai caiq...@gmail.com wrote: 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] a question related to SF-tool
Dear Dialing It looks like that the conversion using the 'auto mode' is successful. The error message might come from the multiple 'Associated datasets '. If no amplitude or intensity are not found in the dataset, an error message will be shown. For a safe conversion, please always use the 'Semi-automatic MTZ conversion to mmCIF', instead of the 'auto mode'. Best regards, Huanwang Dialing Pretty wrote: Dear All, I am trying to convert a PDB and the corresponding mtz file to the mmcif file, and I got the following message: *Converting structure factor to mmCIF format *Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done. Header of the mtz file can be seen from here http://sf-tool.rcsb.org/users_data/dir_14250/mtzdmp_new.log *Click here to see the converted mmCIF file http://sf-tool.rcsb.org/users_data/dir_14250/sf_14250.inp.mmCIF*. Will you please tell me how to solve the problem Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done? Cheers, Dialing
Re: [ccp4bb] [phenixbb] what to do with disordered side chains
If a part of sequence has no density, this part will be cut from coordinates. If the side chain of a residue is lack of density, the opinion is not converged. What about the ligand, if no density is observed? Huanwang Ed Pozharski wrote: The results of the online survey on what to do with disordered side chains (from total of 240 responses): Delete the atoms 43% Let refinement take care of it by inflating B-factors41% Set occupancy to zero12% Other 4% Other suggestions were: - Place atoms in most likely spot based on rotomer and contacts and indicate high positional sigmas on ATMSIG records - To invent refinement that will spread this residues over many rotamers as this is what actually happened - Delet the atoms but retain the original amino acid name - choose the most common rotamer (B-factors don't inflate, they just rise slightly) - Depends. if the disordered region is unteresting, delete atoms. Otherwise, try to model it in one or more disordered model (and then state it clearly in the pdb file) - In case that no density is in the map, model several conformations of the missing segment and insert it into the PDB file with zero occupancies. It is equivalent what the NMR people do. - Model it in and compare the MD simulations with SAXS - I would assumne Dale Tronrod suggestion the best. Sigatm labels. - Let the refinement inflate B-factors, then set occupancy to zero in the last round. Thanks to all for participation, Ed.
Re: [ccp4bb] PDB Submission of SAD data.
Dear Francis You do not have to tell which columns were used for refinement. The program should pick FP/SIGFP. You can deposit the foo.mmcif and your coordinate to the PDB. The alternative to convert/validate your mtz file is to use the server http://pdb-extract.rcsb.org/auto-check/ . It is easy to use. Also the web page is updated faster than the standard alone program. Regards, Huanwang Francis E Reyes wrote: I have a mtz from Autosol/resolve that has the following columns: OVERALL FILE STATISTICS for resolution range 0.002 - 0.261 === Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC 0 37 0 100.00 18.7 18.7 23.68 1.96 H H 2 NONE 0 25 0 100.00 7.3 7.3 23.68 1.96 H K 3 NONE 0 58 0 100.00 20.5 20.5 23.68 1.96 H L 4 NONE2.3 316.2 0 100.0020.3920.39 23.68 1.96 F FP 5 NONE0.117.2 0 100.00 1.77 1.77 23.68 1.96 Q SIGFP 6 NONE -180.0 180.0 0 100.00 6.2489.14 23.68 1.96 P PHIM 7 NONE 0.000 0.998 0 100.000.2830.283 23.68 1.96 W FOMM 8 NONE -10.911.8 0 100.00 0.01 0.46 23.68 1.96 A HLAM 9 NONE -10.720.6 0 100.00 0.00 0.46 23.68 1.96 A HLBM 10 NONE -4.1 4.5 0 100.00-0.00 0.08 23.68 1.96 A HLCM 11 NONE -3.5 3.1 0 100.00 0.00 0.07 23.68 1.96 A HLDM 12 NONE0.0 1.0 0 100.00 0.10 0.10 23.68 1.96 I FreeR_flag 13 BOTH0.0 0.0 0 100.00 0.00 0.00 23.68 1.96 F FC Should I just prepare my mmcif by pdb_extract_sf -dt F -dp MTZ -c 1 -w 1 -iDAT exptl_fobs_phases_freeR_flags.mtz -o foo.mmcif and submit foo.mmcif to the PDB? Do i need to separately indicate which columns (in my case FP/SIGFP) were used for refinement? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D -- *Huanwang Yang Ph.D. * * RCSB Protein Data Bank * * Dep. of Chemistry Chemical Biology, Rutgers University * * 610 Taylor Road, Piscataway, NJ 08854-8087 * * Phone: (732)-445-0103 (ext 240); Fax: (732)-445-4320*
