[ccp4bb] R: [ccp4bb] fit multiple structures into SAXS envelope

You can try with  sculptor http://sculptor.biomachina.org In this pgm you can calculate first a map (a bĺured model)  from saxs model   (dammif) , then load your xray models and fit them simultaneously into the envelope.  for the fitted model you can then calculate the saxs curve and compare with

[ccp4bb] fit multiple structures into SAXS envelope

Dear All, I have a question regarding SAXS, I collected SAXS data on the protein of interest and I can generate the molecular envelope, I also solved x-ray structures of its domains, and I would like to fit my x-ray structures into SAXS envelope, or alternatively find some program which could asse

Re: [ccp4bb] Conversion from PDB-downloaded structure factors to mtz

Of course not claiming it the best, but two options I'm aware of are: phenix.cif_as_mtz file_name.cif phenix.fetch_pdb 1f8t --mtz Pavel On Fri, Nov 4, 2016 at 6:34 PM, Keller, Jacob wrote: > Dear crystallographers, > > > > What program is best used to convert pdb-downloaded sf’s to mtz format

Re: [ccp4bb] Conversion from PDB-downloaded structure factors to mtz

Got to GUI and it will call the appropriate program.. Eleanor On 4 November 2016 at 15:55, Ian Tickle wrote: > cif2mtz > > Cheers > > -- Ian > > > > On 4 November 2016 at 15:34, Keller, Jacob > wrote: > >> Dear crystallographers, >> >> >> >> What program is best used to convert pdb-downloaded s

Re: [ccp4bb] Conversion from PDB-downloaded structure factors to mtz

cif2mtz Cheers -- Ian On 4 November 2016 at 15:34, Keller, Jacob wrote: > Dear crystallographers, > > > > What program is best used to convert pdb-downloaded sf’s to mtz format? > > > > JPK > > > > *** > > Jacob Pearson Keller, PhD > > Research Scienti

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

OK yes it's Phaser: the version you are using is not writing the correct CCP4 space group number in the MTZ header (i.e. the one listed in syminfo.lib), which will confuse many downstream programs using the CCP4 symmetry library. Phaser is using the space group number shown in ITC-A, but that does

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

An MTZ file contains the space group name, space group number, and all the symmetry operators. Space group numbers such as 4005 are an unofficial undocumented extension to International Tables rules and shouldn't be used as reliable information. The name or the operators should take precedence Doe

[ccp4bb] Conversion from PDB-downloaded structure factors to mtz

Dear crystallographers, What program is best used to convert pdb-downloaded sf's to mtz format? JPK *** Jacob Pearson Keller, PhD Research Scientist HHMI Janelia Research Campus / Looger lab Phone: (571)209-4000 x3159 Email: kell...@janelia.hhmi.org

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

Ian, I think I found the issue just by looking through mtzdmp output, but there was a clue from the response I got yesterday: Hi Paul, I have come across this problem before, suddenly what was complete data is only 50% complete. I seem to recall its because I2 is also called space

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

Paul, mtzdump may not give the full header. The best way to get this is to use a text editor on the MTZ file (yes I know it looks like garbage!), scroll to the end where you will find the header starting at 'VERS MTZ:V1.1'. Then copy/paste everything from there to the end (don't worry about forma

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

Hi Paul I just tried Refmac 5.8.0135 (which must be very similar to the version you are using) with an I2 dataset and I don't see this "conversion to C2". I doubt very much that the refinement programs need to convert to C2: I'm pretty sure they can do the refinement perfectly well in I2. I thin

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

Refmac and phenix.refine versions I used both seem to be problematic. Both are I2 in and C2 out. --p On 11/04/2016 08:25 AM, Ian Tickle wrote: Hi Paul This sounds like there might be a recently-introduced bug which should be reported to the author. I have several structures in I2 & I have

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

It seems this happens at the level of the refinement programs. Both seem to convert to C2, but use the I2 cell parameters. They are somewhat older versions, so perhaps it is an old bug and not a new one? I've confirmed that the input mtz I used for both refmac and phenix.refine was in I2 with t

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

Hi Paul This sounds like there might be a recently-introduced bug which should be reported to the author. I have several structures in I2 & I haven't noticed anything like this. Can you tell which program is introducing this error, e.g. by looking at the mtzdump outputs? Cheers -- Ian On 4 No

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

That must mean there is a bug in the reindexing to I2 Eleanor On 4 November 2016 at 12:00, Paul Paukstelis wrote: > Thanks to all that responded. I sorted this out. > > It all appears to stem from the C2->I2 conversion. Forcing everything in > processing to stick with C2 fixes all the issues! >

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

Thanks to all that responded. I sorted this out. It all appears to stem from the C2->I2 conversion. Forcing everything in processing to stick with C2 fixes all the issues! Thanks again, --paul On 11/03/2016 12:39 PM, Paul Paukstelis wrote: CCP4BB, I posted some time back about a DNA olig

[ccp4bb] Symmetry axes

Dear All can some one advise that how to calculate/draw the symmetry axes on the structure. On the deposited structure one can do in the Jmol by selecting the symmetry option but how to do it off line. best Jiri

Re: [ccp4bb] problem with AMPLE

Thank you Daniel.

Re: [ccp4bb] problem with AMPLE

Dear Vikram AMPLE tries to create ensembles by clustering the ab initio models from, in this case, Rosetta. It has failed here because it has not found any pair of models that are similar enough by its criteria to superpose into a cluster. This is a sign that your 500 models are very diverse a