Dear Antony, Have you considered MAIN - www-bmb.ijs.si ? best regards, dusan
On Jun 19, 2014, at 1:06 AM, CCP4BB automatic digest system <lists...@jiscmail.ac.uk> wrote: > There are 6 messages totaling 843 lines in this issue. > > Topics of the day: > > 1. Rotamer Selection in Low Resolution Data (4) > 2. Refinement > 3. [phenixbb] Calculation of RSR for a fragment of PDB > > ---------------------------------------------------------------------- > > Date: Wed, 18 Jun 2014 15:39:02 +0000 > From: Antony Oliver <antony.oli...@sussex.ac.uk> > Subject: Rotamer Selection in Low Resolution Data > > Dear Crystallographic Community, > > Apologies for the cross-posting, but I *do* routinely use programs from all > three software packages. > > I find myself refining a relatively low resolution structure (3.5 Angstrom) - > with 8 molecules in the asymmetric unit. > Is there a *simple* automated way to place “optimal-fit to electron density" > side-chain rotamers into my model? > Preferably in an NCS-independant manner? > > With thanks, > Antony. > > - - - - - - - - - - - - - - - - - - > Dr Antony W Oliver > Senior Research Fellow > CR-UK DNA Repair Enzymes Group > Genome Damage and Stability Centre > Science Park Road > University of Sussex > Falmer, Brighton, BN1 9RQ > - - - - - - - - - - - - - - - - - - > email: antony.oli...@sussex.ac.uk<mailto:antony.oli...@sussex.ac.uk> > > tel (office): +44 (0)1273 678349 > tel (lab): +44 (0)1273 677512 > > http://www.sussex.ac.uk/lifesci/oliverlab > http://tinyurl.com/aw-oliver > - - - - - - - - - - - - - - - - - - > > ------------------------------ > > Date: Wed, 18 Jun 2014 09:13:57 -0700 > From: Pavel Afonine <pafon...@gmail.com> > Subject: Re: Rotamer Selection in Low Resolution Data > > Hi Antony, > > Apologies for the cross-posting, but I *do* routinely use programs from all >> three software packages. >> >> I find myself refining a relatively low resolution structure (3.5 >> Angstrom) - with 8 molecules in the asymmetric unit. >> Is there a *simple* automated way to place “optimal-fit to electron >> density" side-chain rotamers into my model? >> Preferably in an NCS-independant manner? >> > > naively assuming that one of the "three software packages" that you did not > mention by name is Phenix: > yes, you can do it in a number of different ways. Let me know if interested > and I will list all options. > > Pavel > > ------------------------------ > > Date: Wed, 18 Jun 2014 16:21:20 +0000 > From: Antony Oliver <antony.oli...@sussex.ac.uk> > Subject: Re: Rotamer Selection in Low Resolution Data > > Hi Pavel, > > Sorry… the current ‘triumvirate’ is, in no particular order: > > CCP4, Phenix and Buster (Global Phasing). > > Any suggestions would indeed be useful. > > Many thanks, > > Antony. > > - - - - - - - - - - - - - - - - - - > Dr Antony W Oliver > Senior Research Fellow > CR-UK DNA Repair Enzymes Group > Genome Damage and Stability Centre > Science Park Road > University of Sussex > Falmer, Brighton, BN1 9RQ > - - - - - - - - - - - - - - - - - - > email: antony.oli...@sussex.ac.uk<mailto:antony.oli...@sussex.ac.uk> > > tel (office): +44 (0)1273 678349 > tel (lab): +44 (0)1273 677512 > > http://www.sussex.ac.uk/lifesci/oliverlab > http://tinyurl.com/aw-oliver > - - - - - - - - - - - - - - - - - - > > On 18 Jun 2014, at 17:13, Pavel Afonine > <pafon...@gmail.com<mailto:pafon...@gmail.com>> wrote: > > Hi Antony, > > Apologies for the cross-posting, but I *do* routinely use programs from all > three software packages. > > I find myself refining a relatively low resolution structure (3.5 Angstrom) - > with 8 molecules in the asymmetric unit. > Is there a *simple* automated way to place “optimal-fit to electron density" > side-chain rotamers into my model? > Preferably in an NCS-independant manner? > > naively assuming that one of the "three software packages" that you did not > mention by name is Phenix: > yes, you can do it in a number of different ways. Let me know if interested > and I will list all options. > > Pavel > > ------------------------------ > > Date: Wed, 18 Jun 2014 13:25:24 -0400 > From: Remie Fawaz-Touma <remiefa...@gmail.com> > Subject: Refinement > > Hi all, > > I need to refine a structure keeping the ligands or some of the ligands > intact (in same positions as before refinement). > Please give me specific instructions if you are familiar with this procedure. > I am using Refmac 5 in CCP4. > > Thanks so much for your help. > > Remie > > ------------------------------ > > Date: Wed, 18 Jun 2014 14:28:54 -0400 > From: "Edward A. Berry" <ber...@upstate.edu> > Subject: Re: [phenixbb] Calculation of RSR for a fragment of PDB > > On 06/16/2014 04:26 PM, George Devaniranjan wrote: >> Hi everyone, >> >> I apologize at the beginning itself as I am new to using PHENIX/X-ray >> crystallography so this question might not make the most sense but I will >> try and explain it well. >> >> I cut out a part of a map for a PDB fragment using phenix map cut out >> density resulting in a MTZ file. >> >> Now I changed the fragment (changed its phi and psi externally) and want to >> calculate the RSR [real-space R -factor] for the model based on the old >> density (to check if I have made things worse or not). >> >> how can I go about this? I tried using phenix.refine couldn't get it to work. >> >> I have attached the MTZ fragment, the original PDB fragment and the modified >> PDB fragment. >> native: nativeFragment.pdb >> model: modelledFragment.pdb >> MTZ: cut_out_density.MTZ >> >> (I can see mine is worse but I want to quantify that "badness") >> > > I'm sure phenix has tools to do what you want, but if you still have > difficulty > and want to go back to G. Kleywegt's suggestions of using mapman, step by step > instructions are below. > > First you need to understand that an mtz file is not a map- > a map is a list of the value of density at points, like pixels in a digital > picture > but in 3D (voxels) instead of 2D. > The mtz file contains structure factors which are the Fourier transform > coefficients > of the map. With modern computers the map can be calculated rapidly from the > structure > factors, and many applications work directly with mtz files and never save a > map file. > Still the distinction is important- for examples you cannot calculate a CC > between > mtz files in a defined area, because of the all-on-all relation between > reflections and realspace. You can calculate the CC between two maps in a > defined > area, which is what the suggested mapman command does. > > As I understand it, mapman calculates the RSCC and RSR between two maps- the > pdb file is only used to define the area in which the values are calculated. > Since it uses the pdb to define the area, there is no need to cut out density > around the fragment- I recommend using the original mtz to calculate the > "obs" map, > that way you can use the same one for all fragments. > > So you need to calculate > a map from the original mtz covering all the fragments > a map (Fc-Phic) from your fragment > (They presumably must have the same cell parameters and grid spacing) > and give them together with the fragment.pdb to mapman. > > Do this once for nativefragment.pdb > and again for modelledfragment.pdb > and compare the results > Remember phases in the original mtz wil be biased in favor of the original > model, > so if the modified ragment is equally good it will still get a worse score. > > step by step: > > 1. Use fft to calculate a map from the original mtz: > From the ccp4i gui, on the left side, select program list, then under that > fft. > fill in according to the screen shot at http://sb20.lbl.gov/ccp4/RunFFT-1.png > (this is working with your cut-out-density.mtz but I recommend using the > original mtz). see notes below. > > 2. Use sfall to calculate SF's from nativefragment.pdb making > nativefragment.mtz > (http://sb20.lbl.gov/ccp4/RunSFALL.png) > (with a script sfall can make the map directly, don't see that in the > gui) > > 3. use fft to calculate a map from nativefragment.mtz > (http://sb20.lbl.gov/ccp4/RunFFT-2.png) > > 4. run mapman in the directory where these files were created: > > MAPMAN > read m1 cut_out_density.map ccp4 > MAPMAN > read m2 nativefragment.map ccp4 > MAPMAN > RS_fit > Which obs_map ? (m2) m1 > Which calc_map ? (NATIVEFRAGMENT.MAP) m2 > Model PDB file ? (m1.pdb) nativeFragment.pdb > RS-fit list output file ? (rs_fit.list) fragment27CC.txt > > . . > Non-water residues with RSCC : ( 28) > ... Average RSCC for these : ( 0.775) > > Non-water residues with RSR : ( 28) > ... Average RSR for these : ( 0.247) > > 6. now repeat 2 - 4 using modified fragment instead of native fragment > > > Notes- > FFT-1: > Uncheck the box that says "append to an existing . . ." > FFT will probably guess which columns to use, at least if coot was able to > auto-open. > if this is blank and you don't know, send a list of the column labels. > set the resolution say 100 to 2 A. > click the bar that opens up "infrequently used options". You need to > set the grid spacing so it will be the same in both maps, and fine > enough that it doesn't distort either map. Should have no large prime > factors- power of 2 like 64, 128 etc is fine. > (Or let sfall choose grid based on resolution, note what it is and use the > same > in step 3 when you make the other map) > If your original mtz is not P1 and all of the fragments are not in the > asymmetric unit, > you may need to use the option to extend map to cover (whole) pdb > You only need to do this once in that case, for all the fragments. > > sfall: make sure the cell param are the same as in step 1, which will be > determined by orig mtz. > > fft-2: use the same grid as in step 1. cell param taken from the mtz should > be right > > ------------------------------ > > Date: Wed, 18 Jun 2014 15:11:25 -0700 > From: Pavel Afonine <pafon...@gmail.com> > Subject: Re: Rotamer Selection in Low Resolution Data > > Hi Antony, > > (Sorry for replying with Phenix specific suggestions in non-Phenix forum. > Since the whole conversation started here and seems to move on I thought > it's best to keep it here rather than move off-list or to a more tailored > list. Also several people expressed the interest asking directly.) > > ok, here is the list. Some options are not exactly what you want but > relevant and (very) close, some are supposed to do just what you want. > Also, I assume you have the latest version of Phenix. > > *1) Use phenix.real_space_refine:* > > http://phenix-online.org/documentation/reference/real_space_refine.html > For this you need a model (PDB file) and a map in CCP4 format or Fourier > map coefficients. > Since I'm not certain which one is going to work best in your specific > case, I would run it in two ways (sorry, not GUI yet): > > phenix.real_space_refine model.pdb map_coefficients.mtz > phenix.real_space_refine model.pdb map_coefficients.mtz > run=minimization_global+local_grid_search > > Both should tidy up geometry while keeping best fit to the map, and also > result in models with NO rotamer outliers or just a few (if you get > outliers I would be interested to know, as this is not expected). The > second option may run considerably longer. Resulting model should be a good > starting point for usual reciprocal-space refinement in phenix.refine or > other refinement program of your choice. > > map_coefficients.mtz can be MTZ file out of a phenix.refine (it will > contain 2mFo-DFc map coefficients) or any other MTZ file containing an > equivalent map coefficients. You may be prompted to specify them when > running phenix.real_space_refine. Also, you can calculate the map like this > > phenix.maps model.pdb data.mtz > > or using the GUI. > > *2) Idealize model geometry minimally moving the model from starting > (initial) position.* > > This is done using phenix.geometry_minimization (available in the GUI; some > command line defaults may be different in the GUI): > http://phenix-online.org/documentation/reference/geometry_minimization.html > > Using as simple as > > phenix.geometry_minimization model.pdb > > or drop in your file into the GUI, make sure you check "fix rotamers" box, > and run. > > By default it will idealize all usual targets: bond, angle, planarity, > dihedral, chirality, as well as it will use C-beta deviations restraints > and for each residue side chain rotamer outlier it will switch it to the > nearest valid rotamer. On top of that, optionally, you can add > secondary-structure and Ramachandran plot restrains. Ramachandran plot > restrains come in two different flavors, which is a topic of a separate > discussion - let me know if you get to this! > > Important: since diffraction data is not used here, the resulting model can > (potentially) deviate quite a lot from the starting one. Most likely you > don't want this if you want to use this model to continue refinement. To > make sure the model does not deviate much from initial state you can > restrain it to starting point (I don't remember if these parameters are > exposed in the GUI): > > phenix.geometry_minimization model.pdb > reference_restraints.restrain_starting_coord_selection=all > reference_restraints.coordinate_sigma=0.7 > > You can be more specific, and restrain only selected atoms to initial > position: > > phenix.geometry_minimization model.pdb > reference_restraints.restrain_starting_coord_selection="chain A and resseq > 1:123" reference_restraints.coordinate_sigma=0.7 > > *3) Use phenix.refine.* > > In theory a default phenix.refine run includes step #1 above. In reality > I'm yet to optimize how real- and reciprocal-space refinements play > together in most optimal way. This means that while real-space refinement > part of phenix.refine will fix all rotamer outliers, its reciprocal-space > refinement part my not keep them all. Also, in case of large molecule > real-space refinement in phenix.refine may take quite some time. > > *In summary*, my suggestion is to try all three options with all plausible > to your case variants each one offers, and see which one works best. > > Good luck! > Pavel > > > On Wed, Jun 18, 2014 at 9:21 AM, Antony Oliver <antony.oli...@sussex.ac.uk> > wrote: > >> Hi Pavel, >> >> Sorry… the current ‘triumvirate’ is, in no particular order: >> >> CCP4, Phenix and Buster (Global Phasing). >> >> Any suggestions would indeed be useful. >> >> Many thanks, >> >> Antony. >> >> - - - - - - - - - - - - - - - - - - >> Dr Antony W Oliver >> Senior Research Fellow >> CR-UK DNA Repair Enzymes Group >> Genome Damage and Stability Centre >> Science Park Road >> University of Sussex >> Falmer, Brighton, BN1 9RQ >> - - - - - - - - - - - - - - - - - - >> email: antony.oli...@sussex.ac.uk >> >> tel (office): +44 (0)1273 678349 >> tel (lab): +44 (0)1273 677512 >> >> http://www.sussex.ac.uk/lifesci/oliverlab >> http://tinyurl.com/aw-oliver >> - - - - - - - - - - - - - - - - - - >> >> On 18 Jun 2014, at 17:13, Pavel Afonine <pafon...@gmail.com> wrote: >> >> Hi Antony, >> >> Apologies for the cross-posting, but I *do* routinely use programs from >>> all three software packages. >>> >>> I find myself refining a relatively low resolution structure (3.5 >>> Angstrom) - with 8 molecules in the asymmetric unit. >>> Is there a *simple* automated way to place “optimal-fit to electron >>> density" side-chain rotamers into my model? >>> Preferably in an NCS-independant manner? >>> >> >> naively assuming that one of the "three software packages" that you did >> not mention by name is Phenix: >> yes, you can do it in a number of different ways. Let me know if >> interested and I will list all options. >> >> Pavel >> >> >> > > ------------------------------ > > End of CCP4BB Digest - 17 Jun 2014 to 18 Jun 2014 (#2014-166) > ************************************************************* Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS "Jozef Stefan" e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com
