March 2012 - phenixbb - phenix-online.org

links in phenix summary
by Christian Roth 04 Apr '13

04 Apr '13

Dear all, thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions. I have summarised a few things which one might consider if nonstandard links are necessary. Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script: elbow.ligand_linking model.pdb Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary. Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement. For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using iotbx.show_distances your.pdb > all_distances Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix! Christian

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How to include restraints when refining DNA?
by Xun Lu 03 May '12

03 May '12

Dear all, I am refining a protein-DNA complex structure at 2.9A resolution. The R/Rfree is 0.2181/0.2501, which is pretty good, but I can tell that the DNA is not well refined. Some sugar puckers are not right. The distances between some base-paired bases are kind of short (~2.5A). I've tried including a reference model for the DNA, or including a cif file, and I've also tried to turn on the secondary_structure_restraints.... nothing worked. I must have not done it in a correct way. But how to do it? And how to deal with sugar puckers? In refmac, I can set the distances between bases during the refinement, so there must be a way to do it in phenix as well? Any advice is welcome. Thanks! Xun -- Department of Molecular and Structural Biochemistry North Carolina State University

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cut-out mtz edition
by Dialing Pretty 26 Apr '12

26 Apr '12

Dear All, I just cut out a fragment of chain and the corresponding electron density from the whole molecule. Will you please give me some suggestion on how to edit the attached file so that those electron density not from the protein fragment can be erased? Or do you have other methods to produce high quality figure which just shows the fragment chain and the fragment eletron density? Cheers, Dialing

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DEN refinement is crashing
by Mario Sanches 03 Apr '12

03 Apr '12

I am running phenix.refine using the graphical interface. Under "global refinement paramerters..." I am selecting "DEN". The problem is that Python crashes all the time, always at the same point (see portion of the log output below). Is it a known bug? Is DEN incompatible with some of the options in refinement? My resolution is 2.9A by the way. Thank you for your inputs. Mario Sanches ___________________________ Log output final portion: tardy dynamics: number of bodies: 3678 number of degrees of freedom: 3713 number of atoms * 3: 38220 ratio: 0.097 = 1/10.29 temperature degrees of freedom: cartesian (38220) kinetic energy sensitivity to generalized velocities: n: 3713 min: 3.61771e-06 max: 0.0300001 mean: 0.00410663 time step: 0.00100 pico seconds velocity scaling: True suppressing allowed origin shifts: False new target temperature: 2500.00 K step= 1 temperature= 2500.0 rmsd=0.0446 r_work=0.3010 r_free=0.3214 -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches

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very informative - Trends in Data Fabrication
by Bosch, Juergen 31 Mar '12

31 Mar '12

really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen Acta Cryst. (2012). F68, 366-376 doi:10.1107/S1744309112008421<http://dx.doi.org/10.1107/S1744309112008421> Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen B. Rupp<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Rupp,%20B.> Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4>). A variety of analytical tools, including the application of Diederichs plots, R plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/

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Problems fitting NADH
by Phillip Steindel 31 Mar '12

31 Mar '12

Dear all, I'm trying to fit a NADH into a 1.7 Å structure. LigandFit worked with just the three-letter code (NAI), however phenix.refine won't work with just the model. If I use eLBOW to create restraints, meanwhile, the ligand gets distorted during refinement (non-tetrahedral phosphates, mainly). I'm not sure exactly how I'm supposed to be generating these restraints- any help is appreciated. Thank you, Phillip Steindel Theobald Lab Department of Biochemistry Brandeis University

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Re: [phenixbb] [ccp4bb] a small trick for protein and organic compound cocrystallization.
by Bryan Lepore 31 Mar '12

31 Mar '12

On Fri, Mar 30, 2012 at 3:26 PM, Jacob Keller <j-keller2(a)fsm.northwestern.edu> wrote: > What's the harm? have you seen usenet/Google groups? -Bryan

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a small trick for protein and organic compound cocrystallization.
by Kevin Jin 31 Mar '12

31 Mar '12

Dear All, Here is way I have used for protein and hydrophobic organic compound cocrystallization. Via this method, less amount of DMSO will be used to aviod protein ppt. I hope you can use for your research. http://www.jinkai.org/Xtal.html Regards, -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/

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Re: [phenixbb] need help for crystallization
by Kevin Jin 31 Mar '12

31 Mar '12

My pleasure ! Since this may be help for other people, I also cc it to CCP4BBS. According to your email, I guess the buffer is phosphate buffer at pH 7.4. You can do a quick buffer exchange before crystallization. Since PO4 is a competitor in this case, I will also avoid PO4 and Cocodylate buffer from screen kits. Here is what you can do, 1. concentrate your protein using an amicro centrocon with 3KD cutoff. 2. Measure how much buffer has been spin down, then add equal amount of Tris with same pH back to the top. 3. Then, spin down again. 4. Repeat several times, 5 times may be good enough. 5. Most of Phosphate buffer should be removed. That's what I used before. Let me know if it works. Best, Kevin Jin On Fri, Mar 30, 2012 at 9:40 AM, Afshan Begum <afshan490(a)yahoo.com> wrote: > > Dear Kevin > > I have seen your website and come to you to discuss my problem actually i > want to co-crystallized my enzyme with inhibitor but problem is that the > phosphate ion come to the active site and occupied the cavity and my > inhibitor not bind to the active center i purchase this enzyme from a > commercial source and they purify with phosphate buffer that's why also > phosphate is occupied the cavity how can i get ride of it from the active > center could you kindly help me regarding this i would be really thankful to > you. > > > Best Regards > > AFSHAN > =========================================== > Dr. Afshan Begum > University of Hamburg > Institute of Biochemistry and Molecularbiology > Laboratory for Structural Biology of Infection and Imflammation > c/o DESY, Build. 22a > Notkestr. 85 > 22603 Hamburg > Germany > Home phone: +49 40 22888618 > Fax: +49 40 8998-4747 > E-mail: afshan490(a)yahoo.com > -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/

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Re: [phenixbb] phaser_ep
by Airlie McCoy 30 Mar '12

30 Mar '12

Dear Kay, You can control the distance for the atom separation/anisotropy in Phaser with the llgcomplete.clash input parameter. By default llgcomplete.clash is zero, which means Phaser will calculate a value based on the resolution. If a value is set this will override the default. Apologies, this was not explained in the wiki, but is now! Airlie

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