- phenixbb - phenix-online.org

Partially reduced disulfides
by Christopher Wanty 22 Mar '12

22 Mar '12

Hi, I have a structure that appears to have a combination of reduced and oxidised disulfides. >From previous reading on the board I've taken the strategy of dropping the disulfide detection cutoff to 0.1 then added back the disulfides as appropriate using restraints. The problem I now have is that for some of these cysteine pairs there are clearly oxidised and reduced positions in the density. Modelling altloc's for each of these works, but the occupancies do not refine as I expected; the altloc's involved in the disulfide I expected to have the same occupancy as their counterpart in the disulfide. To try to get these to match, I introduced occupancy constraint that look like: constrained_group { selection = (chain A and resseq 276 and altloc B) or (chain A and resseq 286 and altloc B) } But with that the sum of occupancies for altloc 276 (for example) is not adding to 1.00. My thought is that I need to change the occupancy constraints but I'm not sure how to make them do what I want. Any help/advice is appreciated. Regards, Chris ------------------------------------------------------- Dr. Christopher Wanty christopher.wanty(a)uwa.edu.au Research Associate Biomolecular, Biomedical and Chemical Sciences, Building M310 University of Western Australia 35 Stirling Highway Crawley 6009 Western Australia Australia

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Documentation in last Dev versions
by Alexander Batyuk 22 Mar '12

22 Mar '12

Dear developers, Is there any particular reason for missing documentation file in phenix-dev-1008 and up (it could not be found on the website as well)? dev-1005 is fine. Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Hydrogens
by Christopher Wanty 21 Mar '12

21 Mar '12

Hi all, I've been refining with riding hydrogens, and from what I've read hydrogen contribution should be included in Fo calculation automatically for maps. What I'm seeing after refinement is a lot of little bits of green in the difference density that look like they could be explained by hydrogens. I'm working at 1.4A, attached image gives an example and shows contours at 3 sigma for difference map. Is there a setting/parameter I need to adjust to get this to work properly? Kind Regards, Chris ------------------------------------------------------- Dr. Christopher Wanty christopher.wanty(a)uwa.edu.au Research Associate Biomolecular, Biomedical and Chemical Sciences, Building M310 University of Western Australia 35 Stirling Highway Crawley 6009 Western Australia Australia

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building a peptide-like polymer with phenix.elbow
by Geoffrey Feld 21 Mar '12

21 Mar '12

Greetings, I have a co-crystal structure of a protein bound to an interesting polymer -- poly-D-g-glutamic acid (poly glutamic acid with D chirality and gamma linked, rather than alpha linked). In the structure, I have density corresponding to different links, from 1 to 6 (so far). I'd like to build a ligand that has "residues" much like a polypeptide polymer so that I can refine each residue individually (hopefully in COOT). Up till now, I've been using SMILES to generate the different length polymers so I have pdbs and cif files, and then (painstakingly) modelling them into COOT, building restraints for refinement, etc. More recently, I used maestro to build a dimer that at least has the right atom labels you'd expect for a protein. However, I can't use phenix now to generate cif files because it is confused by the GLU. Is there a way to use phenix.elbow to make a multi-residue polymer? I'm also doing some monte carlo minimizations in macromodel to generate models of the various low energy states and would like to use them as building blocks, so an easy order-of-operations would be to generate the files in macromodel and feed them in via pdbs to phenix.elbow to generate cif restraints. Any help on this would be greatly appreciated. Cheers, Geoff -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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a small trick for SDS-Gel storage
by Kevin Jin 20 Mar '12

20 Mar '12

Dear All, Maybe most of you already knew. I just put my understanding of SDS page gel storage here, if you want to make gel yourself and safe some money. http://www.jinkai.org/SDS_page.html If I am wrong, please let me know. Sharing knowledge each other is always joyful. -- Kevin Jin Protein crystallographer and Biopolymer chemist Personal Website: http://www.jinkai.org/

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A possible conjugative relaxase with novel fold for DNA cleavage?
by Kevin Jin 20 Mar '12

20 Mar '12

Dear All, The protein structure of Jann_2411 (PDB 3H0N) from Jannaschia sp. strain CCS1 carries a novel fold for unknown function. Zn-finger is indentified in the C-terminus. However, the N-terminus with a metal binding site presents a novel fold. As the person who solved and characterized this protein, I would like to put some further observation here for your consideration. My analysis is available here: http://www.jinkai.org/Novel_fold_3H0N.html Best regards, Kevin -- Kevin Jin Protein crystallographer and Biopolymer chemist Personal Website: http://www.jinkai.org/

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NCS operators
by Melania Strycharska 19 Mar '12

19 Mar '12

Dear all, I have a bit of a problem applying NCS to my fairly low resolution structure. If I try to look for NCS symmetry automatically - phenix doesn't find any. If I specify sections that I want to be related by NCS, the script usually crashes. I have a dimer in the asymmetric unit, however it appears that one domain is related by 3-fold symmetry while the other is related by 6 fold symmetry. I can "cheat" phenix and generate operators for each of the domains by feeding a stripped pdb file (one that contains only a dimer of one domain or the other) to phenix.simple_ncs_from_pdb and then it easily identifies the ncs operators... unfortunately the simple_ncs_from_pdb.ncs file generated that is meant to be fed into phenix.refine contains only the chain selections, not the actual operators. Is there a way to specify different NCS operators (rotational matrix and translational vector) for specific chain selections in the .eff file or under GUI? or if there isn't, how can I still take advantage of my NCS symmetry? Also, is there any obvious reason why NCS operators that I generated with Phenix do not match the operators that I found using CCP4 Lsqkab? (yes I already accounted for chain A moving onto B or chain B moving onto A) Can I choose to apply NCS symmetry to just my backbone? How would I specify that? thanks so much! Melania

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GUI parameter files
by Leonid Sazanov 19 Mar '12

19 Mar '12

Hi, I have a following problem in dev-874 version: If I restore a previous job in refine GUI, to run it with modified settings, and include a new parameter file .eff with definitinon of secondary structure restrains, these new restrains are combined with previously used restrains. How do i get rid of previous restrains? Older file is not visible in inputs, but its settings are still used. And in general, how can one be sure which parameters are used at the start of each refine run? If older settings loaded from .eff or .param file are not visible, the only way is to look through new .eff file, which takes a lot of time. Has this been solved in latest builds perhaps? Thank you, Leo -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Refinement using data with pseudo translational symmetry
by Bret Wallace 18 Mar '12

18 Mar '12

To all, First I apologize for the long email, but I wont to make sure that I give enough information to describe the problem. I have been working on a structure of two proteins in complex with each other (one forms a homodimer, with each monomer bound to 1 monomer of the other protein), using data, that according to phenix.xtriage contains pseudo translational symmetry (output pasted below). I have done a lot of searching of both the phenixBB and ccp4BB regarding solutions to this problem, but unfortunately most responses seem to be directed at resolving issues with MR. I have successfully performed MR using both phenix phaser, ccp4 phaser (the most updated version), as well as molrep. The issue arises upon structure refinement, where my Rwork and Rfree are essentially stuck at 28 and 33, respectively. I have built the entire structure, including ligands, except for any solvent molecules. Here are the details for the data/structure: SG: P212121 Cell: 72 124 175 90 90 90 Res: 50-2.8 Patterson analyses ------------------ Largest Patterson peak with length larger than 15 Angstrom Frac. coord. : 0.155 0.000 0.500 Distance to origin : 87.222 Height (origin=100) : 34.517 p_value(height) : 6.739e-04 The reported p_value has the following meaning: The probability that a peak of the specified height or larger is found in a Patterson function of a macro molecule that does not have any translational pseudo symmetry is equal to 6.739e-04. p_values smaller than 0.05 might indicate weak translational pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are a very strong indication for the presence of translational pseudo symmetry. Xtriage notes that the if the PTS is crystallographic, that C2221 is a possible SG (x+1/6, y, z+1/2). However, neither XDS or HKL picks orthorhombic C, and the indexing/integrating doesn't work if I force it. I should also not there is no twinning detected by either xtriage or twinning servers. I have done a number of things to try to resolve this: -rescaling in lower symmetry (P21 and P1) -rescaling in the PG P222 and letting the MR program decide the proper space group -shifting origin and re-refining -a number of different refinement protocols (TLS, optimized weights/adp, simulated annealing, several cycles of rigid body, etc.) I have used HKL2000 and XDS to index/integrate/scale the data, both yield the same results, with slightly different completeness and Rmerge values, but refining with either gives similar R factor values. Does any know of any other possible things I should try to refine this data? I am happy to provide additional information upon request. Thanks in advance for any help! Bret

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selectively remove bond length restraints on atoms
by Maxime Cuypers 15 Mar '12

15 Mar '12

hello, What is the best way to selectively remove bond length restraints on some selected atoms for phenix.refine? i found the commands for a .param file: refinement { geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } } but no bond length command in the manual online. http://www.phenix-online.org/version_docs/dev-283/refinement.htm otherwise there is the commands refinement { geometry_restraints.edit { bond { action= *delete change atom_selection_1= (selection1 here) atom_selection_2= (selection2 here) distance_ideal= None } } } is it a good way to deal with the problem ? thanks in advance for your help. Maxime

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