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SA omit map for ligand
by Tjaard Pijning 27 May '11

27 May '11

Hi, I am trying to make an SA-omit Fo-Fc map for a sugar ligand (chain B) bound to protein (structure solved by MR), without doing any rebuilding of protein or ligand – just calculate an Fo-Fc map that I can load into PyMol. So far I used the AutoBuild – Create omit map module with these settings : - input files : model (protein+ligand+waters), data (.mtz), restraints for sugar ligand (.cif) - omit map type : simulated annealing - omit region : omit selection - omit map options : keep input waters, omit chain list : omit_chain_list chainB However, the ligand gets modified even though I use “omit_chain_list chainB”. What are the parameters to set to keep the model (protein, ligand, waters) from being rebuilt ? Furthermore, what is the procedure to load the SA Fo-Fc omit map into pymol ? Phenix version is 1.6.4-486. Thanks in advance, Tjaard Ing. Tjaard Pijning Research Assistant Protein Crystallography Group Nijenborgh 7 9747 AG Groningen The Netherlands (31)(0)50 363 43 85

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get_cc_mtz_pdb results
by Jerome Nwachukwu 27 May '11

27 May '11

Hi: I am using get_cc_mtz_pdb to compare some structural models and found differences in overall CC around ~0.0056 and local CC around 0.0033. How much difference in local and overall CC values between two models is generally considered significant? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

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a new PDB clustering tool available in phenix from nightly build dev-756
by Francois Berenger 26 May '11

26 May '11

Dear Phenix users, Starting from the nightly build dev-756, a new clustering tool called DURANDAL is included in Phenix. It performs exact clustering of proteins in PDB format, fast. It is primarily aimed at people working in protein structure prediction and having to deal with a lot of protein models. The correspondence used to compute CARMSD for a pair of proteins is 1 to 1. If two proteins A and B are to be optimally superposed, both PDB files (A.pdb and B.pdb) must have the same numbers of alpha carbons. The first alpha carbon in A.pdb will be matched to the first alpha carbon in B.pdb, and so on. Clustering up to 20,000 PDB files should work on most machines. Workstations with a lot of memory will be able to cluster even more files. Examples: --------- * to perform exact clustering using a fixed cutoff value of 3.0 Angstroms: durandal.cluster_pdbs -i [file_containing_one_PDB_filename_per_line]\ -d 3.0 -o out -s -v * there is also another tool included, to compute CARMSD of many files versus a reference one (the first in the list is considered the reference): durandal.rank_pdbs [file_containing_one_PDB_filename_per_line] If you want to know more about how the software is working, you can have a look at http://bioinformatics.oxfordjournals.org/content/27/7/939 Don't hesitate to ask if you encounter any problem while using the software. Best regards, Francois Berenger.

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ADP refinement
by Christian Roth 26 May '11

26 May '11

Dear all, I am sorry for this very stupid question, but I probably overlooked the relevant text in the documentation. I requested the refinement of a heavy atom (chloride) with anisotropic ADP. In the log than isotropic refined ADP were set for 0 atoms. I guess I have to define all other chains as isotropic. Is that right. I have a lot of chains, it would be possible but a pain (more than 40 chains). Is there a something like refine anisotropic chain x and all others isotropic? Thanks and best Regards Christian

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Quick PHENIX install question
by Yuri 26 May '11

26 May '11

Hello PHENIXers, I just got a computer with Red Hat workstation 5 running 64-bit architecture. Which build should I install? Thank you -- Yuri Pompeu

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Equations of transformation
by Hena Dutta 25 May '11

25 May '11

Dear Members, Sorry, if my question is out of the field. I want to know the mathematical relations between 2 sets of co-ordinates, one before and one after the rotation. I used COOT to rotate the side chain (containing atoms N1, C2, N3, C4, C5, C6, N6, N7 and C8) of Adenine by 180 degree about the glycosidic bond (C1’-N9). How the initial co-ordinates (Xi, Yi, Zi) and final co-ordinates (Xf, Yf, Zf) are mathematically related? I shall be very grateful if someone can tell me the equations. Regards... Hena

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Refining sucrose
by Priit Eek 23 May '11

23 May '11

Hi, I couldn't find this (probably basic knowledge) in the manual or here, so... I have a problem with refining a sucrose ligand. It is not covalently bound to the protein – just electrostatic interaction. The density isn't the best, but it's still obvious it must be there. LigandFit can find the blob and fits the sucrose in there quite well, but when I run phenix.refine it distorts the geometry of the molecule and complains about it later in MolProbity - Basic Geometry validation in almost every possible way. How can I apply more stringent restraints to the ligand so its geometry wouldn't get so twisted? This might not be the most appropriate list for my second question, but the problem is the same and somebody probably knows: how to manually modify that sucrose in Coot (eg rotate only one ring or a -CH2OH group) or perform real space refinement? Right now I can only rotate/translate the whole sucrose and trying to perform a real space refinement results in an error ("Failed to match (to the dictionary) the following model atom names: SUC C1 C2 C3 C4 C5 C6 O1 O2 O3 O4 O6. That would cause exploding atoms, so the refinement didn't start.") I haven't specified any custom cif libraries as SUC should be present in the built-in library of both Phenix and Coot. I'm using Phenix v1.7.1-743 and Coot v0.6.2-pre-1-rev3450 on OS X 10.6.7. Thank you in advance! Regards, Priit Eek

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Call for articles and short communications for Computational Crystallography Newsletter
by Nigel Moriarty 23 May '11

23 May '11

Dear Colleagues I'm accepting short communications and articles of general interest to crystallographers working on macromolecular systems for the next issue of the Computational Crystallography Newsletter. You can see recent issues at http://www.phenix-online.org/newsletter/ as well as the word template for article submission. The deadline is June 17th but early submission is appreciated. Nigel -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Weird R-free discrepancy.
by Yuri 21 May '11

21 May '11

I was working on a model for at 1.9 A using the previous phenix release (650). I was almost finished r-free was 0.197. I installed the newest release and refined again and my r-free went up to 0.228!!. The values for bsol and ksol look significantly different. I do not understand where the biggest difference is coming from... Below I pasted part of the .log files. Old and new, respectively. =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.90 - 28.74 A; n_refl. = 32203)------------------------------| | | | r_work= 0.1747 r_free= 0.1967 ksol= 0.40 Bsol= 39.70 scale= 0.064 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-1.65,-1.65,3.31,-0.00,0.00,0.00); trace/3= -0.00 | | | | maximum likelihood estimate for coordinate error: 0.21 A | | x-ray target function (ml) for work reflections: 2.567485 | =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.90 - 28.74 A; n_refl. = 34277)------------------------------| | | | r_work= 0.1911 r_free= 0.2279 ksol= 0.40 Bsol= 59.62 scale= 0.063 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-1.73,-1.73,3.47,0.00,0.00,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.55 A | | x-ray target function (ml) for work reflections: 2.591014 | |-----------------------------------------------------------------------------| -- Yuri Pompeu

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BRU error
by Krystle Williams McLaughlin 20 May '11

20 May '11

Hi, I'm using phenix for refinement and I keep getting an error. My DNA strand has a bromo-uridine in it and phenix.refine keeps crashing on this nucleotide. Here is the error: Number of atoms with unknown nonbonded energy type symbols: 40 "ATOM 2770 P BRU P 5 .*. P " "ATOM 2771 O1P BRU P 5 .*. O " "ATOM 2772 O2P BRU P 5 .*. O " "ATOM 2773 O5* BRU P 5 .*. O " "ATOM 2774 C5* BRU P 5 .*. C " "ATOM 2775 C4* BRU P 5 .*. C " "ATOM 2776 O4* BRU P 5 .*. O " "ATOM 2777 C1* BRU P 5 .*. C " "ATOM 2778 N1 BRU P 5 .*. N " "ATOM 2779 C6 BRU P 5 .*. C " ... (remaining 30 not shown) Here is what I have in my pdb: ATOM 2901 P BRU E 5 33.977 -16.324 24.303 1.00 27.21 P ATOM 2902 O1P BRU E 5 34.027 -15.724 22.919 1.00 28.22 O ATOM 2903 O2P BRU E 5 33.857 -15.340 25.393 1.00 25.06 O ATOM 2904 O5* BRU E 5 32.721 -17.236 24.418 1.00 28.02 O ATOM 2905 C5* BRU E 5 32.487 -18.228 23.495 1.00 28.50 C ATOM 2906 C4* BRU E 5 31.047 -18.347 23.082 1.00 32.59 C ATOM 2907 O4* BRU E 5 30.337 -18.858 24.152 1.00 28.61 O ATOM 2908 C1* BRU E 5 29.369 -17.891 24.535 1.00 29.63 C ATOM 2909 N1 BRU E 5 29.279 -17.855 25.962 1.00 29.72 N ATOM 2910 C6 BRU E 5 30.426 -17.755 26.799 1.00 30.57 C ATOM 2911 C5 BRU E 5 30.251 -17.738 28.232 1.00 30.89 C ATOM 2912 BR BRU E 5 31.869 -17.591 29.321 1.00 57.08 Br ATOM 2913 C4 BRU E 5 28.917 -17.845 28.826 1.00 30.70 C ATOM 2914 O4 BRU E 5 28.768 -17.825 30.033 1.00 29.36 O ATOM 2915 N3 BRU E 5 27.785 -17.945 27.981 1.00 29.36 N ATOM 2916 C2 BRU E 5 27.961 -17.966 26.552 1.00 29.05 C ATOM 2917 O2 BRU E 5 26.994 -18.064 25.848 1.00 35.29 O ATOM 2918 C3* BRU E 5 30.464 -17.006 22.751 1.00 34.58 C ATOM 2919 C2* BRU E 5 29.845 -16.605 23.968 1.00 33.10 C ATOM 2920 O3* BRU E 5 29.526 -17.213 21.768 1.00 37.93 O I have already run a BRU molecule through ReadySet and when I use the cif file generated from this phenix.refine will run through but when the Bromine atom is in the structure has a large negative density peak in the Fo-Fc map. I think it may just be a naming thing. BRU is already in the monomer library so I don't understand why I get an error at first also without the readyset cif file. Any suggestions? Thanks, Krystle

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