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How can I add another chain to my PDB by Coot
by Dialing Pretty 14 Nov '11

14 Nov '11

Dear All, By Phenix refine I got a PDB (Only one chain) and mtz output files. After analysis by Coot I find I need to add a protein fragment so that a large blob will disappear. I know I use Baton to construct the protein fragment. Will you please tell me how can I input the sequence file of the protein fragment so that I can refine the protein fragment by Coot? I am looking forward to getting your reply. Regards. Dialing

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twin/pseudo-symmetry question
by Green, Todd 11 Nov '11

11 Nov '11

Hello all- I have a question regarding the possibility of twinning and or psuedo-symmetry. I have a crystal that processes well in R32, ie. less than 6% r-merge at 2.2 angstrom. We collected multiple potential derivatives and were able to get some phasing from one that was good enough to model in the helices. The strange thing is that when looking at the harker sections there were a lot of unexplained strong peaks. And there is a very narrow range of parameters that we could get the sites with Shelx and end up with interpretable maps(i know that this part might not be unusual). My first thought was that there could be twinning. Since there is no twin law for this space group, I thought that it might suggest that there was twinning in a lower symmetry space group and/or that we have a pseudo-R32 crystal. Processing works well in C2 and R3, as expected. In those cases Xtriage suggests that the real symmetry is likely to be R32. In the case of C-2, xtriage suggetss if it is twinned then it is about 45% twinned. That's the background. Fast forward with the help of phenix Autobuild and some manual correction, we have been able to refine the structure with the R32 processed data(with tls) to r_work = 0.1894, r_free = 0.2287, bonds = 0.007, angles = 0.908 at 2.2 angstrom with almost everything accounted for. I think I should be quite comfortable with this. BUT, I'm still wondering about those Harker sections. I've been reading the manuscripts of Dauter regarding twinning and I think I am at this point more curious than anything. But not leaving well enough alone, I went back to the data processed in C2. I can easily do molecular replacement, following refinement at 2.3 angstrom(I need a lot more frames for this sg so the cutoffs are a bit lower but r-merge is ~ the same as R32) with TLS I get r_work = 0.1850, r_free = 0.2249, bonds = 0.007, angles = 0.946. this doesn't seem significant to me. However if I refine with the two possible twin operations, the values drop with one being better than the other. both have the same starting model: r_work = 0.1639 r_free = 0.1880 bonds = 0.006 angles = 0.902 r_work = 0.1582 r_free = 0.1866 bonds = 0.006 angles = 0.891 The twin fraction from the refined pdb header is 0.544 for the better statistical model and the r-values seem too low for 2.3 angstrom data. Is the high twin fraction suggestive of the higher symmetry space group or inconclusive towards that. of interest is that the maps look better to me than the r32 maps. by that i mean that the maps don't have what i would call minor dots of negative density for some(not a lot) of the side chains as we see for some side chains in the R32 case. also some side chains look better in the C2 twin refined case. Lastly for some of the monomers(there are now 6 copies versus 2 in the R32 case), I can add an additional residue or two on the termini which are not seen before. I wonder if this also suggests that the true space group is C2. Are these r-values too low? does the difference in values according to each twin law mean something? In the end, the models are essentially the same in either space group (with the exception of a couple of residues at the termini). So, I don't think I learn much one way or the other. But the curiocity keeps coming back. So is it likely to be R32 or C2 or C2 with a hefty twin fraction? Anyone have an explanation? Thanks in advance- Todd

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peptide link problem solved LINKR in pdb is not recognized but LINK is
by Christian Roth 10 Nov '11

10 Nov '11

Hi, In my pdb from Refmac the keyword LINKR is used but only LINK is interpreted by phenix. I changed this and now it works as it should. Sorry, a careful analysis sometimes help. Regards Christian

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peptide link
by Christian Roth 10 Nov '11

10 Nov '11

Hi, I have an modified aminoacid in my peptide chain (backbone modified). I have a cif file and I refined it previously in Refmac. I put the Link definition in the pdb and Refmac has interpreted the peptide link as I wanted. Now I did a run in phenix to compare the results and the chain is broken I created the SNN cif file with ReadySet Reel and I tried to incorporate the link definition via GUI in the following way apply_cif_link: data_link: TRANS residue_selection_1: chain A and resseq 366 residue_selection_2: chain A and resseq 367 apply_cif_link: data_link: TRANS residue_selection_1: chain A and resseq 367 residue_selection_2: chain A and resseq 368 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7983 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 496, 7926 Unusual residues: {'SNN': 1} Classifications: {'undetermined': 1, 'peptide': 495} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 37, 'TRANS': 456, None: 2} Not linked: pdbres="ASP A 366 " pdbres="SNN A 367 " Not linked: pdbres="SNN A 367 " pdbres="GLY A 368 " Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 This fails with an error message that it cannot interpret the links. In my previous pdbs I have also defined the atoms which I wanted to link. Maybe I have to do this also somhow in Phenix. I have tried to extract the Link definition using phenix.link_edits but the resulting .edits file is empty. How can I resolve issue? Thanks Christian

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Rebetta fragment library
by Wei Shi 10 Nov '11

10 Nov '11

Hi everyone, I am trying to generate a fragment library in Rebetta server for my sequence of interest to use with mr_rosetta. I can open the 9-mer and 3-mer fragment results: aat000_09_05.200_v1_3 and aat000_03_05.200_v1_3, but didn't see link to download these two files. Does anyone know how to download these two files? If I do copy and paste, what file type or format is compatible with mr_rosetta? Thank you so much! Best, Wei

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define angle between groups of atom 'planes' for refinement restraint?
by Francis E Reyes 10 Nov '11

10 Nov '11

Hi all I was wondering if there was language in the monomer restraint libraries (.cif) or a custom phenix.refine geometry restraint a that defines an angle between two planes, where each plane is a group of coplanar atoms. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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nproc for autobuild
by Michael Thompson 09 Nov '11

09 Nov '11

Hello, I apologize if this question seems very basic, but I am new to phenix.autobuild. I would like to set up a series of phenix.autobuild runs on our cluster, and would like to maximize the speed. I am trying to make single rebuilt models using the command below: phenix.autobuild data=data.mtz model=coords.pdb map_file=map_coeffs.mtz multiple_models_number=1 n_cycle_rebuild_max=5 ncycle_refine=5 s_annealing=true refine_with_ncs=True place_waters=True nproc=?? run_command=/home/qsub.sh The AutoBuild documentation says "if you are using rebuild_in_place=False, then use nproc=4" and "if you are using rebuild_in_place=True, then use nproc=5. (Any more will not make any difference)." My interpretation of the documentation is that for the above AutoBuild run with multiple_models_number=1, I should set nproc=5 (or 4?). Is this correct? Also, if I were to change the command so that multiple_models_number=10, should I then use nproc=50 (i.e. 5 processors per model), or is it still the case that setting nproc>5 doesn't make a difference? Thanks in advance for your help! Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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phenix.phaser output .param file
by G Y 08 Nov '11

08 Nov '11

Dear Experts, I run my script for phenix.phaser in bash shell and one of the output file is filename.param (please note there is no "s" at the end of param) There are only two lines inside this file: # [no title set] TNCS IGNORE ON I do not really know what this file doing for. And, if I run the phaser from GUI, I will not find any .param file. What is this file doing for? Is it some kind of redundant information which is not useful at all? What should I edit in input params.eff file to avoid this output file? I would appreciate to any help from you. Thanks. Best, G

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Constrained group refinement
by Christian Roth 08 Nov '11

08 Nov '11

Dear all, I defined the following contrained groups which should a ligand in two alternative forms and an ion at the same position refine to an summed occupancy of 1. constrained_group { selection = chain Z and resname 2CL and altloc A selection = chain Z and resname 2CL and altloc B selection = chain r and resname Cl } constrained_group { selection = chain c and resname 2CL and altloc A selection = chain c and resname 2CL and altloc B selection = chain m and resname Cl } constrained_group { selection = chain N and resseq 69 and altloc A selection = chain N and resseq 69 and altloc B selection = chain o and resname 2Cl } } At the end I get an error because of the very small nonbonded interactions. it seems that my definition are not correct, but I am at the moment unsure why. Could someone point me to the mistake. Thanks in advace for your help Best Regards Christian

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Constrained group refinement Addendum
by Christian Roth 08 Nov '11

08 Nov '11

Do the ions have to be altlocC for the group definition? Best Regards Christian

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