- phenixbb - phenix-online.org

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

1 0

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

2 1

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

2 2

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

5 4

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

2 1

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

3 2

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

2 1

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

1 0

Cross Validation Reflection Set question
by Yuri 07 Nov '11

07 Nov '11

Thanks for the replies. >I just tried doing this, and it looks like the R-free flags will cover >the full resolution range, at least with the current code. By current code, you mean 1.7.2-869 and newer, right? >Is this really necessary in this case (refine against lower res data, >then continue with the whole data set I think I have a backbone shift in this structure (relative to native protein used for MR) so I wanted to do it this way befor trying to go all the way down to 2A. One last question does phnix do NCS averaging to improve maps? -- Yuri Pompeu

6 6

Re: [phenixbb] AutoBuild runtime
by Nathaniel Echols 07 Nov '11

07 Nov '11

On Mon, Nov 7, 2011 at 9:14 AM, Shya Biswas <shyabiswas(a)gmail.com> wrote: > Thanks for the suggestions. Unfortunately my MR solution is not good enough > to get a good map. Autobuild does give me a solution when i put in my > sequence but the map does not look good. I was wondering if the final model > that Autobuild gives has undergone density modification. Strictly speaking, it's the map that undergoes density modification - but yes, this will be done unless you explicitly disable it. -Nat

1 0