- phenixbb - phenix-online.org

eLBOW / REEL and chirality
by L. Costenaro (IBB) 25 Jul '14

25 Jul '14

Dear all, I am making the restraints file (CIF) for a ligand with two chiral carbons, using eLBOW (AM1 QM, output: retain original chirality) from a SMILES description and obtain the following: Atom input_chirality input_smiles output_vol_sign output_R/S output_chirality_pdb C20 S C@H negative S S C37 R C@@H positive S S Although the volume_sign in the output cif file correspond to the input chiralities, the output pdb has the wrong chirality for the carbon C37: S instead of the desired R. I think the "retain original chirality" option is what I need to keep the input chirality, but apparently it doesn't. How should I proceed to get a pdb with the correct chiralities? Best regards, Lionel PS: phenix version 1.9-1692, linux X86_64 PS2: in REEL, the action "Find unique code" make phenix (not REEL) crash (all windows close) without error message

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SFALL in CCP4 and calculate F(model) in Phenix
by PC 25 Jul '14

25 Jul '14

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Re: [phenixbb] [External] RE: phenix.ligandfit does not recognize a list of SDF file names
by Terwilliger, Thomas Charles 23 Jul '14

23 Jul '14

Hi Jason, I fixed ligandfit so that it should now be able to take your list of sdf files and run each file sequentially. Starting with tomorrow's build, you should be able test it out with this regression test: phenix_regression.wizards.test_command_line_ligands test_ligand_list Thanks for pointing out the problem! Let me know if that does not do it. All the best, Tom T On Jul 21, 2014, at 7:11 PM, Phan, Jason wrote: > ________________________________________ > From: phenixbb-bounces(a)phenix-online.org<mailto:[email protected]> [phenixbb-bounces(a)phenix-online.org] on behalf of Phan, Jason [jason.phan(a)vanderbilt.edu] > Sent: Monday, July 21, 2014 4:32 PM > To: phenixbb(a)phenix-online.org<mailto:[email protected]> > Subject: [phenixbb] phenix.ligandfit does not recognize a list of SDF file names > > Hi All, > > I'm trying to fit a list of ligands in SD format with phenix.ligandfit using the ligand=ligand.dat (file containing the ligand file names in the same directory) and the file_or_file_list=file_with_list_of_files flag. It complained that the ligand does not exist. I tested a single ligand, ligand=ligand1.sdf, and it worked fine. I tested a list containing pdb file names and it worked fine. I think phenix.ligandfit does not recognize SD-formatted ligands from a list, although it is fine running as a single ligand. PDB format is fine single or list of names. Any suggestions other than converting SDF to PDB or writing a script to run one SDF at a time? Thanks. > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/phenixbb

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B iso average versus B wilson
by Emily Golden 22 Jul '14

22 Jul '14

Dear All, I have a 1.12 A refined structure with and average B of 11.5 but the wilson B is 6. There are a couple of highly mobile loops and water molecules in the structure that are increasing the average B. What is an acceptable difference between wilson B and average B? Thank you, Emily

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phenix.ligandfit does not recognize a list of SDF file names
by Phan, Jason 22 Jul '14

22 Jul '14

Hi All, I'm trying to fit a list of ligands in SD format with phenix.ligandfit using the ligand=ligand.dat (file containing the ligand file names in the same directory) and the file_or_file_list=file_with_list_of_files flag. It complained that the ligand does not exist. I tested a single ligand, ligand=ligand1.sdf, and it worked fine. I tested a list containing pdb file names and it worked fine. I think phenix.ligandfit does not recognize SD-formatted ligands from a list, although it is fine running as a single ligand. PDB format is fine single or list of names. Any suggestions other than converting SDF to PDB or writing a script to run one SDF at a time? Thanks.

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CCTBX questions
by Morten Grøftehauge 22 Jul '14

22 Jul '14

Hi people, I notice that cctbx.python comes with phenix but as far as I can tell from when I run it, look at imported modules with dir(), and compare to the documentation on Sourceforge the version that comes with phenix is abridged. And possibly not the same version as the sourceforge one but they probably are the same. Will it cause any problems with Phenix if I install cctbx from sourceforge? Is it unnecessary? Second question: Is there any better documentation anywhere? I found James Stroud's wiki but that's mainly for structure factor manipulation. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Long Distant Restraints
by Bradley Hintze 18 Jul '14

18 Jul '14

Hey PHENIX, I am wondering if I can define a distant restraint longer that 3A in a custom restraint file? The conventional way of doing this is to provide : refinement.geometry_restraints.edits { C8_C1=chain C and resid 8 and name C1' D10_C1=chain D and resid 10 and name C1' bond { action = *add atom_selection_1 = $C8_C1 atom_selection_2 = $D10_C1 distance_ideal = 9.1 sigma = 0.02 slack = 0.5 } Obviously this is a distant and not bond restraint. 9.1 exceeds the allowed length of 3 for a bond. Is there a different type of restraint that allows longer distances? Thanks! -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry

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Refinement cycles
by George Devaniranjan 18 Jul '14

18 Jul '14

Hi, I was wondering if there is a reason for setting the default number of refinement cycles to 3 in Phenix refine? is there a number of cycles at which point it becomes unacceptable to run so many ? Thank you, George

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B factors too high for low resolution data refinement
by 李翔 16 Jul '14

16 Jul '14

Hi everyone, I am working on my low-resolution data (~6.5 A). When I was doing refinement with PHENIX, the B factors remain pretty high (~400, not sure whether it is normal for the data with such resolution.) And B factors further increased after group B factor refinement (~500). Does it mean the group B factors refinement not working or is there a way I can somehow define a limit for B-factors? (I read one previous topic a few years ago which indicates the B factor can not be controlled. Not sure whether it is available now). Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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So what is unique?
by Kenneth A. Satyshur 16 Jul '14

16 Jul '14

There is some disagreement on terms used to deposit data. We need a definition and an algorithm for each definition. "Unique Reflections" My definition is all the possible reflections out to the highest resolution reported not related by symmetry. Where can I find this? The .mtz contains a list of all HKL calculated to the highest resolution. Usually, we are not able to measure all these diffraction spots due to limits of the detector, mechanical limits, crystal orientation, etc. 'Total reflections' The depositions server asks for total reflections. I assume it wants only those unique reflections we were able to collect, regardless of the sigma cut off. These are called 'observed'. The total we use in refinement will be a subset of the 'unique observed' that are cut on sigma. However, some crystallographers believe that we should not cut on sigma since some of the intensities may in fact be zero. Is this a question for the Refmac and Phenix people? Please give us some guidance and maybe a reference or two that we can use. thanks -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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