- phenixbb - phenix-online.org

completing the description of a residue according to idealized geometry
by Peter Grey 15 Apr '10

15 Apr '10

Dear Phenix users, My crystals contains many copies of cobalt hexamine (used for SAD phasing). Currently the model contains only the cobalt ions (without the amines) and I am looking for a tool that will use the idealized geometry of cobalt hexamine to complete the description of these resdiues, i.e. add ATOM lines for the amines Is there such a tool ? Hoping, Peter

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Phenix.reflection_file_converter enhancement request
by Schubert, Carsten [PRDUS] 15 Apr '10

15 Apr '10

Hi, would it be possible to enhance the reflection file converter so that it can simultaneously write out IOBS and FOBS into the same mtz file? Right now these options seem to be mutually exclusive. The automatic conversion in phenix.refine handles that task automatically, so it should not be too hard to implement. Thanks Carsten

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Re: [phenixbb] Real Space Refinement with marginal data
by Rongjin 15 Apr '10

15 Apr '10

Hi Pavel can you show me how to select some residues that are excluded from refinement? You suggested this earlier but I did not know how to do it. I looked through the manual and I can see how to select a chain, but do not know how to select some residues. Thanks Rongjin ------------------ Original ------------------ From: "Pavel Afonine"<PAfonine(a)lbl.gov>; Date: Thu, Apr 15, 2010 08:08 AM To: "PHENIX user mailing list"<phenixbb(a)phenix-online.org>; Subject: Re: [phenixbb] Real Space Refinement with marginal data Hi Carsten, I was wondering if anyone had experience/advice for real space refinement with phenix using marginal data to 3A. I just did a run (SA, real-space refinement against diff_map, 2 fold NCS, grouped APD, fix_rotamers enabled) were the resulting structure showed lots of disconnected sidechains and some broken main chains. I am just repeating the run w/o real space refinement, may be the combination of SA and real space refinement was a bit harsh, but am wondering what kind of parameters make most sense to tweak in order to avoid having the molecules fall apart. this could be a weight issue (weight between real-space target and restraints). In general I didn't find it too beneficial doing real-space refinement globally, although I've seen cases where it made a good difference (but at higher than 3A resolution). You may try to switch to "simple" target (to make it run much faster) and turn on the weight optimization: real_space_refinement { mode = *simple diff_map target_weights = value *grid_search gradients_ratio rmsd_max_bonds = 0.05 rmsd_max_angles = 5 grid_search_scales = 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3 } "fix_rotamers=true" (local real-space refinement for the residues that really need it, as determined automatically) is much better option. I thoroughly tested it up to 3A resolution and in all test cases it worked just great. Try it and see what happens for your data. Pavel.

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Real Space Refinement with marginal data
by Schubert, Carsten [PRDUS] 15 Apr '10

15 Apr '10

Hi, I was wondering if anyone had experience/advice for real space refinement with phenix using marginal data to 3A. I just did a run (SA, real-space refinement against diff_map, 2 fold NCS, grouped APD, fix_rotamers enabled) were the resulting structure showed lots of disconnected sidechains and some broken main chains. I am just repeating the run w/o real space refinement, may be the combination of SA and real space refinement was a bit harsh, but am wondering what kind of parameters make most sense to tweak in order to avoid having the molecules fall apart. Cheers Carsten

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Autobuild
by sbiswas2＠ncsu.edu 14 Apr '10

14 Apr '10

Hi all, I was wondering if you are required to delete the tmp.dat file everytime you run autobuild. What is the imporatnce of this file? I tried to run autobuild from the same folder but it did not allow me to run until I deleted this file. Thanks Shya

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xtriage and anomalous difference assessment
by Francis E Reyes 13 Apr '10

13 Apr '10

Hi all Is xtriage's assessment of anomalous signal depend on the space group chosen? (i.e. measuring genuine I+/I- or I+/I- related by symmetry operation) ? Thanks F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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SAD Phasing
by Rajagopalan, Senapathy 12 Apr '10

12 Apr '10

Hi Everyone, I have been trying to solve a structure of a protein-DNA complex using SAD data, but am running into problems and have some questions on how phenix solves it. From Mathews coefficient calculation, I know that my protein binds to the DNA as a dimer in the asymmetric unit. And when I use this information to specify the the number of heavy atoms to look for, I always get more (1.5-2X, depending on what resolution cutoff I use) in the final heavy atom sites pdb file. More importantly, the map looks 'incomplete' in the sense that part of one of the strands in the double stranded DNA is missing. My question is if this is the result of phenix using some incorrect sites (such as with low occupancy) while phasing. If so, then how can I fix it. I have tried deleting the low occupancy sites and reading the edited heavy atom sites file explicitly using sites_file=ha.pdb, but it doesn't seem to help. Also, if I just use solve to find the heavy atom sites, those tend to be different too... Any suggestions here would be appreciated. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Group ADP syntax question
by Peter Grey 12 Apr '10

12 Apr '10

Hi Phenix people, Is it possible to have One B-factor per residue for one part of the structure and for other parts to use One isotropic B per selected group of atoms. For example to have one B-factor for the entire chain A and have One B-factor per each residue in chain B ? Thanks, -- Peter

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sculpt program
by sbiswas2＠ncsu.edu 12 Apr '10

12 Apr '10

Dear all, I was trying to generate a model using the sculpt program in phenix. when I run it with both alignment file and pdb file I get the following message: Processing PDB... Next model: ''... Next chain 'A'... No matching alignment for chain 'A'; delete PDB output requested Executing design... Everything is deleted; output file empty Any help with this... thanks, Shya

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assert n_ncs > 0
by Robert Ng 12 Apr '10

12 Apr '10

Hi again, How about this one ... Traceback (most recent call last): File "/usr/local/phenix-1.6.1-348/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/command_line.py", line 71, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 413, in __init__ self.process_ncs_restraint_groups() File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 672, in process_ncs_restraint_groups log = log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 306, in from_atom_selections log=log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 219, in __init__ assert n_ncs > 0 AssertionError Thanks again, Robert

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