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Average B-factors when using TLS
by Phil Jeffrey 13 Oct '10

13 Oct '10

I'm having a discussion with a colleague here about what we expect to see on a model with and without TLS being used. I had the expectation that if you'd compared both models the Biso values reported in the ATOM line for the same atom w/ and w/o TLS would be somewhat comparable. Not the same, because the ADP model is different, but similar. However in the case of the TLS-refined model the average B-factors are systematically higher over the whole structure (86 A^2 vs 69A^2 for one polypeptide chain). Is this reasonable ? Expected ? Phil Jeffrey Princeton

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Re: [phenixbb] When to freeze crystal?
by miket＠chem.ucla.edu 13 Oct '10

13 Oct '10

Just last week I had crystals on Friday, then by Monday they dissolved back into the drop. I don't really understand how or why this happens, but it does. After experiencing this and complaining about it, I heard several other similar stories from around the department. Lesson learned: if you think you have a decent crystal, freeze it. Having said this, I've also heard of good data being collected from a crystal that was over a year old. Like Bert said, I think that occasionally a crystal survives or even improves over time, but those cases are much more rare than cases where the crystal deteriorates. Do how many crystals do you have? You might try freezing some and saving the others in the drop, then you can see for yourself. Good luck, Mike ----- Original Message ----- From: "Nathaniel Echols" <nechols(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Wednesday, October 13, 2010 8:44:42 AM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] When to freeze crystal? On Wed, Oct 13, 2010 at 4:16 PM, J J <phenix.upitt(a)gmail.com> wrote: > Hi everyone, > Sorry to ask a question that is not really related to phenix. I hope someone > here will be able to help me out. > I have a few crystals at hand right now, but I will not be able to look at > them for at least another month or so due to beamline schedule. Do you think > I should freeze them now or wait till I have my beamtime, or it is crystal > dependent? Thanks in advance. (Bert meant to send this to the list, but since he's using the wrong email address, it went to the list admin instead:) From: "Van Den Berg, Bert" <Lambertus.VandenBerg(a)umassmed.edu> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Wed, 13 Oct 2010 11:27:32 -0400 Subject: Re: [phenixbb] When to freeze crystal? It is crystal dependent, but if they are big enough I would freeze them now. I have seen many crystal forms deteriorate over time and wouldn’t take the risk of that happening. It can happen though that old crystals get better (presumably due to slow dehydration of the drop), but I think these cases are fairly rare. Bert _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- 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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When to freeze crystal?
by J J 13 Oct '10

13 Oct '10

Hi everyone, Sorry to ask a question that is not really related to phenix. I hope someone here will be able to help me out. I have a few crystals at hand right now, but I will not be able to look at them for at least another month or so due to beamline schedule. Do you think I should freeze them now or wait till I have my beamtime, or it is crystal dependent? Thanks in advance. Jason University of Pittsburgh

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Merging low resolution mtz file with high resolution sca file with phenix_reflection_file_editor
by Pei-Chun Lin 13 Oct '10

13 Oct '10

Hi, If I merge my low resolution mtz file with the high resolution sca file with phenix.reflection_file_editor GUI, is it the same as : Merge in hires data phenix.autobuild data=solve_2.mtz hires_file=w1.sca seq_file=seq.dat in Phenix Autobuild? PC

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secondary structure restraints question
by Peter Grey 12 Oct '10

12 Oct '10

Dear Phenix community, I have a very large model with many chains (due to NCS and complexity of model) where chain-id is not unique (e.g. there are several chain A) but segid is. All atom selections (for rigid body refinement, ncs restraints, tls etc...) are defined by segid. When I look at the output of phenix.secondary_structure_restraints I see that these restraints are defined by chain-id and residue number. Does this mean I must have unique chain-id names to correctly apply these secondary structure restraints or am I missing something ? Thank you for your time, Peter

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refine : annealing and bulk solvent
by Lepore, Bryan 11 Oct '10

11 Oct '10

[ phenix 1.6.4-486 ] from the program output, it appears that prior to annealing ( e.g. torsion ), a bulk solvent grid search is run using the initial model. after that ends, all the annealing steps are carried out on the model using the initially optimized bulk solvent. When annealing is done, another search is conducted on the final model. i.e. there are no bulk solvent changes during annealing. is this right? -bryan

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DNA base pairing restraints work for GC only
by Phoebe Rice 07 Oct '10

07 Oct '10

We're trying to refine a large, low-resolution protein-DNA complex structure (4A in the good direction), and we need every restraint we can get, so I'm trying to use secondary structure restraints (in addition to ncs and 3 known substructure models). I found this from the newsletter: phenix.secondary_structure_restraints model.pdb > ss.eff ran it, editted it, and plugged into the gui, where it seems to be taken into account if I also say "yes" to "find automattically". Then I ran torsion angle dynamics to see if things were restrained as requested. It only seems to be restraining G:C pairs - the ATs fly apart! The log file makes a very suspicious set of remarks under "secondary structure": No entry for base pair AT with type WWT (H=False). (repeated about the same # of times as we have AT pairs). I thought maybe it was a nomenclature problem, but if "Gd" is OK I don't see what's wrong with "Ad", and the usual suspect, the thymine methyl, stays coplanar with the rest of its base, so the program must be recognizing our base/atom names. Question 2 is that I wanted to view the restraints in pymol, but this command, also cribbed from the newsletter: phenix.secondary_structure_restraints partry1noss.pdb ss_manual.eff format=pymol > h_bonds.pml seems to overwrite the manual editing in my .eff file. Help? I'm new to phenix, so please be explicit about where I've gone wrong. thanks, Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alph… http://www.rsc.org/shop/books/2008/9780854042722.asp

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maps : scattering corrections
by Lepore, Bryan 07 Oct '10

07 Oct '10

i'd like to define anomalous scattering corrections for phenix.maps, it looks like i'm not doing it right. it appears that simply pasting in various adjustments of : anomalous_scatterers { group { selection = element = Ni f_prime = 2.4 f_double_prime = -0.1 refine = *f_prime *f_double_prime # not sure about this one } in various places in maps.params mostly causes phenix.maps to report "unused parameter", e.g: maps.anomalous_scatterers.group.selection this should work, right? what am i missing here - is there a scope missing, what scope does this go in, did i miss this in the docs... -bryan

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Phenix.refine stops running in the background
by José Trincão 07 Oct '10

07 Oct '10

Hello all, I've been running phenix.refine over ssh on a remote computer, on command line. I always run it in the background (adding & to the command line). If I disconnect the ssh (or it gets disconnected) the job hangs. Any way of leaving it running even after the ssh disconnects? Thank you. Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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phenix.refine : mask
by Lepore, Bryan 07 Oct '10

07 Oct '10

i gather that the only way to define an "a priori" mask of the molecular envelope in phenix.refine is to generate Fmask and combine those in refinement - is that right? i.e. there isn't a more intuitive way using a mama mask or somesuch to keep the bulk solvent from flattening out parts you think are model, besides the model that is being refined in the first place? -bryan

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