- phenixbb - phenix-online.org

Installation problem, please help
by Tiberman Danny 24 May '10

24 May '10

Hello, while trying to install I get the following Error message: "======================================================================== Installing from binary bundle ========================================================================== bundle file: bundle-1.6.1-357-intel-linux-2.6-x86_64.tar.gz PHENIX installation source directory set to: /root/phenix-installer-1.6.1-357 PHENIX installation target directory <PHENIX_LOC > set to: /usr/local/phenix-1.6.1-357 PHENIX installation build directory set to: <PHENIX_LOC > /build/intel-linux-2.6-x86_64 PHENIX temporary build directory set to: build-binary/intel-linux-2.6-x86_64/monst/tmp PHENIX installation log directory set to: build-binary/intel-linux-2.6-x86_64/monst/log ==== warning: "/usr/local/phenix-1.6.1-357" already exists ==== ==== warning: cannot determine installation time-stamp, proceeding ==== installing binary components removing existing files in build-binary/intel-linux-2.6-x86_64/monst/tmp/binary finding installed versions finding binary versions binary components up-to-date the binary package will not be installed setting environment configuring PHENIX components /root/phenix-installer-1.6.1-357/bin/install-from-binary: line 347: 19650 Floating point exception$PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py --current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS >>$PHENIX_LOG/binary.log 2>&1 Error configuring: see /root/phenix-installer-1.6.1-357/build-binary/intel-linux-2.6-x86_64/monst/log/binary.log for details" Thanks

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Re: [phenixbb] Restraining altloc related atoms during refinement
by John Pascal 20 May '10

20 May '10

>I have my doubts about supporting NCS restraints of alternative >conformations; the two seem to be mutually exclusive. But maybe >I don't understand your situtation. Here are some more details on the refinement situation: it is possible for a piece of duplex DNA to be positioned in two conformations in the crystal, and it appears that both conformations are occupied with roughly the same occupancy. The sequence is not completely palindromic, so at some positions a different base is present depending on the random orientation of the DNA. However, the phosphate and ribose atoms occupy the same positions regardless of the orientation, and I want to enforce this. >I can see that NCS restraints of backbone atoms only are useful, >even if the residue names are different. >The trouble is that atoms in two chains need to be matched >unambiguously while allowing for chain breaks. >I could try to simply remove the requirement that the residue names >have to match and go by residue sequence number + insertion code >only. Would that work in your case? Yes, that sounds like it would work. >A potential downside is that people have to be careful >excluding non-matching sidechain atoms. Perhaps it could be that there is an override option after an error message. Thanks for your help. -John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ----- Forwarded message from John.Pascal(a)mail.jci.tju.edu ----- Date: Thu, 20 May 2010 11:54:33 -0400 From: John Pascal <John.Pascal(a)mail.jci.tju.edu> Reply-To: John Pascal <John.Pascal(a)mail.jci.tju.edu> Subject: Restraining altloc related atoms during refinement To: phenixbb(a)phenix-online.org Hello All, I would like to restrain the positions of ribose/phosphate atoms of altloc 'A' to the positions of those in altloc 'B'. Problem is, altloc A and altloc B are different residue types, so phenix.refine exits stating that there are no common atoms when I enter the following NCS-type restraint: selection: chain I and altloc A and resid 1 and (phosphate or ribose) restrain: chain I and altloc B and resid 1 and (phosphate or ribose) I am using the phenix GUI. Is there a better place to enter this type of restraint (rather than NCS) that does not care if a P atom is from a Cd or from a Gd residue type? thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- End forwarded message ----- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Restraining altloc related atoms during refinement
by John Pascal 20 May '10

20 May '10

Hello All, I would like to restrain the positions of ribose/phosphate atoms of altloc 'A' to the positions of those in altloc 'B'. Problem is, altloc A and altloc B are different residue types, so phenix.refine exits stating that there are no common atoms when I enter the following NCS-type restraint: selection: chain I and altloc A and resid 1 and (phosphate or ribose) restrain: chain I and altloc B and resid 1 and (phosphate or ribose) I am using the phenix GUI. Is there a better place to enter this type of restraint (rather than NCS) that does not care if a P atom is from a Cd or from a Gd residue type? thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [phenixbb] all reflections are equal, but some more than others
by Frank von Delft 19 May '10

19 May '10

Are you sure? It's the sigma estimation he talked about, and that does assume it's the same foe both strong and weak, doesn't it? ----- Reply message ----- From: "Phil Evans" <pre(a)mrc-lmb.cam.ac.uk> Date: Wed, May 19, 2010 21:22 Subject: [phenixbb] all reflections are equal, but some more than others To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> If by "scaling" you mean scaling unmerged observations together, I don't think it is right that it assumes a unimodal intensity distribution. In refinement I believe the underlying distributions are assumed to be unimodal, but in data reduction scaling there is no such assumption. That scaling just assumes that the experiment (mainly the diffraction geometry) can be parameterised in such a way that reflections close together in reciprocal space and in measurement time have similar and parameterisable scales. This is independent of the intensity distribution. Phil On 19 May 2010, at 08:44, esko.oksanen(a)helsinki.fi wrote: > Frank, > > Having had a case of such hectic pseudosymmetry, it turns out that the problem originates already from the scaling that assumes a unimodal intensity distribution. The weak reflections then have their sigmas heavily overestimated and the strong ones overestimated. I had to scale the weak and strong reflections separately and ridig-body refine against the weak ones... Of course this type of problem has little to do with issue of treating negative intensities. > > Esko > > Quoting "Frank von Delft" <frank.vondelft(a)sgc.ox.ac.uk>: > >> The philosophical arguments are fine, but is Pavel not justified in asking for real cases where it matters? It's not like he hasn't spent time thinking about it, and it's not like the whole phenix community isn't sitting in his ear about their own favourite missing fix. >> >> I suppose what comes to mind is a case with hectic pseudotranslation causing half the reflections to be systematically almost but not quite zero. But then again, I understand that even if you don't toss the weak ones out, current algorithms don't deal with this well anyway, so it needs special treatment (for now: refine in smaller cell, then rigid-body refine in super-cell). >> >> phx. >> >> >> >> >> >> On 18/05/2010 18:33, Ed Pozharski wrote: >>> On Mon, 2010-05-17 at 16:20 -0700, Peter Zwart wrote: >>> >>>> You make it sound like it is a bad thing. The effect of restraint >>>> weights (ADP, geometry) has most likely a much bigger impact on the >>>> final structure then a small fraction of smallish intensities (*) >>>> >>> Peter, >>> >>> I think discarding data has to be justified. Two points: >>> >>> 1. The fraction of negative intensities is not necessarily small. It >>> depends on resolution cutoff (and you make an excellent point about >>> PTS), but looking at scalepack log-files I can tell that in my hands the >>> fraction is often 10% or more (DISCLAIMER: I belong to I/sigma=1 >>> resolution cutoff cult). >>> >>> 2. Just because these reflections are weak does not mean that they are >>> insignificant. Their contribution to the maps may be small (now I fear >>> another round of "fill-in missing Fobs with Fc for map calculation" >>> discussion), but keeping Fc close to zero for these reflections during >>> refinement seems to be just as important as to keep Fc close to whatever >>> values the strong reflections have. >>> >>> The weak reflections are not fundamentally worse than strong(er) >>> reflections in the same resolution range. They are measured with >>> roughly the same precision. Moreover, the practice of setting negative >>> intensities to zero and then ignoring them in refinement discards those >>> that are barely negative and leaves in those that were (quite randomly) >>> barely positive. >>> >>> You are absolutely right that other factors will have impact on the >>> model. But that does not mean that discarding weak data is justified. >>> Crystallographic refinement is a Rube Goldberg machine, and all the >>> components should be as good as we can make them. Perhaps there could >>> be something better than French&Wilson, but discarding negative >>> intensity reflections is hardly the solution. >>> >>> Cheers, >>> >>> Ed. >>> >>> PS. Personally I have no stake in this, since I always use truncate. >>> >>> >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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View DM map from AutoSol gui?
by Francis E Reyes 19 May '10

19 May '10

I'm not a GUI kind of person but today I'm messing around with it. After AutoSol (with build=False... errr AutoBuild unchecked), I have an opportunity to 'View sites and experimental map' in coot or PyMOL. Wouldn't it be more useful if the gui loaded the DM maps as well? 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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changing TLS groups mid refinement
by Scott Classen 19 May '10

19 May '10

Hello Phenixers, Are there any considerations to changing TLS groups mid refinement? Can I rest assured that after a few rounds of refinement with the new TLS definitions everything will sort itself out or should I do something drastic, like remove all the ANISOU records, reset B factors to some constant value, and start over? Thanks, Scott

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phenix distorts ligand
by Mustafa Koksal 18 May '10

18 May '10

Hi, I have a problem in phenix refinement at 2.25 A resolution, data is 80% complete. I have protein, water, and ions in the .PDB file, and a ligand molecule that is distorted during refinement. I generated the pdb (with H atoms) with ChemDraw3D, edited the atom names etc. I used phenix.elbow to generate the .CIF file. Here is the first problem: Ligand has trans double bonds, which are written out by phenix.elbow as single rotatable bonds although I had correct connect records and H atoms in the .PDB file. I ran phenix.refine, it distorted the ligand, making double bonds not planar and nearly cis. Here is what I have tried: I edited the .CIF file to change these torsion agles to be CONSTANT and 180 or 0 deg. Here is the second problem: phenix.refine still distorted the ligand. Here is what I have tried: I used optimize_wxc/wxu in phenix.refine to optimize the weight, to see if I overweighed the data. Here is the third problem: phenix.refine still distorted the ligand. Is there a way to solve this problem? Is there a way to tighten the constraints for the ligand only? I still do not understand why it even cannot keep the double bonds planar (and trans). I do not want to move back to good old CNS... Thanks to all, Mustafa -- Mustafa Koksal Postdoctoral Fellow University of Pennsylvania Department of Chemistry Roy and Diana Vagelos Laboratories Office: 2090 IAST Office Phone: (215) 898-2227 Mobile Phone: (267) 319-6443 Mail Address: 231 S. 34th St, Philadelphia 19104, USA -- "If you grant me a pen, I shall destroy swords and spears" Mawlana Jalal-ad-Din Rumi --

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geometry_restraints between sym mates?
by Scott Classen 17 May '10

17 May '10

Hi all, Is this possible? # on working model bond { atom_selection_1 = "name SM and chain M and resname SM and resseq 1" atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 313" distance_ideal = 2.5 sigma = 0.2 } # on SYM mol bond { atom_selection_1 = "name SM and chain M and resname SM and resseq 1" atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 285" distance_ideal = 2.5 sigma = 0.2 } I'll find out in a few minutes when I run it through phenix.refine, but I thought to ask anyways. Thanks, Scott

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Looking at omit maps in coot
by xaravich ivan 17 May '10

17 May '10

Hi, Again this is pretty novice and I would apologize in advance. I ran Simulated annealing omit map in PHENIX and it gave me a bunch of files. I started with a partially built model ( I would say most of it was built) and it gave me an edited pdb that I can open in coot but I the composite omit mtz file is not opening in coot. In fact I cannot open any mtz file from the phenix output /OMIT directory and cannot see any map. I am pretty clueless. Thanks, Ivan

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An easier explanation of the regions in omit map
by xaravich ivan 17 May '10

17 May '10

Hi Nat, So I have quite a few regions build by the SA_omit map of phenix. But How do I go about looking at these maps. What am I looking for here. Should I look at the regions where the occupancy was set zero in all these outputs and find if I could build some thing from one of the maps? I guess I am asking, How do I use this information to move forward in refinement? There are 24 regions map and .pdb output in the /OMIT directory. Thanks, Ivan On Fri, May 14, 2010 at 5:52 PM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > On Fri, May 14, 2010 at 5:40 PM, xaravich ivan <xaravich.ivan(a)gmail.com>wrote: > >> Again this is pretty novice and I would apologize in advance. >> I ran Simulated annealing omit map in PHENIX and it gave me a bunch of >> files. I started with a partially built model ( I would say most of it was >> built) and it gave me an edited pdb that I can open in coot but I the >> composite omit mtz file is not opening in coot. In fact I cannot open any >> mtz file from the phenix output /OMIT directory and cannot see any map. >> I am pretty clueless. >> > > Some clarification: > > 1. Which version of Phenix, and which platform? > 2. GUI or command-line? > 3. If you're really making a composite omit map (as opposed to a simple > omit map, e.g. for a ligand), ignore the PDB file output by AutoBuild and > stick to the original. > > One common problem is that on Mac, if you try to open the MTZ file in Coot > (using the "Open MTZ", not auto-open), it will open a window to choose > column labels in the file, but it opens *behind* the main window, which you > need to move to the side temporarily. > > -Nat > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

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