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Re: [phenixbb] phenixbb Digest, Vol 55, Issue 7
by ak2197＠columbia.edu 07 Jun '10

07 Jun '10

Ok Alex Sent from my Verizon Wireless BlackBerry -----Original Message----- From: phenixbb-request(a)phenix-online.org Date: Mon, 07 Jun 2010 12:00:01 To: <phenixbb(a)phenix-online.org> Subject: phenixbb Digest, Vol 55, Issue 7 Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Robert Ng wants to stay in touch on LinkedIn (Robert Ng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 7 Jun 2010 08:57:29 -0700 (PDT) From: Robert Ng <ubi(a)ufl.edu> To: PHENIX list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Robert Ng wants to stay in touch on LinkedIn Message-ID: <1916754023.4088196.1275926249246.JavaMail.app(a)ech3-cdn13.prod> Content-Type: text/plain; charset="utf-8" LinkedIn ------------ PHENIX, I'd like to add you to my professional network on LinkedIn. - Robert Ng Robert Ng Graduate Research Assistant at Department of Biochemistry and Biophysics Gainesville, Florida Area Confirm that you know Robert Ng https://www.linkedin.com/e/isd/1366202655/UCksvc1y/ ------ (c) 2010, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100607/f95d09c5/a…> ------------------------------ _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb End of phenixbb Digest, Vol 55, Issue 7 ***************************************

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Robert Ng wants to stay in touch on LinkedIn
by Robert Ng 07 Jun '10

07 Jun '10

LinkedIn ------------ PHENIX, I'd like to add you to my professional network on LinkedIn. - Robert Ng Robert Ng Graduate Research Assistant at Department of Biochemistry and Biophysics Gainesville, Florida Area Confirm that you know Robert Ng https://www.linkedin.com/e/isd/1366202655/UCksvc1y/ ------ (c) 2010, LinkedIn Corporation

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A couple of questions regarding twinning
by Pietro Roversi 03 Jun '10

03 Jun '10

Dear all, A couple of questions regarding twinning: 1. The structure I work with has multiple twinning domains (4 to be exact, with pseudo-orthorhombic 222 symmetry induced by twinning in P1). I feed the autobuild script the operators using a keyord: input_files.refine_eff_file_list=mytwinrefinement.eff (see attached file) but only the last one seems to be used. Do I guess correctly that there is only provision for two domains adn therefore the last twinning definition overrides any previously defined one? If so, is there a way of specifying and using multiple twinning domains/operators? 2. Output structure factor amplitudes: are they detwinned? Are they detwinned before the density modification in resolve? and during it? Thanks for any clarification/suggestions Regards Pietro

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Re: [phenixbb] NAG-NAG description
by Chris Ulens 02 Jun '10

02 Jun '10

Thanks for the feedback. I would like to refine a NAG-NAG chain attached to residue Asn122 in my structure. There are 5 identical subunits. Could you verify my .params file? I get the following error: Empty atom selection refinement .pdb_interpretation.apply_cif_link.residue_selection_1="chain A and resname NAG and resid 122" Thanks. -Chris On 31 May 2010, at 21:34, Georg Mlynek wrote: > Dear Chris, this did it for me. > > > Create a file which you can call whatever you want even the extension > doesn't matter. E.g.: cif_link.params > > Put in this file your links: (Which Atom of residue1 will be > connected to > which Atom in residue2 is already defined in mon_lib_list.cif) > > > > refinement.pdb_interpretation.apply_cif_link { > data_link = NAG-ASN > residue_selection_1 = chain A and resname NAG and resid 500 > residue_selection_2 = chain A and resname ASN and resid 297 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = BETA1-4 > residue_selection_1 = chain A and resname NAG and resid 500 > residue_selection_2 = chain A and resname NAG and resid 501 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = BETA1-4 > residue_selection_1 = chain A and resname NAG and resid 501 > residue_selection_2 = chain A and resname BMA and resid 502 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = ALPHA1-3. > > residue_selection_1 = chain A and resname BMA and resid 502 > residue_selection_2 = chain A and resname MAN and resid 503 > } > > 4) add this file in the GUI > > > Or run % phenix.refine model.pdb data.hkl cif_link.params > > > 5)Trouble shooting > > a)run iotbx.phil cif_link.params (this checks if the syntax is > right) > > b) check .eff file the links should be added there. You can also > check the . > geo file if you see anything strange. > > c)Having unknown to phenix.refine item in PDB file (novel ligand, > etc... > (BMA is also not there) ). phenix.refine uses the CCP4 Monomer > Library as > the source of stereochemical information for building geometry > restraints > and reporting statistics. If phenix.refine is unable to match an > item in > input PDB file against the Monomer Library it will stop with "Sorry" > message > explaining what to do and listing the problem atoms. If this > happened, it is > necessary to obtain a cif file (parameter file, describing unknown > molecule) > by either making it manually or having eLBOW program to generate it: > > phenix.elbow model.pdb --do-all --output=all_ligands > > this will ask eLBOW to inspect the model_new.pdb file, find all > unknown > items in it and create one cif file for them all_ligands.cif. > Alternatively, > one can specify a three-letters name for the unknown residue: > > phenix.elbow model.pdb --residue=MAN --output=man > > !Check the file if everything is ok! > > > Please correct if this is not ok, or there is an easier way now. > > Kind regards George. > > > -----Ursprüngliche Nachricht----- > Von: phenixbb-bounces(a)phenix-online.org > [mailto:[email protected]] Im Auftrag von Chris Ulens > Gesendet: Monday, May 31, 2010 9:14 PM > An: PHENIX user mailing list > Betreff: Re: [phenixbb] NAG-NAG description > > Dear glycobiologists and phenixfriends. > > I am trying to refine a NAG-NAG chain attached to an Asn122 in my > (pentameric) structure. > What is the proper description in the cif_link.params that is the > equivalent of the pdb description pasted below that phenix so kindly > ignores? > Also, what is the proper way to define the cif_link.params file in the > GUI? > > Thank you. > -Chris > > > LINK ND2 ASN A 122 C1 NAG A 834 1555 > 1555 1.37 > LINK O4 NAG A 834 C1 NAG A 835 1555 > 1555 1.43 > LINK ND2 ASN B 122 C1 NAG B 834 1555 > 1555 1.37 > LINK O4 NAG B 834 C1 NAG B 835 1555 > 1555 1.43 > LINK ND2 ASN C 122 C1 NAG C 834 1555 > 1555 1.37 > LINK O4 NAG C 834 C1 NAG C 835 1555 > 1555 1.43 > LINK ND2 ASN D 122 C1 NAG D 834 1555 > 1555 1.37 > LINK O4 NAG D 834 C1 NAG D 835 1555 > 1555 1.43 > LINK ND2 ASN E 122 C1 NAG E 834 1555 > 1555 1.37 > LINK O4 NAG E 834 C1 NAG E 835 1555 > 1555 1.43 > > --------------------------------------------------- > Chris Ulens, Ph.D. > Lab of Structural Neurobiology > Department of Molecular Cell Biology > Campus Gasthuisberg, ON1 > Herestraat 49, PB 601 > B-3000 Leuven > Belgium > e chris.ulens(a)med.kuleuven.be > t +32 16 345812 > f +32 16 345699 > w http://www.xtal.be > > _______________________________________________ > 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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segmentation fault
by Harry M. Greenblatt 01 Jun '10

01 Jun '10

BS"D Dear All, We had the phenix 1.6.1 GUI running on a fedora core 12 machine; it was thought, for different reasons, that a kernel upgrade would address certain issues unrelated to phenix. The machine is now running 2.6.32.12-115.fc12 (64 bit) and phenix now gives a segmentation fault. Any suggestions? Thanks Harry ------------------------------------------------------------------------ - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenblatt(a)weizmann.ac.il Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel

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Weight optimization
by Jianghai Zhu 28 May '10

28 May '10

Hi, I am using the optimize_wxc=true and optimize_wxu=true in my last refinement. The R and Rfree went down but the RMSDs were way too large. I wonder if phenix.refine still targets the geometry when it optimizes the R and Rfree. Here are the results from almost two identical runs except the weight optimization. 1) optimize_wxc = False optimize_wxu = False wxc_scale=0.08 wxu_scale=1.66 results: R=0.2294 R-free=0.2709 angl=1.087 bond=0.006 2) optimize_wxc = True optimize_wxu = True wxc_scale=0.08 wxu_scale=1.66 results: R=0.2141 R-free=0.2628 angl=2.894 bond=0.033 I am using the dev-412 version. Thanks. -- Jianghai

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offtopic: Problem with Pymol showing maps
by Tatyana Sysoeva 28 May '10

28 May '10

Hi all, if somebody is still not on the memorial day weekend, I have a short question off-topic for Pymol-users I have several maps from Phenix and want to draw some pictures in Pymol. I am opening the files, renamed to ccp4 or map, or not, and all I am getting is just a box, which is not even a unit cell boundary. If you know some nice simple program to do nice pictures of the electron densities- share your knowledge please! Sincerely Tanya

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Super: Rotation and translation
by J. Fleming 28 May '10

28 May '10

Hello, I've been using 'super' to align the c-alphas within one domain of two different models of the same protein while leaving the second domain to move freely. I can do this using: super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca) What I would like to do is determine the rotation and translation of model B's second domain as it moves away from A's second domain. I can output a matrix after running super using: print cmd.get_object_matrix("A") How do I go from the matrix to an angle and distance? Thanks for any thoughts, Jon

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Re: [phenixbb] Autobuild submitted jobs
by Mark A Saper 27 May '10

27 May '10

Tom -- It turns out that each of the omit region's jobs submits another job, but that latter job is only the "test run_command" job. Why test the run_command if no subsequent jobs are submitted? Our solution, thanks to an extremely savvy cluster manager, was to install the qsub (Torque?) package on each of the computing nodes (117). Also we ran the top-level process on the head (scheduler) node, so as not to tie up a computing node while it waits for its sibling jobs (the omit regions) to finish the calculation. Overall wall-time with a separate node allocated for each omit region was about 50 minutes. Interestingly, although each node has 8 processors, the OMIT region jobs seems to only use one processor! Interestingly when phenix.refine jobs are run on my Macbook Pro, the operating system is savvy enough to spread it over 2 processors. -Mark ______________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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How to turn off mask optimization
by Schubert, Carsten [PRDUS] 26 May '10

26 May '10

Hi, Is there a way to turn off the mask optimization step in 393? I tried 'main.optimize_mask = False' but that does not work. The program spends a substantial amount of time in repeated mask optimizations and I am trying to shave off a couple minutes for each run... Cheers, Carsten

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Autobuild submitted jobs
by Mark A Saper 26 May '10

26 May '10

Dear Tom and colleagues, We're running Autobuild composite omit on a large cluster, each node has 8 processors. Autobuild submits jobs with the "run_command". And it appears that each of those jobs submit other jobs. Are the latter jobs necessary? That is, are there situtations where they wouldn't be submitted as separate jobs but run as subprocesses? Currently nodes in our cluster don't have capability of qsubing new jobs, but we are in the process of changing this. Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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atom selection syntax for ALT atoms?
by Scott Classen 25 May '10

25 May '10

This is the selection for the atom I'm interested in: atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 160" I want to try a refinement with an alternate conformation at GLU160 . Can someone please help me with the proper syntax. Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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PDB Deposition Question
by Alexander Hirschi 25 May '10

25 May '10

Hi all - I refined a structure using Phenix 1.4-3 and now I need to submit it to the PDB. When I try to run sfcheck on the .mtz that Phenix generated, sfcheck can't read the file. I also tried to convert the .mtz to .cns using phenix.reflection_file_converter. This time, sfcheck could "not find IOBS or FOBS in your file". Any advice would be greatly appreciated. -Alex

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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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Building DNA
by Rajagopalan, Senapathy 15 May '10

15 May '10

Dear Phenix developers, I am solving a protein-dna complex and Autobuild is able to build both the protein as well as DNA chain (one at a time). However, when I try to do the refinement, I get an error saying "Phenix could not find the geometry restraints in the standard monomer library for one or more residues in the pdb file... DG: 6 copies, DA: 3 copies, DT: 43 copies". It seems like Autobuid uses the nomenclature DA, DC, DG and DT for the DNA bases while Phenix.Refine either doesn't like the nomenclature or the restraint files uses a different one. It still however lets me do the refinement...although I don't know if it just ignores the DNA part. Can someone enlighten me on this. Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA and doesn't like the above phenix style. In order to manipulate in coot, I had to rename all the bases...is it possible to have a format that is compatible both in Phenix and Coot or am I missing something obvious here. Thanks and Have a great weekend! 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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Improved refinement method for low resolution data
by Florian Nachon 14 May '10

14 May '10

Hi all, Axel Brunger just published a paper in Nature (http://www.nature.com/nature/journal/v464/n7292/abs/nature08892.html) about a new method to improve models despite low-resolution data. It is implemented in CNS 1.3. It might be a bit early, but is there any plan to implement that method in phenix? Florian.

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