- phenixbb - phenix-online.org

Elbow problem
by Jerome Nwachukwu 11 Mar '11

11 Mar '11

Hi all: For some reason, phenix.elbow converts a specific double-bond (C=C) in my ligand to a single bond (C-C) and therefore generates a wrong .cif file. Is there away to avoid or correct this problem? Thank you, -Jerome Jerome C. Nwachukwu, PhD Kendall Nettles' Lab Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

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Binary Installation failure on Ubuntu
by Katherine Sippel 11 Mar '11

11 Mar '11

Hi all, I am trying to install the latest nightly build (dev-694) using the Kernel 2.6 (64-bit; Fedora Core 3) binary. The OS is Ubuntu 10.10 installed as a dual boot through Wubi. I get as far as configuring PHENIX components at which point it heaves out a binary.log file. I can send the whole file to anyone whose interested but it's a bit too large for the bb. The juicy bit is as follows... Could not find platform independent libraries <prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site How can I determine which libraries are missing? Thanks for any help you can provide, Katherine

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Average maps (*not* NCS averaging)
by Stephen Graham 11 Mar '11

11 Mar '11

Hi there, I'd like to average 2Fo-Fc maps from 2 (approximately) isomorphous data sets (one with ligand, one without) to see whether I get better density for some of the noisier bits of the structure. I don't want to do any kind of solvent flattening, histogram matching, cyclical averaging, etc; I just want to sum the equivalent pixels and divide by 2. Is it possible to do this easily using any of the phenix tools? It seems like all the required plumbing is there with get_cc_mtz_mtz or superpose_maps, but I can't find a phenix utility for averaging two superposed maps. Thanks, Stephen -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

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Re: [phenixbb] [ccp4bb] Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
by Francois Berenger 10 Mar '11

10 Mar '11

Sorry, I forgot to mention about what is the .obj file I need. It is a pure ASCII geometric description of a polyhedra. Cf. http://en.wikipedia.org/wiki/Wavefront_.obj_file It looks rather easy to parse compared to some VRML file, for example. Thanks, F. Francois Berenger wrote: > Hello, > > What are the good software to do this? > > I already know of Pymol and Jmol. > > Both can export the result to a .obj file, which is interesting for > later processing. > > However, Pymol's algorithm is not exactly what Connolly described, > cf. > http://www.mail-archive.com/[email protected]/msg00179.html > > Also, Pymol will save the surface with some translation and rotation > which are not present in the PDB read in, which is a real pain. > > For Jmol, sometimes the surface is not a closed polyhedra, so > it is kind of useless for my purpose. > > I know of MSMS, but I don't think it is that robust (I read some source > code where someone was using MSMS, the source code had many dirty things > in order to try handling the apparently many cases where MSMS was > crashing). > > Is there something freely usable for research, using beta shapes > internally, for example? That should be a robust approach. > > A robust software would be much appreciated (not crashing, whatever > the PDB we give it as input). > Open source and not in Fortran would be heaven. ;) > > Thanks a lot for suggestions, > F.

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Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
by Francois Berenger 10 Mar '11

10 Mar '11

(was posted on CCP4 bb also) Hello, What are the good software to do this? I already know of Pymol and Jmol. Both can export the result to a .obj file, which is interesting for later processing. However, Pymol's algorithm is not exactly what Connolly described, cf. http://www.mail-archive.com/[email protected]/msg00179.html Also, Pymol will save the surface with some translation and rotation which are not present in the PDB read in, which is a real pain. For Jmol, sometimes the surface is not a closed polyhedra, so it is kind of useless for my purpose. I know of MSMS, but I don't think it is that robust (I read some source code where someone was using MSMS, the source code had many dirty things in order to try handling the apparently many cases where MSMS was crashing). Is there something freely usable for research, using beta shapes internally, for example? That should be a robust approach. A robust software would be much appreciated (not crashing, whatever the PDB we give it as input). Open source and not in Fortran would be heaven. ;) Thanks a lot for suggestions, F.

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automr renumbered all residues to 0 for final solution in dev-674
by Francis E Reyes 10 Mar '11

10 Mar '11

Is this fixed in a later version? Thanks! F --------------------------------------------- Francis E. 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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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Sorry, I meant judging by distances it is not experiencing interaction in the form of H-bonds. Which I think is concerning.

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Hi Pavel, What I meant it was just that the 2mFo-2DFc map looks really great and corroborates experimental data as far as the stereochemistry. But I dont understand ehy the carbonyl moiety of the ligand would be where it is now, no "driving force to be here". And when I look at my averaged kick and SA omit map it looks ambiguous. Any help?

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ambiguous ligand density
by Pompeu,Yuri Alexey Andreiw 09 Mar '11

09 Mar '11

Hello everyone, I have this strucuture I solved by Molecular replacement. It is a single mutant of previously solved enzyme. I started refining it and fit the ligand in a way that gives me the experimental stereochemistry. The final map 2mFo-2DFc looks great. After further examination I noticed, I have a carbonyl that does not seem to be bound to anything !!! I started looking at my average kick and SA composit omit-map prior to modeling in the ligand and now I am really lost. Could anyone help? Thank you

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Important change in phenix.refine output: MTZ file with data and map coefficients
by Pavel Afonine 04 Mar '11

04 Mar '11

Hi Everyone, starting development version dev-686: http://www.phenix-online.org/download/nightly_builds.cgi phenix.refine does not output *map_coeffs.mtz file. Instead, it creates prefix_serial.mtz file (example: lysozime_001.mtz) containing four sections: - section 1: Original input data (Iobs or Fobs, and HL coefficients if provided) and flags (as supplied in input); - section 2: Experimental data used in refinement (labels: F-obs-filtered, SIGF-obs-filtered). This can be different from "Original data" due to Iobs->Fobs conversion (if input data are intensities) and outliers filtering; - section 3: Contains total model structure factors (labels: F-model, PHIF-model) used everywhere in refinement (for the formula, see: http://www.phenix-online.org/documentation/fmodel.htm). In the future, this section might be extended to explicitly list all contributions to Fmodel, such as Fcalc (corresponding to atomic model), Fbulk (bulk solvent contribution), and so on. - section 4: Fourier map coefficients (exactly the same as used to be in *map_coeffs.mtz file). This change is meant to reduce the confusion when people tended to use *map_coeffs.mtz file for refinement and PDB deposition, and facilitates the reproduction of refinement statistics (R-factors, for example). Also, thanks to Jeff Headd, by default phenix.refine now converts input intensities (Iobs) to amplitudes (Fobs) using French & Wilson method (Acta Cryst A34, 517, 1978), so no need to run a specific program (Truncate, for example) to do this. To see the content of a MTZ file use phenix.mtz.dump command: phenix.mtz.dump data.mtz Pavel.

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Geometry problem with sugars refined in phenix
by Tirumala Kumar Chowdary 03 Mar '11

03 Mar '11

Hi, I have refined a structure with NAGs linked to ASNs at 3 places in my structure. I used the right link definitions and the NAG definitions are from Phenix library. Phenix refined all the sugars right and made the right links between the NAGs. However, while submitting, PDB found problem with the geometry of NAGs linked to the ASN at two places. This is the issue -the atoms around C1 atom of the sugar molecule NAG A #810 and NAG A #1670 are on a plane and the C1 atom center is far off to be tetrahedral. Please, verify the chirality of C1 and provide the correct coordinates if necessary.- Any ideas on how to fix the geometry of these sugars will be of great help. Regularization and real space refine in Coot is not working or I don't know how to do it. I am looking for alternative ways to fix this problem. Thank You Tirumal

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Re: [phenixbb] number of cycles
by Maia Cherney 01 Mar '11

01 Mar '11

Hi, I am using now the latest phenix version and I am curious how to understand these lines: Flipped N/Q/H residues before refinement: A 28 HIS A 72 HIS A 141 GLN A 202 GLN A 296 ASN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 388 HIS Maia

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[Fwd: Re: number of cycles]
by Maia Cherney 01 Mar '11

01 Mar '11

-------- Original Message -------- Subject: Re: [phenixbb] number of cycles Date: Tue, 01 Mar 2011 19:50:57 -0700 From: Maia Cherney <chern(a)ualberta.ca> To: Jeff Headd <jjheadd(a)lbl.gov> References: <40FBFA09-3C52-460A-A6A1-7D08F6496AD2(a)umich.edu> <AANLkTin=8_ddvihNSDyLp9k1iSpV9fVj6A2ndvoUTJ6O(a)mail.gmail.com> <0171D39299ABC14AAAA75ABABDD0BBB63868BF23AA(a)NIHMLBX12.nih.gov> <A8FA87FE-7DF1-48BE-AA44-E19BB7D0E6E0(a)crystal.harvard.edu> <4CAC89B8.9090909(a)lbl.gov> <4D12B58C.1030604(a)ualberta.ca> <4D12E866.9070602(a)lbl.gov> <4D138B20.5050001(a)ualberta.ca> <4D14E51F.2040305(a)lbl.gov> <4D164065.3050709(a)ualberta.ca> <4D165AE5.8090905(a)lbl.gov> <4D6C0DB1.5040003(a)ualberta.ca> <4D6C9271.6000301(a)lbl.gov> <4D6DA14C.6060806(a)ualberta.ca> <AANLkTi=GXvoGWsB+3+NNBNFvVtzc0Q0ag1Ln_U6FqHqO(a)mail.gmail.com> Thanks, Jeff. Though I don't see any clashes for any orientations. But this feature is really great. Jeff Headd wrote: > Hi Maia, > > Phenix.refine analyzes Asn, Gln, and His residues at each macrocycle > and determines which orientation is likely correct given the local > environment of the sidechain. The best orientation will have no steric > clashes and satisfy local H-bond donors/acceptors. In cases where > there are other model errors in the region of the sidechain and both > orientations clash significantly, you'll see the **PLEASE CHECK > MANUALLY** warning which indicates that there are likely multiple > misfit sidechains that need to be corrected, and refinement alone is > not powerful enough to escape the false minimum. > > If you want to turn this feature off, you can add main.nqh_flips=False > to your refinement call or > > main { > nqh_flips=False > } > > to your param file. However, we highly recommend leaving this option > on as it is an excellent diagnostic of model errors. > > If you have any further questions please let me know. > > Thanks, > Jeff > > On Tue, Mar 1, 2011 at 5:45 PM, Maia Cherney <chern(a)ualberta.ca> wrote: > >> Hi, >> >> I am using now the latest phenix version and I am curious how to understand >> these lines: >> >> >> Flipped N/Q/H residues before refinement: >> A 28 HIS >> A 72 HIS >> A 141 GLN >> A 202 GLN >> A 296 ASN >> ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** >> ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** >> A 353 ASN >> A 388 HIS >> >> Maia >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> > > >

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Glycan Links/Restraints
by Damian Ekiert 01 Mar '11

01 Mar '11

Sorry to bring up an old topic again but I can't find any documentation of glycan refinement on the Phenix website and previous threads don't seem to answer my question. I am refining a structure with N-linked glycans. I have inserted several "apply_cif_link" records to my .eff file to define the glycan topologies (see below) and fed in a cif file for BMA. After fiddling for quite some time now, I have managed to get around all the error messages people have described previously to disappear. Yet, 1) none of my linkages appear to be enforced and 2) even the restraints on the individual sugars appear to be unenforced (or at least, insufficiently so). For example, some rings are rendered almost flat, or flipped into boat or otherwise distorted conformations, and glycosidic bonds stretch to >2 A. No obvious signs of trouble in the log file, running the latest version (1.7, also tried 1.6.4), but my glycans look terrible (despite some of the best density I have ever seen! :-) ) Any suggestions would be appreciated! Thanks, Damian Ekiert >From my .eff file: apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain X and resname NAG and resid 401 residue_selection_2 = chain A and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Y and resname NAG and resid 401 residue_selection_2 = chain C and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Z and resname NAG and resid 401 residue_selection_2 = chain E and resname ASN and resid 91 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain X and resname NAG and resid 402 residue_selection_2 = chain X and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname NAG and resid 402 residue_selection_2 = chain Y and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Z and resname NAG and resid 402 residue_selection_2 = chain Z and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname BMA and resid 403 residue_selection_2 = chain Y and resname NAG and resid 402 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain Y and resname MAN and resid 404 residue_selection_2 = chain Y and resname BMA and resid 403 }

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Implementation of French & Wilson data correction?
by Joseph Noel 01 Mar '11

01 Mar '11

Hi All, Any pointers on implementing the new option in the latest build for French & Wilson correction? Does scala output negative intensities so that a proper scaling with this new option can be used? Also, what column labels should be used particularly for proper treatment of anomalous data? Can one use the labels output by scala? Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Bay Area and Beyond Phenix User Meeting
by Paul Adams 01 Mar '11

01 Mar '11

Dear Colleagues, On Thursday March 17th, a Bay Area and Beyond Phenix User Meeting will be held at Lawrence Berkeley Lab. During the workshop, the Phenix developers will give lectures on the latest developments and Phenix usage. Half of the user meeting will be in the form of informal hands on sessions, allowing participants to work with the developers. Participants are encouraged to bring their own (reduced) data to be used during hands on sessions, but tutorial data will also be available. Due to the highly interactive format of the meeting there will be space for approximately 20 participants. If I have missed any of your colleagues on this invitation please feel free to pass on the message. To apply, researchers should send a email to NEchols(a)lbl.gov and PDAdams(a)lbl.gov by Monday March 7th. Unfortunately we are unable to provide any funds to support student travel to the meeting. Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ KLMoody(a)lbl.gov ][ 1-510-495-2506 ] --

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how to cut off side chain from a model
by crystallogrphy 01 Mar '11

01 Mar '11

Hi, I am refining a low resolution data (4.7A). I want to cut off all side chains from my model because they cannot be seen from the density. Phenix pdbtools can only keep the backbone, but cannot keep the Cbeta atom. What program I can use to cut off all the side chain, but keep the Cbeta atoms? Thanks!

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ICSG 2011 early registration and abstracts submission open until March 4
by Tom Terwilliger 01 Mar '11

01 Mar '11

Dear Colleagues, We hope that you are planning to attend the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. Due to technical difficulties with the registration page, we have extended both the early registration and abstract submission deadlines. Abstract submission and early bird registration will now end Friday March 4th at 11:59pm EST. Please visit http://www.icsg2011.org for ICSG 2011 meeting and workshop registration details and to submit your abstract. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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Question about Adding Hydrogens
by Louis Lazar 01 Mar '11

01 Mar '11

All, I was curious if there is a way to add hydrogens to an individual residue. For example, rather than running the command: phenix.ready_set model.pdb, run something like: phenix.ready_set model.pdb resid=X or phenix.ready_set=resid 10 model.pdb Any thoughts/recommendations on the subject are greatly appreciated. Thanks in advance. Louis

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ICSG 2011 Early Registration Deadline Feb 28, 2011
by Thomas C. Terwilliger 25 Feb '11

25 Feb '11

ICSG 2011 Abstract and Early Registration Deadline Feb 28, 2011 Dear Colleagues, We hope that you are planning to attend the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics, structural/chemical biology, and their impact on research in biology, medicine and disease. There are many speaking slots still open that will be chosen from submitted poster abstracts. We invite you to submit your abstract by February 28, 2011. Please also note that early registration will end on February 28, 2011, so we invite you to register now in order to take advantage of the reduced registration fee. In addition to the main ICSG meeting, there will be a whole day of free concurrent satellite workshops (May 10, 2011), including: Small Molecule Screening Workshop- This hands-on workshop will allow participants to screen a protein of their choice for binding of selected compounds, using thermal shift assays. Eukaryotic Gene Expression Systems Workshop - This workshop will provide participants with a detailed understanding of the state-of-the-art for production of eukaryotic proteins destined for biochemical, biophysical, and structural analyses. iSee: Interactive 3D Documents for the Dissemination of Structural Biology - This hands-on workshop will familiarize participants with the iSEE 3D graphical software which allows interactive viewing of 3 dimensional molecular structures and is currently used by journals such as Nature Structural & Molecular Biology and PLoS Biology and PLoS ONE. Workshop on NMR Methods for Structural Biology- This workshop will survey technologies for structure/function investigations of proteins, developed in (or in collaboration with) structural genomics projects, that are ready for widespread use by the wider biological community. Phenix Crystallography Software Workshop - This workshop will introduce the PHENIX software for macromolecular structure determination and the core algorithms that it uses. It will provide hands-on tutorials for crystallographers of all levels. Please visit http://www.icsg2011.org for ICSG 2011 meeting and workshop registration details and to submit your abstract. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

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composite omit map problem
by Morgan Thompson 23 Feb '11

23 Feb '11

Hi, I am having trouble generating a composite omit map using the AutoBuild GUI. I am using Phenix version 1.7-650 on Ubuntu and I am able to run AutoBuild to make a simulated annealing composite omit map using my experimental data .mtz file and a reasonably refined model (R/R-free of 24/29% at 3.3 Angstrom). However, when I load the map - resolve_composite_map.mtz - into Coot (version 0.6.1) along with the starting model it looks terrible. There is quite a bit of density between each molecule within the ASU but very little density surrounding the model itself. However, I am able to open any of the .mtz_OMIT_REGION_XX files and they look really good. Any suggestions? Thanks, Morgan Biochemistry Department Dartmouth College

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questions on refinement
by Hena Dutta 23 Feb '11

23 Feb '11

Hello, I have a question on refinement of macromolecules. I like to apply 180 degree rotation to the side chain of a particular residue about a particular bond and see, which one (before or after applying rotation) agrees well with the observed x-ray data (based on R factors and electron density map). Can someone advise, what could be the best way to do this? I like to do the same operation on multiple structures which are already refined. Regards, hena

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phenix find tls groups
by Kendall Nettles 23 Feb '11

23 Feb '11

is there a command line interface to have phenix find TLS groups ? Best regards, Kendall Nettles

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Deadline March 1, 2011: Travel Fellowships for XXII IUCr Congress, Madrid, August 22-31, 2011
by Gloria Borgstahl 21 Feb '11

21 Feb '11

Please visit the USNC/Cr website for more information. *http://sites.nationalacademies.org/pga/biso/IUCr/*<http://sites.nationalacademies.org/pga/biso/IUCr/>

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adding ligands to model
by Geoffrey Feld 21 Feb '11

21 Feb '11

Greetings, I have a few structures I am trying to refine that have density for ligands, and I'm having trouble getting phenix to refine them properly. There are two unique scenarios, so I'll go in order of difficulty. 1) There are non-water solvent molecules (i.e. probably PEGs) that are here and there in the structure. I used phenix.elbow with SMILES notation to build the requested ligands and placed / real space refined them into the density using COOT. Now I cannot get phenix to refine the structure, every time I get the message "Number of atoms with unknown nonbonded energy type symbols: XX Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). where XX can be any variation of a number, depending on how I set up the phenix.refine run. This is what I've tried: a) adding the .cif files into my .def file I'm using for refinement parameters b) adding the .cif files on the command line c) running phenix.ready_set to generate .cif files for the unknown ligands and then inputing the .cif files from that on the command line d) running phenix.elbow with --add_all and the pdb to generate .cif files for unknown ligands, then doing as in (c) from the command line None of these seem to get phenix.refine to skip the error mentioned above and start refining. There are 3 different ligands, one of which is repeated 4x, but each has its own chain number in the same chain (I've even tried them each with their own unique chain). Any advice on getting these ligand restraints into phenix so it will happily refine? 2) I have an intramolecular crosslink in another structure, basically I crosslinked two cysteines with 1,3-dichloroacetone, giving a Cys-S-CH2C(=O)CH2-S-Cys linkage. How can I get restraints for this crosslink so it will refine as one covalent chain? So far, I've placed the acetone in between the two Cysteines, but it would be nice for it to be a part of the chain so I can refine it in real space, the density is not so good since the crosslink adds flexibility to the bond as apposed to just a disulfide. Any ideas here? I thought maybe the best way to do it is to just modify one of the cys to contain the extra atoms and call it a new residue, then add bond restraints for the 2nd link, however, then I'm still stuck with the extra hydrogen. Thanks! Geoff -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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