- phenixbb - phenix-online.org

Phaser not writting out ligands
by Yarrow Madrona 09 Dec '11

09 Dec '11

Hello, I am having trouble with Phaser not writing out my ligands (HEME and small molecule) to it's output PDB even though they are in the input PDB. I am running through the GUI using Phenix version 1.7.3-921. Phenix refine recognizes HEME from the CCP4 library I think so I am not sure why I at least do not get a HEME in the output PDB. Thanks for your help. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

2 1

Please apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 09 Dec '11

09 Dec '11

We are offering RapiData 2012, the fourteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the tenth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 22 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

1 0

map output from ncs_average
by Ursula Schulze-Gahmen 09 Dec '11

09 Dec '11

I used ncs_average to create an averaged fo-fc map. From the manual I thought that the output map is a CCP4 map. I have however difficulties to read it into Pymol as ccp4 map. It is not recognized. Any suggestions? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

3 4

print_sequence
by Bradley Hintze 09 Dec '11

09 Dec '11

Hi, I am analyzing many PDBs vai a script. Thus, I am feeding print_sequence the full path of the given PDB. This has the unfortunate effect of having a filename more than 80 char. As such the '>filename' line is split into two lines making parsing less than ideal. Is there a way I can avoid having the full path on the '>' line and still give print_sequence the full path? Or can that feature be added? Thanks, -- Bradley

2 1

excluding atoms from refinement
by Crystal VanderZanden 08 Dec '11

08 Dec '11

Does anybody know if there a general code that will allow us to exclude something from refinement? I would like to specify that there is a particular part of my structure that I don't want to refine the position. I've thought about deleting those atoms from the pdb file, but then that phasing information is excluded from the refinement. Any ideas? Thanks, Crystal

3 2

Re: [phenixbb] Autosol problems
by Tom Terwilliger 08 Dec '11

08 Dec '11

Hi Stacy, I'm sorry for the trouble! Normally autosol should not have problems with resolve, so this indicates that either (1) the data are unusual or (2) there is some problem in autosol. Can you possibly send along (terwilliger(a)lanl.gov) the log file from autosol and the LAST.log file if there is one? Also what version of phenix is this? (type "phenix.version") Thanks! -Tom T On Dec 8, 2011, at 8:55 AM, stacy William wrote: > Dear All... > I am new user for Phenix. I am right now working with SAD data. I had run Ausol in GUI interface with my SAD anamolous data. but when i am using the output file for my autobuild program it is giving problems with Resolve... n terminating with an error message suggesting to check resolve file. Do i need to change some parameters in Autosol to produce right output files which in turn can work as input files for Autobuild program > Thanks > Stacy > > 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

1 0

automr wizard: searching for all plausible space groups option
by Vitali Stanevich 08 Dec '11

08 Dec '11

Hi, I'm trying to solve structure by MR with phenix 1.6.1-357 version. I have 100% identity search model and can find solution without problem in ccp4i in P212121 sg. But, I can't do it in phenix.automr command line because program looks only for P222 space group (pointed out by Randy Read). I use .sca from hkl2000 and running program from parameters file. I tried: ... all_plausible_sg_list = True use_all_plausible_sg = True ... all_plausible_sg_list = P222 P2221 P21212 P212121 use_all_plausible_sg = True ... space_group = "P 21 21 21" ... They lead to report that no solution found or program being stalled (last variant). What should I do to make phaser search for all space groups in P222 point group? Thanks, Vitali

3 2

rosetta mr
by Shya Biswas 07 Dec '11

07 Dec '11

Hi all, I was wondering how to generate .ali file that I need to run rosetta MR. I have most of the files for the run except this one. the documentation did not help a lot. thanks, Shya

3 3

pseudo-merohedral twinning
by Zhou, Tongqing (NIH/VRC) [E] 07 Dec '11

07 Dec '11

Hi Pavel, I just collected a 2.85 A dataset with space group P212121, MR went well, however, the refinement was not fine: (eg: Rigid body r=48%, it won't go down anymore). I then ran xtriage, it turned out the my data was pseudo-merohedral twinned. The twin fraction is ~0.02. Twin_law=k,h,-l. It there a way to de-twin the data and then do the refinement or just use the twin_law="k,h,-l" at the command line? Is there a way to specify twin_fraction in the paramenter file? Also re-processed data in P41212 or P43212, the ~25% Rsym indicated the data should still be in P222. Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

4 3

pdbtools
by Bradley Hintze 06 Dec '11

06 Dec '11

Developers, I am doing some automated analysis on many pdbs. My analysis is contained to a single chain in a given pdb. Aa such, to cut down on computing time I am generating many pdbs cut to the desired chain. When using pdbtools I get the following Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 46 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). Is there a way around this without creating a CIF file or another tool to cut pdbs? Thanks, Bradley -- Bradley J. Hintze Duke University Graduate Student Department of Biochemistry

2 1

Rfree flag transfer
by Zhang yu 06 Dec '11

06 Dec '11

Hi, I am using phenix_1.7.1-743 GUI. I would like to transfer Rfree tag from one dataset to the other one, but had the following error, "The uni cell for the Miller array /***/*** (186.326, 103.98, 297.48, 90, 98.465, 90)" is significantly different than the output unit cell (183.486, 103.5, 295.416, 90, 98.828, 90)" Two datasets are from same kind of crystal, but with slight different cells. I guess that is why "Reflection file editor" refused to do it. Could anyone tell me how to avoid the error? Thanks Yu

2 3

autoMR wizard
by Vitali Stanevich 06 Dec '11

06 Dec '11

Hi, I'm trying to solve structure by molecular replacement. We already have structure for this protein and new is exactly the same thing with a ligand soaked. I can solve it without a problem with ccp4 gui (tfz=47.7), but not with phenix.automr, which is disappointing. Can somebody point me out what's wrong with my data input? I did it with this command: phenix.automr output.sca complex_search.pdb identity=90 mass=93500 copies=1 or with .eff file (attached) Thanks, Vitali

2 1

H related bond deviaion
by Dialing Pretty 06 Dec '11

06 Dec '11

Dear All, I did a Phenix refine, and before the refine all the H were added. MolProbity analysis demonstrated that almost everything are acceptable after the refinement. However when I did the geometry analysis by the COOT validation, I find all the residues having a significant deviation bond involving H. with z score higher than 7. I am looking forward to getting an explanation from you on it,including how to avoid it. Cheers, Dialing

3 2

bond deviation deected by Coot
by Dialing Pretty 05 Dec '11

05 Dec '11

Dear All, After Pheneix refine, the quality of the structure improved significantly as analyzed by Molprobity. However the bond deviation increased significantly after the refinement. Will you please tell me which refine function can be used to reduce the bond deviation detected by the Coot geometry analysis? Cheers, Dialing

3 3

rotamer outlier reduction by coot
by Dialing Pretty 05 Dec '11

05 Dec '11

Dear All, I am leaning rotamer outlier reduction by Coot. After select a rotamer and acception, I find some hydrogens in the outlier rotamer will be isolated from the rotamer, and the rotamer will have new hydrogens at its new position. Is any influence by further refine by phenix? After new rotamer acception, I have did the rotamer auto-fit, I find there is a trend on that several oxygens can pack together. How to process this problem? After I save the new PDB file by coot after I selected the new rotamers to replace the outlier rotamers, I did a Phenix refine. There is an error message at the start says "Number of atoms with unknown nonbonded energy typensymbol: 2228". What does it mean and how to solve the problem? Is any simple method by which I can do the rotamer outlier reduction by Coot? I am looking forward to getting your reply. Dialing

3 2

documents explaining parameter settings in phenix-1.7.2
by Ruan Wenjie 05 Dec '11

05 Dec '11

Hi, I want to know, about the new Phenix-1.7.2 version, whether I can find some detailed documents explaining how to set the parameters..since there are so many options and I'm not clear their meaning..Thanks~ best, wenjie

6 9

Job Opportunity - Head of the Berkeley Center for Structural Biology
by Paul Adams 04 Dec '11

04 Dec '11

The Physical Biosciences Division at Lawrence Berkeley National Laboratory is seeking candidates for the Head of the Berkeley Center for Structural Biology. This position provides scientific, technical and operational oversight of the BCSB at the Advanced Light Source (ALS), a third generation synchrotron facility. The BCSB is a user resource for structural biology experiments and consists of 5 beamlines at 2 sectors of the ALS, with a staff of 16. This Staff Scientist position will provide leadership and direction to develop methodology and instrumentation for collecting and analyzing crystallographic data using synchrotron radiation, and on projects involving the structure determination of biological molecules using X-ray crystallography. This position focuses on the field of crystallography, and involves interactions and collaborations with researchers from multiple scientific disciplines including chemistry, crystallography, biochemistry, biology, physics and computational sciences. For full details please visit the job application link at: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=73970 Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more about the Lab at http://www.lbl.gov. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area 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: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

1 0

pdb hierarchy
by Bradley Hintze 04 Dec '11

04 Dec '11

Hi Phenix, I have a hierarchy question. I was using the hierarchy and got something that I did not expect. when running this: pdb_io = pdb.input(pdbfile) hierarchy = pdb_io.construct_hierarchy() for model in hierarchy.models(): print model.id for chain in model.chains(): print ' ' + chain.id When I do this I expect the chains in pdbfile to be printed once for each model in pdbfile. However, when I ran this I got, for example, chain 'A' printed four times under the same model. Why is this? Thanks, Bradley

3 2

Writing PDB
by Bradley Hintze 04 Dec '11

04 Dec '11

Hi again, I am trying to take a pdb and write out a new pdb with just a specified chain. I am trying to do this with the hierarchy but am unfamiliar with its functions How do I do this? Thanks, Bradley

3 2

the Ming dial
by Dialing Pretty 04 Dec '11

04 Dec '11

Dear All, In the Ming dial, there is a occupancy (%), which indication of excellent , good, etc. Does it mean if I choose the "occupancy" of excellent, the rotamer outlier ratio will be lowered? My crystal has a resolution of 2.8, and I find no matter how I turn the dial, the original fits the map best. Currently my rotamer outlier is 8%, thus I need the way to have it solved. In addition, for Coot and Ming, which is much convenient to reduce rotamer outlier? I am looking forward to getting your reply. Cheers, Fenghui

2 3

on the rotamer optimization
by Dialing Pretty 03 Dec '11

03 Dec '11

Dear All, Besides Coot and Ming, is any software or server which could further optimize the side chain outliers? I am looking forward to getting your reply. Cheers, Dialing

1 0

solvent model in phenix.refine
by Weiergräber, Oliver H. 01 Dec '11

01 Dec '11

Hello, the ordered_solvent option in phenix.refine apparently uses these parameters by default: min_model_peak_dist = 1.8 max_model_peak_dist = 6.0 min_peak_peak_dist = 1.8 I was wondering about the justification for this (extremely relaxed) set of limits. As far as I know, the shortest hydrogen bonds (if defined as donor-acceptor distance) are about 2 A, and even these are considered exceptional and rare. Similarly, anything in excess of 3.5 A is quite unlikely to be significant energetically, so why use 6 A as an upper limit? Even if max_model_peak_dist was only meant to limit the extent of the outer solvent shell, there is no such thing as max_peak_peak_dist to avoid unreasonably long individual bonds. My personal suggestion would be a range of about 2.3 - 3.2 A for a significant hydrogen bond, with the lower limit exemplified by charged interactions (carboxyl-water or oxonium-water), which tend to be shorter - and stronger - than average. On the other hand, I do frequently observe elongated densities which, in accordance with the default parameters, are typically interpreted by phenix.refine as two water molecules about 2 A apart. So the question arises whether this is a realistic assumption, compared to a "sliding water" model in which the position of a single molecule is just ill-defined in a certain direction (due to a competition of adjacent binding sites for example)? Best regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

Clashing alternative conformations
by Sozanne Solmaz 01 Dec '11

01 Dec '11

Dear all, I have the following problem: I have a homodimer of two protein chains A and B, which I refine in Phenix, and one residue has 2 alternate conformations (a and b) for each chain. If the residues of both chains A and B are in the alternative conformation b, they clash. However, I would expect that never both residues are in conformation b, and therefore only the combinations aa, ab and ba of alternative conformations exist. My problem is, that during the refinement, the two b conformations of the residues clash, which drives the clash-score of the overall structure to a very high value and repulsion pushes the two b-conformations apart during refinement, therefore I cannot model them properly. Is it possible in Phenix to define these two conformations as non-clashing and non-repulsive? Thank you, best regards, Sozanne Solmaz.

2 1

"nproc" in phenix.refine
by Jonathan Elegheert 30 Nov '11

30 Nov '11

Dear all, I have a question regarding the "nproc" parameter in phenix.refine; We have the software installed on our university HPC cluster, which has nodes built up of 8 processors each. Submission works via a queuing system ("qsub"). I understand that compiling with OpenMP renders the nproc parameter disfunctional. Does this then imply that I will be limited to 1 node (8 processors) if compiled without OpenMP, since there is no "message passing" to other nodes? Or is there a way to make use of more of the available nodes, for example by compiling with OpenMP and then specifying many nodes with 1 processor? Best regards, Jonathan Elegheert PhD Student Unit for Structural Biology & Biophysics Ghent University jonathan.elegheert(a)ugent.be

2 1

Nitric Oxide ligand keeps getting pushed far away from specified links in CIF
by Yarrow Madrona 30 Nov '11

30 Nov '11

Hello, I am having some trouble refining a structure with Nitric Oxide coordinated to the Heme Fe. I attempted to merge two Cif files. One for another ligand (CNL) and one for NO (NO.cif). I have saved the merged file as CinNO2.cif. In the defualt refinement I type the following into the command line: Mymodel.mtz mymodel.pdb CinNO2.cif Phenix refine runs fine without any errors but pushes the NO much further than the 1.9 angstrom specified by the links in the cif file. I have pasted the contents of the cif file below. The NO, Fe links are at the end of the file. Thank you for any help you can provide. -Yarrow # Files merged : Tue Oct 4 10:11:22 2011 # # CNL.cif # NO.cif # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level CNL CNL Unknown ligand 29 11 . NO NO Unknown ligand 2 2 . # data_comp_CNL # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z CNL C1 C CT . 55.3085 -9.1280 -43.0216 CNL C2 C CH2 . 55.6432 -10.5699 -43.1750 CNL C3 C CH2 . 54.6509 -11.3139 -43.9725 CNL C4 C CH1 . 53.4902 -10.4784 -44.3504 CNL C5 C CH2 . 53.9278 -9.3349 -45.0693 CNL C6 C CH2 . 54.8932 -8.4964 -44.3064 CNL C7 C CH3 . 56.3801 -8.3679 -42.3275 CNL C8 C CT . 52.9353 -9.9244 -43.0573 CNL C9 C CH3 . 52.3495 -11.0301 -42.2453 CNL C10 C CH3 . 51.8314 -8.9341 -43.2982 CNL O O O2 . 54.1049 -9.2461 -42.2221 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd CNL C1 C2 single 1.488 0.020 CNL C1 C6 single 1.491 0.020 CNL C1 C7 single 1.486 0.020 CNL C1 O single 1.450 0.020 CNL C2 C3 single 1.475 0.020 CNL C3 C4 single 1.479 0.020 CNL C4 C5 single 1.420 0.020 CNL C4 C8 single 1.512 0.020 CNL C5 C6 single 1.489 0.020 CNL C8 C9 single 1.492 0.020 CNL C8 C10 single 1.502 0.020 CNL C8 O single 1.589 0.020 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd CNL C3 C2 C1 113.16 3.000 CNL C5 C6 C1 112.56 3.000 CNL C8 O C1 110.85 3.000 CNL C6 C1 C2 112.60 3.000 CNL C7 C1 C2 112.43 3.000 CNL O C1 C2 99.48 3.000 CNL C4 C3 C2 112.41 3.000 CNL C5 C4 C3 110.02 3.000 CNL C8 C4 C3 106.05 3.000 CNL C6 C5 C4 113.20 3.000 CNL C9 C8 C4 109.75 3.000 CNL C10 C8 C4 111.96 3.000 CNL O C8 C4 109.61 3.000 CNL C8 C4 C5 104.53 3.000 CNL C7 C1 C6 112.76 3.000 CNL O C1 C6 106.18 3.000 CNL O C1 C7 112.51 3.000 CNL C10 C8 C9 106.70 3.000 CNL O C8 C9 108.62 3.000 CNL O C8 C10 110.10 3.000 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period CNL Var_01 C4 C8 O C1 10.40 30.0 3 CNL Var_02 C9 C8 O C1 130.31 30.0 3 CNL Var_03 C10 C8 O C1 -113.19 30.0 3 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign CNL chir_01 C1 C6 C7 O both CNL chir_02 C4 C3 C5 C8 both # data_comp__NO # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z NO N N N . -5.7690 4.3760 32.3600 NO O O O . -4.8990 5.2460 32.3600 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd NO N O double 1.150 0.02 # data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name HEM-CYS HEM . . CYS . . bond_CYS-SG_=_HEM-FE NO -HEM HEM . . NO . . bond_HEM-FE_=_NO-N # data_link_HEM-CYS # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd HEM-CYS 1 FE 2 SG . 2.300000 0.020 # loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd HEM-CYS 2 SG 1 FE 1 NC 109.471221 3.000 HEM-CYS 1 FE 2 SG 2 CB 109.471221 3.000 # data_link_NO -HEM # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd NO -HEM 1 N 2 FE . 1.900000 0.020 # loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd NO -HEM 2 FE 1 N 1 O 140 3.000 NO -HEM 1 N 2 FE 2 NC 103 3.000 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

4 6