- phenixbb - phenix-online.org

restricted simulated annealing
by Raja Dey 13 Nov '08

13 Nov '08

Dear Friends, How can I restrict simulated annealing in phenix on part of my molecule, say 2 chains out of 3 or part of a particular chain? Thanking you in advance for your reply... Raja

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Failed to carry out AutoBuild
by Joao Renato Carvalho Muniz 12 Nov '08

12 Nov '08

Dear Phenix community, I started an AutoBuild run using the Phenix GUI (ver 1.3 final) on linux. However, I noticed 2 weird things: 1st, Phenix seems that can not handle with alignment between the residues from pdb and sequence.seq, flagging the "Rebuild in place not recommended as identity * fraction_aligned is 0.0%" message but still trying to build the structure with the option "include_input_model=False" I guess(?)... and 2nd, after quite a while I obtained the following error message: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/RUN_FILE_1' /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log: File exists. ******************************************************************************** The alignment between MR.1.pdb and sequence.seq should be something like 80%+! Also tried to run using the followed command line: phenix.autobuild data=MR.1.mtz model=MR.1.pdb include_input_model=True n_cycle_rebuild_max=5 seq_file=sequence.seq Same problem as above. Could anyone please tell me what to do to prevent this error and get phenix get its job finished? Many thanks in advance, Joao.

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refine occupancies for MET/MSE double conformations
by Anastassis Perrakis 12 Nov '08

12 Nov '08

Hi there - I was pleased to read in the manual: if no selections are provided (refine.occupancies.individual=None and refine.occupancies.group=None) then phenix.refine by default will refine individual occupancies for atoms that have partial occupancy values in input PDB file (except zeros) and it will perform group constrained occupancy refinement for all atoms in alternative conformations. Occupancies of all other atoms will be fixed. If selections are provided (refine.occupancies.individual=atom_selection or refine.occupancies.group=atom_selection) then the selected atoms will be added to the list of atoms defined above (atoms with partial occupancies or those in alternative conformations). See this document for examples of atom_selection syntax. However, I want to refine my MET residues in double conformations, one as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy to start with. When I try that I get: == ----------Initial model statistics (before refinement)---------- ... |-Occupancies statistics------------------------------------------------------| Sorry: There are atoms with negative occupancies. Check input PDB file. === The PDB file has 0.5 and 1.0 occupancies only. I am also using: == refinement.refine.strategy=tls+individual_sites+individual_adp +group_anomalous refinement.refine.adp.tls="chain A" refinement.refine.adp.tls="chain B" refinement.main.number_of_macro_cycles=4 refinement.simulated_annealing.start_temperature=5000 refinement.refine.adp.individual.anisotropic =" chain C" refinement .input .xray_data .labels=I_Mystery(+),SIGI_Mystery(+),I_Mystery(-),SIGI_Mystery(-),merged refinement.refine.anomalous_scatterers { group { selection = "name ZN " f_prime = -0.3 f_double_prime = 2.5 refine = *f_prime *f_double_prime } group { selection = "name SE " f_prime = -5.2 f_double_prime = 3.8 refine = *f_prime *f_double_prime } } == Any hints on how to proceed ? Should I define groups for the occupancy refinement explicitely and not rely to automatic assignment? And if so how? How do people treat this partial Se-Met issue ? We solved the structure with SeSAD ... if I out MSE I get pretty large negative density peaks on the Se ... if I put MET I get positive peaks ;-) And there are good reasons to believe in partial Se- substitution in this case. Thanks in advance, Tassos

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cis peptide
by Jianghai Zhu 09 Nov '08

09 Nov '08

Hi, Does phenix.refine restrain cis peptide? How do I know if the refined pdb file contain any cis peptide? Thanks. -- Jianghai

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User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 05 Nov '08

05 Nov '08

Dear Users, Through the Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source, scientists can send protein crystals to Berkeley Center for Structural biology (BCSB) staff researchers for data collection and analysis. The CC Pilot Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Click on "protein crystallography" to begin proposal. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for January/February 2009 allocation period, proposals must be submitted by November 15, 2008. The deadline for CC proposals for the time period March/April 2009 will be January 15, 2009. Regards, Banumathi Sankaran

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weight optimization
by Raja Dey 03 Nov '08

03 Nov '08

Hi, I was trying to optimize weights as follows, but it came out with the error given below. Can anyone tell me what's wrong? I used phenix.refine ../p65_nat.mtz ../p65_136.1.pdb optimize_wxc=true optimize_wxu=true output.prefix=136.1 ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' Thanks... Raja

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DNA sugar pucker
by Laura Murray 26 Oct '08

26 Oct '08

Hi. I'm one of the Richardsons' people. I have more experience with RNA, but have looked at DNA some as well. 1. On C2'-endo and C3'-exo being equivalent: no, not quite equivalent, but related. If you do have C1', C4', and O4' in the plane, then "popping" C2' out on one side or C3' out on the other is relatively similar (sort of) and there's a recognized "twist" conformation where you've got them both out of plane a bit. However, you can really get C3' mostly in-plane with the other three and have a conformation that's distinctly a C2' endo pucker rather than looking like it could be either one. If you're building ideal B-form DNA, it would be better to use a real C2'-endo pucker than the twist, and certainly better than using the C3'-exo. 2. I'm afraid I don't know the appropriate format for use with PHENIX, but there are pucker-specific parameters available on the Nucleic Acid Database site: http://ndbserver.rutgers.edu -- specifically, here: http://ndbserver.rutgers.edu/standards/parameter.html -- these are set up for XPLOR, but the values should help. At any rate, these files distinguish the dihedrals for C2'-endo and C3'-endo sugar puckers. (The set for higher resolution also provides slightly different bond lengths and angles for them, since the ring strains are a bit different.) And I don't think they make a habit of turning up C3'-exo. Laura Murray

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sugar puckering in an ideal B-DNA
by chern 26 Oct '08

26 Oct '08

Hi all, does anybody know why coot and sybil (and may be others that I don't know about) generate an ideal dna with C3*-exo puckers instead of C2*-endo, as text books say. maia

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phenix.refine output map format
by Paul Emsley 25 Oct '08

25 Oct '08

Dear Phenixers, Is is possible for phenix.refine to output a ccp4 map? If so, how? Thanks, Paul.

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elbow
by chern 24 Oct '08

24 Oct '08

Dear all, could I use eLBOW to create a .cif file for a B-DNA to restrain sugar puckers? Maia

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sugar puckering in DNA
by Maia Cherney 24 Oct '08

24 Oct '08

Hi Yu Seon. I would appreciate it very much if you send me your added restraints to the cif file. Maia YS. Chung wrote: > Hi Maia, > I had the same problem when I was refining with phenix. I ended up > looking at the torsions that were used in 3DNA (the program I used to > analyze the puckerings) and manually added the restraints to the .cif > files used in phenix. I can send you an example if you'd like. The > puckerings improved a lot when I used the modified .cif files. > Yu Seon > > On Fri, 24 Oct 2008 10:43:44 -0600 > "chern" <chern(a)ualberta.ca> wrote: > >> Sorry, I gave a wrong subject name in my previous e-mails. Should've >> been sugar puckering in DNA. >> I am wondering why the default .cif file for DNA does not include all >> >> information about sugar puckers. >> I do not have some fancy nucleotides. They are regular. >> >> Maia >> >> ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" >> <rwgk(a)cci.lbl.gov> >> To: <phenixbb(a)phenix-online.org> >> Sent: Friday, October 24, 2008 10:03 AM >> Subject: Re: [phenixbb] elbow >> >> >> >>>> The answer is yes but there may be better options. Ralf is the >>>> >> best >> >>>> person to answer this question but one option is to start with the >>>> >> .cif >> >>>> file in the monomer library. >>>> >>> This is more a chemistry question than a formatting question. >>> Since I'm not deeply familiar with the DNA chemistry, I was >>> >> pointing >> >>> Maia to phenixbb in hopes that someone may already have figured out >>> the list of torsion angle restraints to fix sugar puckers. >>> >>> What Maia really wants is: >>> >>> >>>> could you please send me a specific example of how to modify a cif >>>> >> file >> >>>> to specify the sugar puckers in DNA (I want them C2'-endo). >>>> >>> Has anyone on this list done this already? >>> >>> Ralf >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > >

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Re: [phenixbb] phenix.autobuild
by Matthew Chu 24 Oct '08

24 Oct '08

Thank you for the detailed information Tom, my autobuild job is actually running properly! Just some more minors questions: 1. AutoBuild Wizard will use phenix.elbow to generate geometries for any ligands that are not recognized, but how can I find out which ligands that can actually be recognized by phenix? Or to be save, we better run elbow to generate the libraries for every single ligands? 2. eLBOW can automatically add hydrogens to the input molecules if there are less than a quarter of the possible hydrogens, however this command doesn't work: phenix.elbow input_file.pdb --add-hydrogens=True, and I can't find this option under the elbow manual? And actually I would like to remove those hydrogens so it should be "add-hydrogens=false"? I am now using phenix-1.3-rc2. Thanks again! Matt -- ---------------------------------------------------------------------------- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester ----------------------------------------------------------------------------

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NAG-ASN link geometry
by nihmayerm 23 Oct '08

23 Oct '08

We are refining a 2.7 A structure with multiple ASN-NAG links using phenix-1.3-final. The torsion angle between the Asn amide and the sugar is quite variable, while from the chemistry of this link we would expect a value close to 180°, as reported in the PDB survey by Imberty & Perez (Protein Engineering 8:669-709). A quick look at some entries in the PDB revealed close to textbook geometry for the NAG-ASN link in structures around 1Å resolution (e.g. 1UWC) and gets much worse in some lower resolution structures, including those refined with PHENIX. The NAG-ASN link used by PHENIX does not contain a torsion angle definition, and I would like to ask (i) if its appropriate to use one in refinement, and if so (2) could people share their cif file for this link. Thanks - MLM

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optimize weights error
by Sean Johnson 23 Oct '08

23 Oct '08

I just tried optimizing weights in phenix.refine using optimize_wxc=true and optimize_wxu=true in the command line. I got the following error: ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc5/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/driver.py", line 1150, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/strategies.py", line 446, in refinement_machine log = log) File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/weight_xray_chem.py", line 252, in __init__ self.wxc_optimization() File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/weight_xray_chem.py", line 507, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' Any suggestions? Thanks, Sean -- Sean Johnson, PhD R. Gaurth Hansen Assistant Professor Utah State University Department of Chemistry and Biochemistry 0300 Old Main Hill Logan, UT 84322-0300 (435) 797-2089 (435) 797-3390 (fax) sean.johnson(a)usu.edu

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phenix.autobuild
by Matthew Chu 22 Oct '08

22 Oct '08

Dear all, I tried to rebuild my structure from a refined model (by refmac) by phenix.autobuild. I am not sure if it runs properly since this is my first time to run this module....it took like almost a day to just finish the run_1 (there should be five runs by default?), which means it will take me another 4 days to finish the whole thing. My protein has around 350 residues and in the refined model, I have omitted some loops (about 80 residues) because I cannot see the electron density of those regions. I have put the seq.dat file with the full sequence (~350 residues) and the commands "place_water=Yes" and "s_annealing=True". The resolution is 2.4 A. Should it be taken so long to run? Thanks in advance! Kind regards, Matt -- ---------------------------------------------------------------------------- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester ----------------------------------------------------------------------------

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phenix.pdbtools question
by Simon Kolstoe 21 Oct '08

21 Oct '08

Dear phenix list, I am wanting to model a poly-proline structure. I created the file in PyMOL, saved it as a pdb, and then tried to regularize it with: phenix.pdbtools polypro.pdb --geometry_regularization However the program reported (snipped to the last few lines): ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C ATOM 69 2HD PRO 6 -2.824 2.626 -3.453 1.00 0.00 H Distance model: 1.09209 (ideal: 0.97) ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C ATOM 70 3HD PRO 6 -4.165 3.171 -2.396 1.00 0.00 H Distance model: 1.44721 (ideal: 1.473) ATOM 57 N PRO 6 -2.321 4.145 -2.118 1.00 0.00 N ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C Distance model: 1.53855 (ideal: 1.525) ATOM 58 CA PRO 6 -1.810 5.407 -2.632 1.00 0.00 C ATOM 59 C PRO 6 -2.332 6.603 -1.817 1.00 0.00 C Distance model: 1.23088 (ideal: 1.231) ATOM 59 C PRO 6 -2.332 6.603 -1.817 1.00 0.00 C ATOM 60 O PRO 6 -3.080 6.424 -0.856 1.00 0.00 O Sorry: Number of bonds with excessive lengths: 74 I thought the whole purpose of geometry regularization was to get rid of excessive lengths, not just tell me they are there!! How do I get the program to really regularize my geometry? Thanks, Simon

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phenix.reduce (v1.3) changes
by Mark Collins 21 Oct '08

21 Oct '08

Hi Did the --ALLALT command change. I thought the --help gave the flag description as "builds hydrogens for all conformations" but no it says "process adjustments for all conformations" And by default (-ONLYA) so I only have conf A with hydrogens using the --ALLALT flag. Long and short of it I think something is up? Thanks Mark

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postdoc position in LBNL
by Peter Zwart 21 Oct '08

21 Oct '08

Dear All, We would like to bring the following postdoctoral research position to your attention. Within Lawrence Berkeley Laboratory, we have an opening for a postdoc to work on the development of new software for the analysis of small angle X-ray scattering (SAXS) data. The availability of user friendly, robust software analysis tools for SAXS data is of growing importance as the biological community is increasingly using SAXS as a standard method to analyze complex biological systems. We are developing a new set of tools, including a software library, for SAXS data analysis. The successful candidate will have the opportunity to work with experienced software developers in the field of biophysics and interact with users and beamline staff on SAXS beamline 7.3.3 at the Advanced Light Source (ALS) in Berkeley California. Interested candidates can contact me (Peter Zwart, PHZwart(a)lbl.gov) for more details, or visit the LBL job site at: http://jobs.lbl.gov/ Sincerely, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Twin refinement with anomalous pairs
by Francis E Reyes 21 Oct '08

21 Oct '08

All How does phenix.refine handle the twin refinement target when refining against F+/F-? I'm specifically asking for the proper assignment of F +/F- for twin related reflections (e.g. 10.1107/S0907444902021704). My data is currently in P41 with friedel pairs as output by scala. Thanks FR --------------------------------------------- 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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Re: [phenixbb] sa_omit-map
by mathieu Coincon 19 Oct '08

19 Oct '08

Hi, omit-map works fine for me but I have two items on my wish list. 1) Can we compute a difference-map (mFo-DFc map instead of 2mFo-DFc map) ? 2) Is it possible to play with the size of the area omitted around the selection ? Thanks again. A true phenix-fan -------------- Mathieu Coincon PhD Student Universite de Montreal Biochemistry 514-343-6111 #5352

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phenix.refine: including modifications
by Patrick Loll 17 Oct '08

17 Oct '08

Hi all, I'm starting to use phenix.refine and have some questions about defining modifications during refinement: I want to refine a structure that includes several alpha-D-mannose residues. I see that mon_lib_list.cif contains, under the "LIST OF RECOGNIZED MODIFIED MONOMERS," the following line: MAN-a-D MAN-b-D SUG-a-D MAN alpha_D_mannose D-pyranose Question: Where/how do I invoke this modification? I.e., how do I tell the refinement program that a particular sugar is an alpha, and not a beta, mannose? Clearly I can't label the residue MAN-a-D in the PDB file, as this would step on the chain identifier. I'm guessing that I label each sugar MAN in the PDB file, and then insert some instructions about applying the modification in the CIF file that I supply to the refinement program. However, I'm not able to find an example of the appropriate syntax. Thanks, Pat Loll ------------------------------------------------------------------------ --------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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Hydrogen occupancy issue?
by Mischa Machius 17 Oct '08

17 Oct '08

Hi - I have a problem regarding occupancies of hydrogens in residues with alternate conformations. Specifically, when a residue exists in alternate conformations, the H hydrogen of the following residue (the one attached to the N) also exists in the same number of alternate locations. The occupancies of these hydrogens do not add up to 1.00 like the occupancies of the hydrogens for the preceding residue do. In fact, these occupancies are all 1.00. Is that a bug, a feature, or did I commit a user error somehow? Example: ... ATOM 956 H AHIS A 293 6.967 -36.722 8.227 1.00 15.31 H ATOM 957 H BHIS A 293 6.913 -36.667 8.216 1.00 15.31 H ATOM 958 H CHIS A 293 6.888 -36.648 8.202 1.00 15.31 H ... The preceding Ser A 292 exists in three alternate conformations with occupancies A=0.53, B=0.18, C=0.29; sum = 1.00 The corresponding hydrogens have occupancies A=0.52, B=0.19, C=0.29; sum = 1.00 (I can accept that they have somewhat different occupancies than the attached heavy atoms, based on a previous thread about this issue, although the discrepancies are now much smaller in the 1.3- final version compared to 1.3-rc2) The H hydrogens of the following residue (His A 293) have occupancies A=1.00, B=1.00, C=1.00; sum = 3.00, and the RCSB starts yelling. Should I just manually edit the values and set them to the occupancies of the hydrogens in the preceding residue? Any help appreciated. Thanks so much. Best - MM -------------------------------------------------------------------------------- Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353

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Weighted phase combination in phenix.refine?
by Francis E Reyes 17 Oct '08

17 Oct '08

Hi all I have experimental phases and a preliminary model. Will phenix.refine do phase combination while weighting the experimental phase and model phases (which also has NCS) ? By default? Thanks FR --------------------------------------------- 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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high temperature factor refinement
by allbette＠gmail.com 17 Oct '08

17 Oct '08

Hi All, I just refined a structure at 2.95A and getting a good R-work and R-free(0.236 and 0.274). When I checked the PDB, I found many residues have high temperature factor over 100. How can I use Phenix or CNS fix those high temperature factor for further refinment? Thank you Jason

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Re: [phenixbb] sa_omit-map -- it's fine
by Thomas C. Terwilliger 17 Oct '08

17 Oct '08

Hi again Pavel and Vladimir, The omit maps are fine. I'm sorry for the false alarm; I had run a tiny test structure with too few omit boxes so that the omitted regions were way too much of the structure and it looked really bad. Using more omit regions fixed the problem. A regular structure (nsf-d2 from the PHENIX structure library) gets a fine sa-omit map with the defaults. A further-improved map can be obtained with a higher-than-default value of "n_box_target=32" (default=12, note that you don't necessarily get exactly the number you ask for as it has to be something that the asymmetric unit can be divided into.) All the best, Tom T Hi Pavel and Vladimir, After all this discussion...I think there is something wrong with the composite omit maps in the current version. They do not finish correctly...I will check this out. If you instead just omit around the atoms in a pdb file with "omit_box_pdb=target.pdb" that seems fine however. I'm sorry for the problem. All the best, Tom T > Hi Tom, > > don't we need to add "maps_only=True" as well (as Manual suggests in section "Just make maps; don't do any building."; > http://www.phenix-online.org/documentation/autobuild.htm) ? > > I'm asking because the original question was specific about it: compute map and "nothing extra". > > Thanks, > Pavel. > > On 10/13/2008 2:17 PM, Thomas C. Terwilliger wrote: >> Hi Vladimir, >> You can do this with: >> >> phenix.autobuild data=data.mtz model=coords.pdb >> composite_omit_type=sa_omit nproc=4 >> >> All the best, >> Tom T >> >> >> >>> After phenix.refine stage I would like to get just the sa_omit map for the >>> whole assymetric unit (nothing extra). How can I do it? >>> Regards. >>> Vladimir >>> >>> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >>> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >

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