- phenixbb - phenix-online.org

Unrestrained refinement and reported RMSD values
by Yuri 10 Apr '12

10 Apr '12

Hi all, I wonder if there is a way of turning off (loosening) restraints for certain residues and a ligand specifically, and will the bond/angle rmsd be printed out somewhere? Thanks -- Yuri Pompeu

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Limit Ramachandran restrain to certain region
by Nian Huang 04 Apr '12

04 Apr '12

Dear all, Is it possible to limit Ramachandran restrain to specified residues in phenix.refine? I have a couple of loops with very poor density. The refinement process always made some residues fall out of ramachandran plot no matter how I tightened the weight and adjusted the residues back. Because the diffraction is about 2.3 A, I don't want the ramachandran restrain to impact the rest of structure. Thanks. Nian Huang

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modelling a flexible peptide
by intekhab alam 04 Apr '12

04 Apr '12

Hi All I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt 60 and 8 Kda respectively. Molecular repalcement (60Kda protein as template) with Phaser gave a solution with 6 molecules in ASU. A continuous density is also obersved near two different chains which i consider as the second protein. I refined the density using a poly Alanine model but still i can't recognise the side chains confidently for modelling. Considering the fact that the smaller protein partner is rich in lysine, arginine, Asp and Glutamate with only 3 tyr and 4 phe, i tried to modell fragments one by one but the B-factor of the segments are quite high (in the range of 110) what will be the best strategy to improve the map for modelling. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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fwd: Application deadline approaching: CCP4 summer school at APS, in USA
by Nathaniel Echols 04 Apr '12

04 Apr '12

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "'phenixbb(a)phenix-online.org'" <phenixbb(a)phenix-online.org> Cc: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> Date: Tue, 3 Apr 2012 17:19:36 -0500 Subject: Application deadline approaching: CCP4 summer school at APS, in USA Dear Colleagues, We would like to point out that the application deadline for the 5th annual CCP4 Summer School “From data collection to structure refinement and beyond” is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will cover all aspects of macromolecular structure determination and validation. Some of the world’s leading experts will be providing instruction and hand-on help. We are looking forward to another productive school this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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Trueblood Award Nominations
by Paul Adams 04 Apr '12

04 Apr '12

Dear Colleagues, on behalf of the selection committee I'd like to draw your attention to the the Trueblood award: http://www.amercrystalassn.org/content/pages/main-award-descriptions This will next be awarded in 2013, however nominations are sought now so that the winner can be announcement this Summer. The award will be presented at the 2013 ACA meeting. Please follow this link to obtain the nomination form: http://www.amercrystalassn.org/documents/ACAnomNEW.pdf Note that the deadline for nominations is May 1st, which should be sent to marcia(a)hwi.buffalo.edu. Here is a summary of the award: Kenneth N. Trueblood Award To recognize exceptional achievement in computational or chemical crystallography. The award is established in memory of Professor Kenneth N. Trueblood, UCLA 1949-1998, who was a major force in the early use of computers and the development of crystallographic computer programs. He applied these programs to the examination of chemical and molecular details of many structures at the frontiers of research. His contribution to the famous work on vitamin B12 is one example. Professor Trueblood was a leader in the development of techniques for analysis of anisotropic motion and was also a superb teacher and a lucid author. Established in 2001, the award will be given every three years and consist of an honorarium of $1,500 and up to $1,500 in travel expenses to accept the award. -- 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 ] --

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Exhaustive List of Phenix Commands
by Matthew J. Whitley 04 Apr '12

04 Apr '12

Hello all, I was wondering if somewhere, either on the web or in hardcopy, there is an exhaustive or nearly exhaustive list of Phenix commands. For example, from a Phenix BB thread earlier in the day I learned of the existence of the phenix.r_factor_statistics command for gaining insight into where your R/Rfree values place you in regard to structures of similar resolution. As I read more of the messages posted to the Phenix BB, I become aware of more and more nifty things that Phenix can do that I simply was not aware of, and I was wondering if some kind of master list of Phenix commands is available somewhere. Thanks to all the developers for making this amazing program available to the x-ray community. Thanks, Matthew --- Matthew J. Whitley, Ph.D. Postdoctoral Research Fellow Angela Gronenborn Lab Department of Structural Biology University of Pittsburgh School of Medicine

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amazing good statistics add
by Christian Roth 04 Apr '12

04 Apr '12

In general the Rvalues of course fit very well Rmerge. A good sign that it should be fine, as far as I remember correctly about the theoretical limits for the Rvalues after refinement compared to the experiment. Best Regards Christian

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Creating dictionary restraints for a LINK
by Mario Sanches 04 Apr '12

04 Apr '12

I have a question regarding link dictionary generation. Nigel helped me with a molecule dictionary last week (thank you Nigel) so the molecule is refining well now. This molecule is covalently bound to on of the residues. I tried generating a dictionary that describes both the molecule and the link but so far phenix.refine is ignoring it. Again, the molecule itself refines very well but the link is not there. What is the best way to define it? Thank you very much. -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches

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DEN refinement is crashing
by Mario Sanches 03 Apr '12

03 Apr '12

I am running phenix.refine using the graphical interface. Under "global refinement paramerters..." I am selecting "DEN". The problem is that Python crashes all the time, always at the same point (see portion of the log output below). Is it a known bug? Is DEN incompatible with some of the options in refinement? My resolution is 2.9A by the way. Thank you for your inputs. Mario Sanches ___________________________ Log output final portion: tardy dynamics: number of bodies: 3678 number of degrees of freedom: 3713 number of atoms * 3: 38220 ratio: 0.097 = 1/10.29 temperature degrees of freedom: cartesian (38220) kinetic energy sensitivity to generalized velocities: n: 3713 min: 3.61771e-06 max: 0.0300001 mean: 0.00410663 time step: 0.00100 pico seconds velocity scaling: True suppressing allowed origin shifts: False new target temperature: 2500.00 K step= 1 temperature= 2500.0 rmsd=0.0446 r_work=0.3010 r_free=0.3214 -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches

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labelit.index is too precise not to allow 0.000001 deg difference
by fukamitka＠chugai-pharm.co.jp 03 Apr '12

03 Apr '12

Dear Phenix developers, I had a problem in indexing by labelit.index in phenix-1.7.3-928, getting the error below: InputFileError: Input error: All images must have same oscillation range (delta phi). My dataset was collected by inhouse R-axis with 0.8 deg oscillation. Image header values of oscillation range fluctuate between 0.799999 - 0.800004 degrees. When I specified two images whose delta phi angles were different, say 0.799999 and 0.800003, labelit.index stopped with the error above. I don't think a goniometer have such a precision, therefore I think line 249 in /phenix-1.7.3-928/labelit/command_line/imagefiles.py should be modified not to use == instead of similar_delta_phi() or something. 246 if False in [similar_wavelength(self.images[0],self.images[x]) for x in xrange(1,Nimages)]: 247 raise InputFileError("""All images must have similar wavelength.""") 248 249 if False in [self.images[0].deltaphi==self.images[x].deltaphi for x in xrange(1,Nimages)]: 250 raise InputFileError("""All images must have same oscillation range (delta phi).""") Best regards, Takaaki Fukami ----- Dr. Takaaki Fukami (mailto:[email protected]) Discovery Research Dept. (Biostructure Gr.) Roche Group: Chugai Pharmaceutical Co.,Ltd.

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very informative - Trends in Data Fabrication
by Bosch, Juergen 31 Mar '12

31 Mar '12

really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen Acta Cryst. (2012). F68, 366-376 doi:10.1107/S1744309112008421<http://dx.doi.org/10.1107/S1744309112008421> Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen B. Rupp<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Rupp,%20B.> Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4>). A variety of analytical tools, including the application of Diederichs plots, R plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/

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Problems fitting NADH
by Phillip Steindel 31 Mar '12

31 Mar '12

Dear all, I'm trying to fit a NADH into a 1.7 Å structure. LigandFit worked with just the three-letter code (NAI), however phenix.refine won't work with just the model. If I use eLBOW to create restraints, meanwhile, the ligand gets distorted during refinement (non-tetrahedral phosphates, mainly). I'm not sure exactly how I'm supposed to be generating these restraints- any help is appreciated. Thank you, Phillip Steindel Theobald Lab Department of Biochemistry Brandeis University

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Re: [phenixbb] [ccp4bb] a small trick for protein and organic compound cocrystallization.
by Bryan Lepore 31 Mar '12

31 Mar '12

On Fri, Mar 30, 2012 at 3:26 PM, Jacob Keller <j-keller2(a)fsm.northwestern.edu> wrote: > What's the harm? have you seen usenet/Google groups? -Bryan

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a small trick for protein and organic compound cocrystallization.
by Kevin Jin 31 Mar '12

31 Mar '12

Dear All, Here is way I have used for protein and hydrophobic organic compound cocrystallization. Via this method, less amount of DMSO will be used to aviod protein ppt. I hope you can use for your research. http://www.jinkai.org/Xtal.html Regards, -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/

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Re: [phenixbb] need help for crystallization
by Kevin Jin 31 Mar '12

31 Mar '12

My pleasure ! Since this may be help for other people, I also cc it to CCP4BBS. According to your email, I guess the buffer is phosphate buffer at pH 7.4. You can do a quick buffer exchange before crystallization. Since PO4 is a competitor in this case, I will also avoid PO4 and Cocodylate buffer from screen kits. Here is what you can do, 1. concentrate your protein using an amicro centrocon with 3KD cutoff. 2. Measure how much buffer has been spin down, then add equal amount of Tris with same pH back to the top. 3. Then, spin down again. 4. Repeat several times, 5 times may be good enough. 5. Most of Phosphate buffer should be removed. That's what I used before. Let me know if it works. Best, Kevin Jin On Fri, Mar 30, 2012 at 9:40 AM, Afshan Begum <afshan490(a)yahoo.com> wrote: > > Dear Kevin > > I have seen your website and come to you to discuss my problem actually i > want to co-crystallized my enzyme with inhibitor but problem is that the > phosphate ion come to the active site and occupied the cavity and my > inhibitor not bind to the active center i purchase this enzyme from a > commercial source and they purify with phosphate buffer that's why also > phosphate is occupied the cavity how can i get ride of it from the active > center could you kindly help me regarding this i would be really thankful to > you. > > > Best Regards > > AFSHAN > =========================================== > Dr. Afshan Begum > University of Hamburg > Institute of Biochemistry and Molecularbiology > Laboratory for Structural Biology of Infection and Imflammation > c/o DESY, Build. 22a > Notkestr. 85 > 22603 Hamburg > Germany > Home phone: +49 40 22888618 > Fax: +49 40 8998-4747 > E-mail: afshan490(a)yahoo.com > -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/

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Re: [phenixbb] phaser_ep
by Airlie McCoy 30 Mar '12

30 Mar '12

Dear Kay, You can control the distance for the atom separation/anisotropy in Phaser with the llgcomplete.clash input parameter. By default llgcomplete.clash is zero, which means Phaser will calculate a value based on the resolution. If a value is set this will override the default. Apologies, this was not explained in the wiki, but is now! Airlie

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phaser_ep
by Kay Diederichs 30 Mar '12

30 Mar '12

Dear all, is there a way to modify the decision constants in phaser_ep? Specifically, I want to refine against heavy-atom derivative with one strong site. The resolution of the data is 3.6A; the substructure (4 sites) was solved at 8A. Upon refinement, phaser finds two more sites at distances of ~3.5A to the strongest site. Furthermore, it finds two holes at distances of ~3.5A to the strongest site. Now I would like phaser to treat the site as anisotropic. However, the distances are beyond its decision constant (~2.54A), so it chooses to add two sites to my HA model, but they refine poorly. How is the decision constant calculated? Can I influence the calculation? I found nothing in the phaser wiki. Alternatively: how can I tell phaser_ep that it should refine a given input atom anisotropically? I tried to add a ANISOU line to the PDB file but the program seems to ignore it. thanks, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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A small trick to make cover glass extremely hydrophilic for hanging drop
by Kevin Jin 30 Mar '12

30 Mar '12

Dear All, Making the surface of cover glass hydrophilic could let drop with organic solvent (MPD, etc) shrink into a ball shape, not spread out. Here is the method I used before. http://www.jinkai.org/Xtal.html Kevin -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/

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a strategy for endotoxin removal
by Kevin Jin 30 Mar '12

30 Mar '12

Dear All, I developed a method to remove endotoxin before and it worked pretty well. Here is the strategy for this protocol. http://www.jinkai.org/Endotoxin.html I hope it is useful. Best, Kevin -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/

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reference model restraints now support multiple reference model files
by Jeff Headd 29 Mar '12

29 Mar '12

Hi PHENIX users, After numerous user requests, we've added support to phenix.refine for multiple reference model input files. If you are refining a complex and have reference models for individual components, you may now input as many files as necessary. A parameter file would include: refinement { reference_model { file = "reference_A.pdb" file = "reference_B.pdb" } } Chain matching is still carried out automatically, so simply specifying the file paths is usually enough for the restraints to be generated for refinement. Details of chain matches are printed in the .log file, as well as in the reference_model scope in the .eff file. If anyone has questions, please let me know. Thanks! Jeff

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positive density around heavy metals
by Subhani Bandara 29 Mar '12

29 Mar '12

Hi everyone, I have refined a protein with a metal-chelate complex at 1.4 resolution and saw positive density around some metals that are on a two fold. I refined those chelator complexes with fixed occupancy to avoid the negative density seen around it as they are partially occupied. Also I had to avoid xyz refinement after fixing them on special position, to avoid moving away from two fold. I have attached a figure of one of those complexes. If I increase occupancy then it shows negative density. How can I get rid of this positive density. Thanks in advance for the help Subhani

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Re: [phenixbb] merging in hires data in AutoBuild
by Desiree Ho-Chi Fong, Ms 28 Mar '12

28 Mar '12

It works! Thank you. Desiree

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Generating a list of peak heights in a Bijvoet difference Fourier
by John Rose 28 Mar '12

28 Mar '12

Hi, Is there a way to get a print out of the peak positions and their heights from a Bijvoet difference Fourier map? I can generate the map and see the peals but I would like a listing also. Thanks, John Rose John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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merging in hires data in AutoBuild
by Desiree Ho-Chi Fong, Ms 27 Mar '12

27 Mar '12

Hello all, I am using PHENIX 1.7.3-928 and I am trying to merge a high resolution native data set with a MAD data set in AutoBuild. I have run AutoBuild through the GUI as well as on the command line. Here is the command I used: phenix.autobuild data=AutoSol_run_1_/exptl_fobs_phases_freeR_flags_1.mtz hires_file=hires.mtz model=AutoSol_run_1_/overall_best.pdb rebuld_in_place=True The data file, exptl_fobs_phases_freeR_flags.mtz from AutoBuild only includes data to the resolution of the MAD data set. The higher resolution native data was not incorporated into this mtz file. Looking at the log file, the hires data was merged with expel_fobs_phases_freeR_flags_1.mtz from AutoSol (with AutoBuild after) and followed by anisotropy correction. This was then used for density modification. However, the high resolution data was never included in the mtz file for refinement in AutoBuild. My understanding is that if hires data is specified in AutoBuild, the phases would be extended and included in map calculation as well as subsequent refinement. The output exptl_fobs_phases_freeR_flags.mtz from AutoBuild would also include the hires data for subsequent refinement. Is this correct? Thank you for your help. Desiree

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R value difference in model vs data vs refinement
by Christian Roth 24 Mar '12

24 Mar '12

Dear all, I refined a structure in phenix quite good resolution (1.4 Ang.) After the last refinement I created the "table 1" to extract all data. Interestingly I got a warning due to small changes in the R values R/Rfree after Refinement. 15,46/18,16 Phenix modelvs.data gives me R/Rfree 15,34/18,07 Interestingly this is nearly exactly the value which I got after the first OHS scattering optimization from phenix R/Rfree 15,43/18,03 The differences are of course very small and negeligible, but I wonder why it happens. Esspecially taking into account that it was refined with phenix and in this case I would expect that both values match exactly. Thank you very much in advance Best Regards Christian

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sequence file for DNA-Protein complex
by Sita Ram Meena 24 Mar '12

24 Mar '12

Hello Everyone. As per my knowledge we gives the Protein sequence .SEQ OR .DAT file format having only protein sequence in Caps and no gaps now, Please suggest me how we can give a sequence file for double stranded DNA-Protein Complex for the use in Phenix autobuild. Thank you. Best Regards Sita Ram

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error generating output file overal_best pdb
by Andres PALENCIA 24 Mar '12

24 Mar '12

Dear Phenix users, I have been running Phenix_Autobuild successfully for the last houra. The program generates the corresponding Autobuild_run_** folders as usually, however I got an error message when the program was trying to generate the overal_best.pdb file after the Autobuild cycle 3. I copy below the error message that I got, thank you in advance for any help: OSError : [Errno 2] No such file or directory: '/user/palencia' Traceback (most recent call last): File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Home/Jobs.py", line 170, in OnTimer self.project.refresh_detached_jobs() File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Tracking.py", line 72, in refresh_detached_jobs tmp_dir = self.get_tmp_dir() File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/phenix/tracking/project.py", line 97, in get_tmp_dir os.makedirs(tmp_dir) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 2] No such file or directory: '/user/palencia' Platform info: __FILE__ = /net/anaconda/scratch1/phenix/phenix-1.7.3-928/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Dec 6 2011 __TIME__ = 04:18:10 __x86_64__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_48 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.5 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.18-238.9.1.el5-x86_64-with-redhat-5.7-Final platform.architecture(): ('64bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 24 Memory total: 25,263,722,496 Memory free: 20,157,317,120 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Ã

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Rosetta and disulphides
by Morten Groftehauge 24 Mar '12

24 Mar '12

Hi phenix-bb'ers, Is there anyway to make phenix.mr_rosetta take disulphide bridges into account? It's a rather enormous restraint on conformational space after all (wait is that a constraint or restraint? I get confused). Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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about readyset
by Ming 24 Mar '12

24 Mar '12

Dear all, I was using ready set to get my pdb ready. It automatically built the ligand cif file from scratch too. And the phenix.refine was fine with the files from ready set. Then I tried another method in which I threw everything that phenix.refine needs, including pdb file, ligand cif file, ligand pdb file, mtz. And phenix.refine ran smoothly again. But the refinement results were different between these two ways. The R fac is 1% different. I think ready set is only making the phenix.refine easier by generating ligand and building H, but if I do all the work of ready set and prepare the files for phenix.refine. Aren't they supposed to give the same results back? Can anyone help me here? Thanks a lot. -- Ming

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Partially reduced disulfides
by Christopher Wanty 23 Mar '12

23 Mar '12

Hi, I have a structure that appears to have a combination of reduced and oxidised disulfides. >From previous reading on the board I've taken the strategy of dropping the disulfide detection cutoff to 0.1 then added back the disulfides as appropriate using restraints. The problem I now have is that for some of these cysteine pairs there are clearly oxidised and reduced positions in the density. Modelling altloc's for each of these works, but the occupancies do not refine as I expected; the altloc's involved in the disulfide I expected to have the same occupancy as their counterpart in the disulfide. To try to get these to match, I introduced occupancy constraint that look like: constrained_group { selection = (chain A and resseq 276 and altloc B) or (chain A and resseq 286 and altloc B) } But with that the sum of occupancies for altloc 276 (for example) is not adding to 1.00. My thought is that I need to change the occupancy constraints but I'm not sure how to make them do what I want. Any help/advice is appreciated. Regards, Chris ------------------------------------------------------- Dr. Christopher Wanty christopher.wanty(a)uwa.edu.au Research Associate Biomolecular, Biomedical and Chemical Sciences, Building M310 University of Western Australia 35 Stirling Highway Crawley 6009 Western Australia Australia

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Documentation in last Dev versions
by Alexander Batyuk 22 Mar '12

22 Mar '12

Dear developers, Is there any particular reason for missing documentation file in phenix-dev-1008 and up (it could not be found on the website as well)? dev-1005 is fine. Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Hydrogens
by Christopher Wanty 21 Mar '12

21 Mar '12

Hi all, I've been refining with riding hydrogens, and from what I've read hydrogen contribution should be included in Fo calculation automatically for maps. What I'm seeing after refinement is a lot of little bits of green in the difference density that look like they could be explained by hydrogens. I'm working at 1.4A, attached image gives an example and shows contours at 3 sigma for difference map. Is there a setting/parameter I need to adjust to get this to work properly? Kind Regards, Chris ------------------------------------------------------- Dr. Christopher Wanty christopher.wanty(a)uwa.edu.au Research Associate Biomolecular, Biomedical and Chemical Sciences, Building M310 University of Western Australia 35 Stirling Highway Crawley 6009 Western Australia Australia

3 2

building a peptide-like polymer with phenix.elbow
by Geoffrey Feld 21 Mar '12

21 Mar '12

Greetings, I have a co-crystal structure of a protein bound to an interesting polymer -- poly-D-g-glutamic acid (poly glutamic acid with D chirality and gamma linked, rather than alpha linked). In the structure, I have density corresponding to different links, from 1 to 6 (so far). I'd like to build a ligand that has "residues" much like a polypeptide polymer so that I can refine each residue individually (hopefully in COOT). Up till now, I've been using SMILES to generate the different length polymers so I have pdbs and cif files, and then (painstakingly) modelling them into COOT, building restraints for refinement, etc. More recently, I used maestro to build a dimer that at least has the right atom labels you'd expect for a protein. However, I can't use phenix now to generate cif files because it is confused by the GLU. Is there a way to use phenix.elbow to make a multi-residue polymer? I'm also doing some monte carlo minimizations in macromodel to generate models of the various low energy states and would like to use them as building blocks, so an easy order-of-operations would be to generate the files in macromodel and feed them in via pdbs to phenix.elbow to generate cif restraints. Any help on this would be greatly appreciated. Cheers, Geoff -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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a small trick for SDS-Gel storage
by Kevin Jin 21 Mar '12

21 Mar '12

Dear All, Maybe most of you already knew. I just put my understanding of SDS page gel storage here, if you want to make gel yourself and safe some money. http://www.jinkai.org/SDS_page.html If I am wrong, please let me know. Sharing knowledge each other is always joyful. -- Kevin Jin Protein crystallographer and Biopolymer chemist Personal Website: http://www.jinkai.org/

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A possible conjugative relaxase with novel fold for DNA cleavage?
by Kevin Jin 21 Mar '12

21 Mar '12

Dear All, The protein structure of Jann_2411 (PDB 3H0N) from Jannaschia sp. strain CCS1 carries a novel fold for unknown function. Zn-finger is indentified in the C-terminus. However, the N-terminus with a metal binding site presents a novel fold. As the person who solved and characterized this protein, I would like to put some further observation here for your consideration. My analysis is available here: http://www.jinkai.org/Novel_fold_3H0N.html Best regards, Kevin -- Kevin Jin Protein crystallographer and Biopolymer chemist Personal Website: http://www.jinkai.org/

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NCS operators
by Melania Strycharska 20 Mar '12

20 Mar '12

Dear all, I have a bit of a problem applying NCS to my fairly low resolution structure. If I try to look for NCS symmetry automatically - phenix doesn't find any. If I specify sections that I want to be related by NCS, the script usually crashes. I have a dimer in the asymmetric unit, however it appears that one domain is related by 3-fold symmetry while the other is related by 6 fold symmetry. I can "cheat" phenix and generate operators for each of the domains by feeding a stripped pdb file (one that contains only a dimer of one domain or the other) to phenix.simple_ncs_from_pdb and then it easily identifies the ncs operators... unfortunately the simple_ncs_from_pdb.ncs file generated that is meant to be fed into phenix.refine contains only the chain selections, not the actual operators. Is there a way to specify different NCS operators (rotational matrix and translational vector) for specific chain selections in the .eff file or under GUI? or if there isn't, how can I still take advantage of my NCS symmetry? Also, is there any obvious reason why NCS operators that I generated with Phenix do not match the operators that I found using CCP4 Lsqkab? (yes I already accounted for chain A moving onto B or chain B moving onto A) Can I choose to apply NCS symmetry to just my backbone? How would I specify that? thanks so much! Melania

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GUI parameter files
by Leonid Sazanov 20 Mar '12

20 Mar '12

Hi, I have a following problem in dev-874 version: If I restore a previous job in refine GUI, to run it with modified settings, and include a new parameter file .eff with definitinon of secondary structure restrains, these new restrains are combined with previously used restrains. How do i get rid of previous restrains? Older file is not visible in inputs, but its settings are still used. And in general, how can one be sure which parameters are used at the start of each refine run? If older settings loaded from .eff or .param file are not visible, the only way is to look through new .eff file, which takes a lot of time. Has this been solved in latest builds perhaps? Thank you, Leo -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Refinement using data with pseudo translational symmetry
by Bret Wallace 19 Mar '12

19 Mar '12

To all, First I apologize for the long email, but I wont to make sure that I give enough information to describe the problem. I have been working on a structure of two proteins in complex with each other (one forms a homodimer, with each monomer bound to 1 monomer of the other protein), using data, that according to phenix.xtriage contains pseudo translational symmetry (output pasted below). I have done a lot of searching of both the phenixBB and ccp4BB regarding solutions to this problem, but unfortunately most responses seem to be directed at resolving issues with MR. I have successfully performed MR using both phenix phaser, ccp4 phaser (the most updated version), as well as molrep. The issue arises upon structure refinement, where my Rwork and Rfree are essentially stuck at 28 and 33, respectively. I have built the entire structure, including ligands, except for any solvent molecules. Here are the details for the data/structure: SG: P212121 Cell: 72 124 175 90 90 90 Res: 50-2.8 Patterson analyses ------------------ Largest Patterson peak with length larger than 15 Angstrom Frac. coord. : 0.155 0.000 0.500 Distance to origin : 87.222 Height (origin=100) : 34.517 p_value(height) : 6.739e-04 The reported p_value has the following meaning: The probability that a peak of the specified height or larger is found in a Patterson function of a macro molecule that does not have any translational pseudo symmetry is equal to 6.739e-04. p_values smaller than 0.05 might indicate weak translational pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are a very strong indication for the presence of translational pseudo symmetry. Xtriage notes that the if the PTS is crystallographic, that C2221 is a possible SG (x+1/6, y, z+1/2). However, neither XDS or HKL picks orthorhombic C, and the indexing/integrating doesn't work if I force it. I should also not there is no twinning detected by either xtriage or twinning servers. I have done a number of things to try to resolve this: -rescaling in lower symmetry (P21 and P1) -rescaling in the PG P222 and letting the MR program decide the proper space group -shifting origin and re-refining -a number of different refinement protocols (TLS, optimized weights/adp, simulated annealing, several cycles of rigid body, etc.) I have used HKL2000 and XDS to index/integrate/scale the data, both yield the same results, with slightly different completeness and Rmerge values, but refining with either gives similar R factor values. Does any know of any other possible things I should try to refine this data? I am happy to provide additional information upon request. Thanks in advance for any help! Bret

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selectively remove bond length restraints on atoms
by Maxime Cuypers 16 Mar '12

16 Mar '12

hello, What is the best way to selectively remove bond length restraints on some selected atoms for phenix.refine? i found the commands for a .param file: refinement { geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } } but no bond length command in the manual online. http://www.phenix-online.org/version_docs/dev-283/refinement.htm otherwise there is the commands refinement { geometry_restraints.edit { bond { action= *delete change atom_selection_1= (selection1 here) atom_selection_2= (selection2 here) distance_ideal= None } } } is it a good way to deal with the problem ? thanks in advance for your help. Maxime

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crystal packing pattern
by bsubedi＠btk.fi 15 Mar '12

15 Mar '12

Hi All, Could someone help me with a program/tool to see the pattern of protein packing in the crystal. I would like to make comparative study between regions of the protein in two different chains and if crystal packing has some effect on conformational alteration. Kind regards, World

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Reminder: BCA/CCP4 Summer School 2012
by Airlie McCoy 15 Mar '12

15 Mar '12

This is a reminder that applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 28th August to Sunday 2nd September 2012. Applications close 1st May 2012. The course is suitable for PhD students in macromolecular crystallography who started in or before October 2011, and postdocs new to macromolecular crystallography. Please note that references from supervisors are also due by 1st May 2012, so don't leave your application until the last minute! For more information see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012.html Application form: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012/Application-Pag…

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Transfer to new computer
by Colin Levy 15 Mar '12

15 Mar '12

Hi, Is it possible to transfer Phenix along with it's archive to a new computer? I have a fresh install of Phenix on the new machine and a copy of all the original files and folders from the old machine but cant figure how to point Phenix to the correct place. Thanks Colin

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March 15, 2012 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 15 Mar '12

15 Mar '12

Dear Users, The deadline for May/June 2012 Collaborative Crystallography proposals will be *Mar 15, 2012. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC 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; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 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 learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for May/June 2012 allocation period, proposals must be submitted by *March 15, 2012.* The deadline for CC proposals for the time period July/August 2012 will be May 15, 2012. Regards, Banumathi Sankaran

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David Sayre
by Paul Adams 13 Mar '12

13 Mar '12

On behalf of the Phenix development team: We regret deeply the passing of David Sayre on Feb. 23, 2012. David Sayre made profound contributions to crystallography and scientific computing that continue to have a major impact decades later. An obituary summarizing his many achievements was posted by Physics Today (http://www.physicstoday.org/1.2732466). In crystallography, Sayre’s fundamental insight into the implications of the atomic nature of crystal structures and the relationships between crystallographic structure factors allowed him to develop in 1952 the brilliantly simple Sayre equation relating each structure factor to all other structure factors. The Sayre equation has had a well-known yet greatly under-appreciated significance in small-molecule crystallography, both in its original form and in the equivalent probabilistic forms implemented later as part of direct methods. These methods have profoundly affected macromolecular crystallography in the last decade because of their astounding power for determination of heavy-atom substructures. The use of direct methods has made possible solution of the positions of as many as 160 selenium atoms in large macromolecular structures. To appreciate the feat that this represents, it is useful to consider that many macromolecular crystallographers were initially hesitant to use the seleno-methionine approach at all for structures that had more than about 10 selenium atoms for fear that the substructure could not be solved. Sayre’s recent work on phasing X-ray diffraction data from single large objects such as a yeast cell and single small objects such as a single protein molecule was groundbreaking in a different way. This work is revolutionary because of its boldness, and because of the elegantly simple approach to phase determination that Sayre developed. Once again Sayre took a fundamental real-space feature of the diffraction image and used it to obtain phase relationships. In this case the diffraction forms a continuous pattern from a single object, and the feature is the lack of contrast outside of the object. While the idea of using a mask of the object (the “support”) to define phases has been used for some time in many contexts, it was far from obvious that this could be done with a single cell or with a single protein molecule. Sayre and his colleagues systematically showed theoretically and then experimentally that each step in this process can be carried out and that the required signal can be extracted to obtain an X-ray image of microdots and later even a yeast cell. Others have followed up his ideas for phasing data from a single protein molecule. This work was of fundamental and transforming importance because few would have believed that the ideas were remotely feasible, and now they have a sound theoretical basis and experimental demonstrations, allowing anyone to think of new and powerful ways to use these approaches. The breadth of Sayre's intellectual spectrum reached far beyond crystallography. He was also a member of the IBM team that developed the original Fortran compiler, the first high-level programming tool (see http://www.ibm.com/ibm100/us/en/icons/fortran/team/ for more details). Currently, 55 years after the first commercial release of Fortran, this language is still in wide use. The history of crystallographic computing, and scientific computing in general, cannot be separated from the success of Fortran, made possible by the amazing IBM team that included Sayre. In spite of his great accomplishments, David Sayre was modest and approachable in person, and he was generous in sharing credit with his colleagues. He will be greatly missed. -- 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 ] --

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phenix.elbow problem
by Simon Kolstoe 13 Mar '12

13 Mar '12

Hi there, Who's the best person to talk to when phenix.elbow is not assigning correct geometry to a molecule? Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Wolfson Drug Discovery Unit University College London Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------

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error after adp refinement
by Christian Roth 10 Mar '12

10 Mar '12

Dear Phenix Team, I started a refinement with anisotropic adp and weight optimization and directly after the optimization step an error appeared which never appeared befor for me. The previous steps of mask optimization and xyz refinement worked well. Best Regards Christian AssertionError : Traceback: File "/userdata-2/christian/phenix- dev-979/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/userdata-2/christian/phenix- dev-979/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/runtime.py", line 68, in __call__ call_back_handler=callback) File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/command_line.py", line 97, in run call_back_handler=call_back_handler) File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/driver.py", line 1494, in run ncs_manager = self.ncs_manager) File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/strategies.py", line 1046, in refinement_machine h_params = h_params) File "/userdata-2/christian/phenix- dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 212, in __init__ nproc = nproc) File "/userdata-2/christian/phenix- dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 389, in __init__ compute_gradients=False).target_work()) Platform info: __FILE__ = /net/longnose/scratch2/phenix/phenix- dev-979/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Feb 7 2012 __TIME__ = 02:05:24 __i386__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 BOOST_LIB_VERSION = 1_48 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 12 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.10.1 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.31-23-generic-pae-i686-with-debian-squeeze-sid platform.architecture(): ('32bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 8 Memory total: 25,405,636,608 Memory free: 20,305,633,280 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å

5 11

Calculating Bijvoet difference Fourier map
by John Rose 08 Mar '12

08 Mar '12

Hi, I am some what new to PHENIX and using the Mac GUI. I want to compute a Bijvoet difference Fourier map. Any help would be appreciated. John Rose

2 1

autobuild omit map as Fo-Fc
by Ursula Schulze-Gahmen 08 Mar '12

08 Mar '12

I calculated an omit-map for my model using the following command inpt: phenix.autobuild data=HKL2000+R.mtz model=ptefb_A4_refine_43.pdb omit_region_specification=omit_around_pdb omit_box_pdb_list=G_chain.pdb composite_omit_type=refine_omit maps_only=true I would like to display a 2Fo-Fc and Fo-Fc map but I cannot find the overall_best_refine_map_coeffs.mtz output file that should have these coefficients according to the manual. I only see the overall_best_denmod_map_coeffs.mtz file. Can somebody tell how to best get to an omit Fo-Fc or 2Fo-Fc map? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

2 1

bins in phenix.refine
by Jianghai Zhu 07 Mar '12

07 Mar '12

Hi, A colleague asked me a question if phenix.refine can use user-input resolution bins for R and Rfree calculation. I am not sure if such parameters exist. -- Jianghai

3 3

where is the fo-fc omit map?
by Yu, Hongjun 07 Mar '12

07 Mar '12

hello, It is so good that phenix can caculate sa-omit map so easily. But I am new to this. When I finish caculating, I can only get acess to 2fo-fc map whe I use coot to open the file: resolve_composite_map.mtz . How can I open the fo-fc omit map? I notice this from phenix.autobuild manual page "Note 1: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz". I don't understand this because the omit_regin.mtz seem to be the omit box I specify. Is this correlated with my problem? Any advice is appreciated. Thank you in advance! Sincerely, Hongjun

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