March 2012 - phenixbb - phenix-online.org

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 29 Mar '12

29 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 29 Mar '12

29 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 28 Mar '12

28 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 28 Mar '12

28 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 27 Mar '12

27 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 27 Mar '12

27 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 26 Mar '12

26 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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