- phenixbb - phenix-online.org

Autobuild error
by Nora Cronin 21 Oct '13

21 Oct '13

Whilst running Autobuild SA omit map using 40 segments one OMIT region fail and the program quits. Error as follow: Can you help? Summary of output files for Solution 1 from rebuild cycle 2 --- Model (PDB file) --- pdb_file: /local/ncronin/phenix/APC4/Autobuild_20131018/AutoBuild_run_2_/TEMP0/AutoBuild_run_5_/overall_best.pdb --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- refine_data: /local/ncronin/phenix/APC4/Autobuild_20131018/AutoBuild_run_2_/TEMP0/AutoBuild_run_5_/overall_best_refine_data.mtz AutoBuild_build_cycle AutoBuild Run 5 Fri Oct 18 13:30:32 2013 Ending these rebuild cycles as the limit is reached All done with build cycles in this region AutoBuild_set_up_build AutoBuild Run 5 Fri Oct 18 13:30:32 2013 Traceback (most recent call last): File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 2146, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1832, in AutoBuild_set_up_build self.AutoBuild_finish_current_region() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1909, in AutoBuild_finish_current_region self.AutoBuild_update_ncs() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 5567, in AutoBuild_update_ncs ],quiet=True,out=f) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 324, in __init__ self.read_ncs_as_file(params,out=out) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 511, in read_ncs_as_file quiet=self.quiet,log=null_out()) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 546, in __init__ starting_residue_numbers) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 1326, in find_invariant_groups minimum_size=min_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 35, in __init__ minimum_size=minimum_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 70, in process size, index = self.find_largest( matches, used ) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 168, in find_largest max_size = flex.max( sizes ) RuntimeError: unidentifiable C++ exception Traceback (most recent call last): File "/common/app/phenix/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/autobuild.py", line 230, in <module> run_autobuild=run_autobuild(args=sys.argv[1:]) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 564, in __init__ self.RunWizard() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 1000, in RunWizard self.runWizard.run() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 838, in Run self.DoNextMethod() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 1003, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 2146, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1832, in AutoBuild_set_up_build self.AutoBuild_finish_current_region() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1909, in AutoBuild_finish_current_region self.AutoBuild_update_ncs() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 5567, in AutoBuild_update_ncs ],quiet=True,out=f) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 324, in __init__ self.read_ncs_as_file(params,out=out) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 511, in read_ncs_as_file quiet=self.quiet,log=null_out()) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 546, in __init__ starting_residue_numbers) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 1326, in find_invariant_groups minimum_size=min_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 35, in __init__ minimum_size=minimum_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 70, in process size, index = self.find_largest( matches, used ) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 168, in find_largest max_size = flex.max( sizes ) RuntimeError: unidentifiable C++ exception Best regards Nora Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5456 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

3 2

anisotropic refinement based on B values
by Yarrow Madrona 20 Oct '13

20 Oct '13

I'm sure that this has probably already been covered but I am having some problem finding out how to tell phenix to make a decision whether to refine isotropically or anisotropically based on B factor values. Is this something you can do with a python script? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] increasing NCS restraints
by Mark van Raaij 17 Oct '13

17 Oct '13

Oops, 1 vote for making phenixbb default reply to sender only.... Mark van Raaij <mjvanraaij(a)cnb.csic.es> wrote: >Dont worry about it, we are alli diots...even without commuting 4 hrs a day > >Yarrow Madrona <amadrona(a)uci.edu> wrote: > >>Hi Dale, >> >>That is right! And that is what I concluded yesterday yet I somehow forgot >>all that overnight. Starting a new job and commuting 4 hours a day has >>taken a toll on my brain. I am an idiot. >> >>-Yarrow >> >>> >>> I'm puzzled. Didn't you say that the translation of your ncs >>> two-fold was not equal to half the "a" cell edge? If it is not >>> a translation of 1/2 (in fractional coordinates) then it cannot >>> be a crystallographic symmetry element and your space group cannot >>> be P212121. Unless this condition is met, the similarity of your >>> molecules is unimportant. >>> >>> Dale Tronrud >>> >>> On 10/17/2013 12:48 PM, Yarrow Madrona wrote: >>>> I am doing restrained NCS refinement and would like to know how to set >>>> the >>>> target weight of the cartesian restraint in the command line? I also >>>> found >>>> a sigma value in the GUI. I read that I can decrease it in order to >>>> increase the NCS restraints. However, I have seen this under Torsional >>>> restraints. Does this also apply to cartesian restraints? >>>> >>>> I am doing this so that I can look at the differences in position and >>>> B-factors of two molecules in the ASU that I am trying to determine are >>>> related by a perfect or imperfect 2(1) screw axis. (I posted a question >>>> about this on the CCP4 bullitan board.) If the values between molecules >>>> are exactly the same then presumably the space group is actually P212121 >>>> with 1molecule in the asu instead of P21 with two molecules. I already >>>> know that the P21 dimer superimposes almost exactly on the P212121 >>>> monomer >>>> and it's symmetry mate. I just don't know how "perfectly" they align and >>>> I >>>> am hoping this approach will tell me. I hope this makes some sense. >>>> >>>> -Yarrow >>>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>> >> >> >>-- >>Yarrow Madrona >> >>Graduate Student >>Molecular Biology and Biochemistry Dept. >>University of California, Irvine >>Natural Sciences I, Rm 2403 >>Irvine, CA 92697 >> >> >> >>_______________________________________________ >>phenixbb mailing list >>phenixbb(a)phenix-online.org >>http://phenix-online.org/mailman/listinfo/phenixbb >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb

1 0

Re: [phenixbb] increasing NCS restraints
by Mark van Raaij 17 Oct '13

17 Oct '13

Dont worry about it, we are alli diots...even without commuting 4 hrs a day Yarrow Madrona <amadrona(a)uci.edu> wrote: >Hi Dale, > >That is right! And that is what I concluded yesterday yet I somehow forgot >all that overnight. Starting a new job and commuting 4 hours a day has >taken a toll on my brain. I am an idiot. > >-Yarrow > >> >> I'm puzzled. Didn't you say that the translation of your ncs >> two-fold was not equal to half the "a" cell edge? If it is not >> a translation of 1/2 (in fractional coordinates) then it cannot >> be a crystallographic symmetry element and your space group cannot >> be P212121. Unless this condition is met, the similarity of your >> molecules is unimportant. >> >> Dale Tronrud >> >> On 10/17/2013 12:48 PM, Yarrow Madrona wrote: >>> I am doing restrained NCS refinement and would like to know how to set >>> the >>> target weight of the cartesian restraint in the command line? I also >>> found >>> a sigma value in the GUI. I read that I can decrease it in order to >>> increase the NCS restraints. However, I have seen this under Torsional >>> restraints. Does this also apply to cartesian restraints? >>> >>> I am doing this so that I can look at the differences in position and >>> B-factors of two molecules in the ASU that I am trying to determine are >>> related by a perfect or imperfect 2(1) screw axis. (I posted a question >>> about this on the CCP4 bullitan board.) If the values between molecules >>> are exactly the same then presumably the space group is actually P212121 >>> with 1molecule in the asu instead of P21 with two molecules. I already >>> know that the P21 dimer superimposes almost exactly on the P212121 >>> monomer >>> and it's symmetry mate. I just don't know how "perfectly" they align and >>> I >>> am hoping this approach will tell me. I hope this makes some sense. >>> >>> -Yarrow >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> > > >-- >Yarrow Madrona > >Graduate Student >Molecular Biology and Biochemistry Dept. >University of California, Irvine >Natural Sciences I, Rm 2403 >Irvine, CA 92697 > > > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb

1 0

increasing NCS restraints
by Yarrow Madrona 17 Oct '13

17 Oct '13

I am doing restrained NCS refinement and would like to know how to set the target weight of the cartesian restraint in the command line? I also found a sigma value in the GUI. I read that I can decrease it in order to increase the NCS restraints. However, I have seen this under Torsional restraints. Does this also apply to cartesian restraints? I am doing this so that I can look at the differences in position and B-factors of two molecules in the ASU that I am trying to determine are related by a perfect or imperfect 2(1) screw axis. (I posted a question about this on the CCP4 bullitan board.) If the values between molecules are exactly the same then presumably the space group is actually P212121 with 1molecule in the asu instead of P21 with two molecules. I already know that the P21 dimer superimposes almost exactly on the P212121 monomer and it's symmetry mate. I just don't know how "perfectly" they align and I am hoping this approach will tell me. I hope this makes some sense. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] Need help with atom selection for anisotropic refinement
by Nathaniel Echols 16 Oct '13

16 Oct '13

I think the problem is with the boolean logic ("and"/"or"). First, the isotropic: optional (element H or element D or resname HOH or chain E or chain F or > chain A or chain B) > This will be processed okay but it's going to select all atoms in chains A/B/E/F in addition to all H/D and waters, which probably isn't what you really want since the anisotropic selection includes chains A and B. I'm not sure what will actually happen here, but it's better not to rely on the atom selections being processed in a particular order (and better not to rely on the code automatically handling the problem of overlapping selections). chain A and chain B and not (element H or element D or resname HOH or chain > E or chain F or chain A resseq 5:11 or chain A resseq 66:72 or chain A > resseq 117:138 or chain A resseq 152:184 or chain A resseq 196:210 or chain > A resseq 249:251 or chain B resseq 3:6 or chain B resseq 66:72 or chain B > resseq 166:210 or chain B resseq 249:251) > The problem here is that you have specified that the atoms match "chain A and chain B", which is impossible. You probably want this: (chain A or chain B) and not (....) -Nat

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phenix.rosetta_refine
by Guenter Fritz 14 Oct '13

14 Oct '13

Dear Phenix developers, I am working on a 3.6 A structure and want to try the latest joint development of phenix and rosetta. Is there are kind of "how_to" available online? Some do's and don'ts? Best, Guenter

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Phenix on Ubuntu12.3
by Swastik Phulera 12 Oct '13

12 Oct '13

Dear All, I am setting up a computer with ubuntu(12.3) installed on it. running "uname -rm" gives me 3.8.0-31-generic x86_64. I am trying to install phenix on this machine, as recommended I downloaded the 64 bit kernel 2.3 (64bit fedora 3 ) command line installer. I then ran ./install and source the required file by: source /usr/local/phenix-1.8.4-1496/phenix_env.sh but some how phenix refuses to start, following is the error phenix Traceback (most recent call last): File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/../../phenix/wxGUI2/command_line/main.py", line 22, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/../../phenix/wxGUI2/command_line/main.py", line 16, in run from wxGUI2 import App File "/usr/local/phenix-1.8.4-1496/phenix/wxGUI2/App.py", line 15, in <module> import wx File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory Any suggestions would be welcome. regards Swastik

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Re: [phenixbb] Problem in reducing R-factor
by Nathaniel Echols 12 Oct '13

12 Oct '13

On Fri, Oct 11, 2013 at 6:19 PM, Ryan Spencer <rspencer(a)uci.edu> wrote: > For high resolution structures, below 1.5 Å, is there a set of > rules > for best practices for refinement? > Not really rules that I'm aware of... just general guidelines, and not well-codified. I've wanted for a long time for us to write some sort of extensive how-to across all resolution ranges, but like everything else, this has to compete with writing code and "real" papers. As Pavel mentioned, these resolution limits are somewhat subjective depending on completeness, how aggressively you process the data, etc. But, a few basic suggestions: - you will probably not want to use real-space refinement after the first couple of rounds - start parameterizing conservatively, then get more aggressive as you near the end of refinement (if nothing else, it's faster this way) - don't use any restraints other than the default geometry restraints plus whatever custom bonds are required by the chemistry (e.g. prosthetic groups) - use hydrogens by the end of refinement, but riding only until you're at subatomic resolution - the automatic weighting is probably going to work great; weight optimization might help for the final round, but probably not necessary - below 1.5Å, try making non-water/non-hydrogen anisotropic (and compare to purely isotropic); below 1.2Å, you can start thinking about making all non-H/D anisotropic. (Also note that heavier atoms can become anisotropic even earlier, so in your case, refining individual anisotropic B-factors for iodine and TLS for everything else would be a reasonable alternative.) - you should probably be able to get rid of all geometry outliers, including clashes - but you may see real (correct) Ramachandran or rotamer outliers at this point - you're inevitably going to see more blobs in the difference map that you can't explain than usual. don't sweat it. - you should definitely see a fair number of alternate conformations - I don't know what is expected statistically but I'd say at least 10% of protein residues will have them - pay attention to waters with close contacts to oxygen - these may be sodium (or other) ions I've attached a few slides that give *very approximate* suggestions - basically just reframing what Pavel and others have said over the years. Although some of these are pretty clear-cut (e.g. you absolutely do not want to use a reference model), you will always need to experiment somewhat to find out what is best for *your* model and data. I think based on your R-factors and statistics that you're headed in the right direction. I'd try to get the clashscore as close to zero as possible, though. I've been toying with different parameters and found that the > weighting didn't make a huge difference, which is probably expected, with a > 1.3 Å dataset. Do stereochemical/ADP weights have any effect? > Do you mean weight optimization? I wouldn't expect it to make much difference. > For the particular data set I'm working with, I'm refining directly > against anomalous data, more specifically against 12 Iodines. Refining the > f' and f" has worked well, generating a beautiful density map. > Good idea. Also consider looking at the anomalous residual map (map_type=anom_residual), which may show weaker anomalous scatterers like chloride or sulfur. (It will be flattened around the iodines if you refine their f'' values.) Refining against the model with hydrogens increased the Rfree/Rwork > values by about 2 points. From what I've read previously I thought refining > hydrogens in a non-"riding" model was only valid below ~1.0 Å. > I'm not sure what you mean here. Did you use the riding model and it increased R-free? Or only when you let them refine individually? The default is now to switch to individual only at 0.9Å or less. > by a few points. For water, I assume that at this resolution there is a > combination of anisotropic (big banana looking density) and isotropic > waters > and that one cannot simply rely entirely on the water_update option. > Yes, at some point you will need to complete the waters yourself. Those bananas may not be simply anisotropic waters, but split sites. You may see other small ligands too. The twin law has worked great, usually dropping Rfree/Rwork values > by 5 points or so. > Just remember to be careful when interpreting the effect of twin law application - I think in this case it's probably quite reasonable, but at lower resolution and with a worse model it can be extremely deceptive. I apologize if any of this is common knowledge and shows my relative > inexperience when it comes to best practices for crystal refinement. > No need to apologize - it is all oral tradition anyways. It is much better to ask questions now than to do something blindly and regret it later. -Nat

1 0

Problem in reducing R-factor
by Singh, Bishal 12 Oct '13

12 Oct '13

Hi all, I am solving a crystal structure at 1.3Å. Completeness of the data-set and Figure of merit at this resolution are 99.5% and 0.62 respectively. Structure has two molecules per asymmetric unit. I used TLS parameters and NCS restraints. WXC_scale and WXU_scale are 0.50 and 1.0 respectively. Rwork and Rfree are 18.09 and 19.62 respectively. I tried with reducing WXC_scale and WXU scale to 0.25 and 0.30 respectively but it did not help. Please suggest me if I need to change some parameters. I shall be grateful for your help. Thanking you, Bishal Singh Graduate student University of Heidelberg, Germany

5 5

special positions Refinement crash
by Yarrow Madrona 11 Oct '13

11 Oct '13

Hello, I am trying to do a refinement and I get an error that I think means I have atoms on special positions. The refinement stops and gives the following output given below. Any help would be appreciated. I am not sure how to exactly determine which atoms are at special positions. Thank you. -Yarrow |-real space refinement (target=simple)---------------------------------------| | start: r_work=0.5500 r_free=0.5441 rmsd: bonds=0.019 angles= 1.68 weight= 50| | final: r_work=0.5309 r_free=0.5358 rmsd: bonds=0.029 angles= 2.45 weight= 80| | --------------------------------------------------------------------------- | ==================== Compute data/restraints target weights =================== Traceback (most recent call last): File "/usr/bin/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py", line 159, in run call_back_handler=call_back_handler) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py", line 1593, in run reference_model_manager = self.reference_model_manager).result File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/strategies.py", line 171, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py", line 87, in __init__ self.call(self.weight, "Compute data/restraints target weights") File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py", line 137, in call func(prefix = prefix) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py", line 302, in weight log = self.log) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weights.py", line 20, in run log = log) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py", line 368, in __init__ self.xyz_weights_result = self.xyz_weights() File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py", line 411, in xyz_weights log=self.log) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py", line 294, in __init__ verbose=0) File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/memory_eraser.py", line 29, in shake_sites max_iterations = max_iterations)) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py", line 43, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py", line 259, in run log) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py", line 127, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py", line 89, in compute_functional_and_gradients self.apply_shifts() File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py", line 70, in apply_shifts site_cart=self.tmp.sites_shifted[i_seq]) File "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/__init__.py", line 609, in correct_special_position raise AssertionError(error_message) AssertionError: Excessive special position correction: unit_cell: (56.278, 67.256, 106.26, 90, 90, 90) space_group_info: P 21 2 2 special_op: 1/2,y,1/2 site_frac: (0.5090941495765681, 0.42722892547242985, 0.5083083194012079) site_special_frac: (0.5, 0.42722892547242985, 0.5) distance_moved: 1.02047 Phenix v. 1.8.4-1496 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

4 5

r-free output by resolution shell
by Ursula Schulze-Gahmen 11 Oct '13

11 Oct '13

Where can I find an output of Rfree in resolution shells? I ran phenix.model_vs_data and I don't see it there. I also didn't find it in the log-files of refinement. Maybe I am just overlooking it. Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

3 2

Project Database Location
by David Shin 10 Oct '13

10 Oct '13

Hi - I had a computer disk go down and want/need to migrate files over manually. I just reinstalled a 1.8.3 version of phenix from a disk image onto OS X 10.6.8. Upon launch, it appears it cannot find my old project database. I was wondering if this is something that can relatively easily migrated over from my backup disk, and where it lives. Thanks, Dave -- David Shin, Ph.D Lawrence Berkeley National Labs 1 Cyclotron Road MS 83-R0101 Berkeley, CA 94720 USA

2 1

Worse R factor with newer version of phenix
by Jan van Agthoven 09 Oct '13

09 Oct '13

Hi everyone, I've been working on a low resolution structure (3.6A) which was previously refined with phenix 1.8_1069 (with a reference model, strategy=individual_sites,individual_adp ). I used the same input files and parameters and ended up with significantly different R factors. Start: r_work = 0.2850 r_free = 0.3189 bonds = 0.005 angles = 1.059 Final: r_work = 0.2609 r_free = 0.3160 bonds = 0.003 angles = 0.997 For the old version and Start: r_work = 0.2779 r_free = 0.3183 bonds = 0.006 angles = 1.141 Final: r_work = 0.2889 r_free = 0.3303 bonds = 0.021 angles = 2.737 with the new version 1.8.4 Remarkably it also came with an increased number of C-beta deviation (0 against 16!). Adding tls refinement or ramachandran restrains did not help. Now because I was using the .eff file of an old version of phenix, it came with a long list of unused parameters. These parameters however were all used by default. What should I do? Should I go back to this old phenix, or is there a way to improve the result? Thanks,

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Phenix version 1.8.4 released
by Paul Adams 09 Oct '13

09 Oct '13

The Phenix developers are pleased to announce that version 1.8.4 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights from this version: Automated MR/ligand fitting/refinement pipeline (phenix.ligand_pipeline), improved determination of bulk solvent masks, improved real space refinement, GUI for ERRASER, improvements to AutoSol and AutoBuild, improvements to Phaser, improvements to Guided Ligand Replacement, 64-bit Windows 7 installer. Graphical interface: ==================== - New GUIs: ERRASER, phenix.dynamics - Pause/resume function for most programs on Mac/Linux - Utilities for conversion to/from mmCIF General: ======== - Multiple bug fixes - 64-bit Windows 7 installer - Improved bulk solvent mask calculations (phenix.refine, phenix.maps, etc.): - analyzes mFo-DFc map to identify spurious negative density blobs in bulk solvent regions and applies correction, can decrease R-factors by 0.5-2.0% Refinement: =========== - phenix.refine: - bug fixes in occupancy refinement, hydrogen addition - new local and global real-space refinement (RSR) methods: - Global RSR (refine all atoms, as before) runs only if: d_min > 1.5, r_work > 0.25, and not neutron data or "individual_sites_real_space" is the only selected strategy - Local RSR: residue-by-residue, replaces old fix_rotamers option - fits both main chain and sidechain - only applies to residues with rotamer outlier, poor CC, or clashes - new residue fit serves as torsion restrains for subsequent macro-cycle - normally not performed when explicit hydrogens present - added omit_selection keyword: sets atom occupancies for a selection to zero prior to refinement - optional harmonic restraints on starting positions - used to maintain structure close to starting model during simulated annealing omit map calculation - alpha feature: placement of elemental ions (place_ions=True) - looks for Mg, Cl, Ca, and Zn by default; specify elements=Cl,Ni,... to give explicit list (recommended) - works best with anomalous data Experimental Phasing and Model Building: ======================================== - AutoSol: - overall_best_refine_data.mtz now contains uncorrected F+,sigF+,F-,sigF- data and uncorrected FP,SIGFP. Previously only the FP,SIGFP was uncorrected, and F+,sigF+,F -,sigF- had been corrected for anisotropy and sharpened. Note that output map files from phenix.autosol and phenix.autobuild are still sharpened and corrected for anisotropy. - For MIR, if quick=True then as soon as a good solution is found with HySS all other derivatives are solved by difference Fouriers. This can speed up MIR structure solution. You can disable this feature with skip_hyss_other_derivs_if_quick=False. - AutoSol and AutoBuild: - It is now possible to specify a different number of copies of different chains in the sequence file. If the sequence file has n copies of chain A and m of chain B, it is now assumed that the stoichiometry is ncs_copies * (nA, mB). Previously it had been assumed always that the stoichiometry was ncs_copies *(A, B). - For structure determination with extremely little phase information there is a new keyword extreme_dm=True (default is False). This allows density modification to use parameters optimized for very poor phasing if the FOM of phasing is less than fom_for_extreme_dm. - AutoBuild - phenix.autobuild now requires that if a hires (or refinement) file is supplied, it must have a complete set of free R flags (test set) if the datafile also has a test set. In this case the test set from the datafile is ignored and the one from the hires/refinement file is used. - You can use the Phenix GUI to extend the test set from your datafile to match the data in your hires/refinement file if necessary. Molecular Replacement: ====================== - Phaser: - various speed enhancements - new normal modes analysis features for domain finding (phaser.splitter) - bug fixes - MR-Rosetta: - You can now tell mr_rosetta to ignore long-running sub-processes and just go on with the finished jobs. New commands: ============= - phenix.dynamics (new command): - simple Cartesian dynamics, replaces equivalent function in PDBTools - phenix.parallel_autobuild (new command): - a tool for running phenix.autobuild many times in parallel, picking the best results, and iterating with the new maps as a starting point. - can make effective use of as many as 40 processors. Ligands: ======== - phenix.ligand_pipeline: - numerous bug fixes - more flexible handling of input sequence files - optional Sculptor step prior to MR to fix residue identities - sidechain pruning enabled by default - interactive mode now includes ligand selection - phenix.guided_ligand_replacement: - Guided Ligand Replacement (GLR) can now search for a protein-ligand complex suitable for the guided fitting using web services on the PDB website or in a local directory. - GLR ligand input has been reworked to allow the use of the three-letter code relying on eLBOW to generate the restraints. - REEL: - simplification and improvement of molecule building - support for cis/trans E/Z enantiomers - view .geo files Miscellaneous: ============== - PDBTools: - simple dynamics option moved to new command, phenix.dynamics - remove_alt_confs and truncate_to_poly_ala options made compatible with other model modifications - HySS: - converted to use standard Phenix parameter syntax - Many new optional features: - Parallel pre-scoring of 2-site solutions - Parallel completion and scoring - Comparison with a fixed solution - Resolution cutoff for Phaser rescoring - Top-scoring solution written even if no matches found - All solutions written - Skip direct methods completion - LLG completion sigma cutoff - Scoring of input sites - Randomization of input sites For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- 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 Building 80, Room 247 Building 978, Room 4126 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

bad density for part of the electron density map
by Wei Shi 08 Oct '13

08 Oct '13

Hi all, I am working with a dataset in space P212121, resolution 2.8 amstrong, total completeness of the data 96.2% (98.1%), I/sigma 5.2 (3.1). This is a structure of a transcriptional factor (dimer) with the ligand. Upon ligand binding, there is conformational change in some part of the protein and I used the apo protein structure as a search model, and get a molecular replacement solution. After some rounds of refinement and rebuild (mainly in a region in the C-terminal ligand binding domain), the best refinement I have is as follows. But the electron density map for the C-terminal DNA binding (about 80 residues) is still very bad.... I tried to mutate them to alanine and do refinement and also tried to delete the whole region to do refinement, but both of the strategies didn't give me better density which I could use to rebuild the residues manually. I am wondering whether any of you have any ideas about what might go wrong and any suggestions about what to check or try next. Thank you so much! start final --------------------------------------- R-work: 0.3220 0.3100 R-free: 0.3916 0.3884 RMS(angles): 2.50 1.39 RMS(bonds): 0.016 0.010 Ramachandran outliers: 1.8% (Goal: < 0.2%) Ramachandran favored: 89.0% (Goal: > 98%) Rotamer outliers: 5.4% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 11.50 Overall score: 2.71 Best, Wei

2 5

Re: [phenixbb] metal coordination restrain on alternative conformation
by Zhang yu 07 Oct '13

07 Oct '13

Hi Nigel, Another question. How do I let phenix.refine know that all atoms in my ligand should have the same occupancy for one conformation? The occupancy refinement in phenix.refine assigned different occupancies to atoms in one conformation. Thanks Yu On Tue, Oct 1, 2013 at 6:10 PM, Zhang yu <phenixzyfish(a)gmail.com> wrote: > Thanks > > > On Tue, Oct 1, 2013 at 1:54 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: > >> I ran >> >> phenix.metal_coordination >> >> and got the attached. Pass it to phenix.refine. >> >> >> On Mon, Sep 30, 2013 at 6:53 PM, Zhang yu <phenixzyfish(a)gmail.com> wrote: >> >>> Hi Nigel, >>> >>> Thanks. Please see attached PDB file. The structure has two molecules in >>> one ASU. Each of molecule contains 6 protein chains and three Nucleic-acid >>> chains (i.e. chain A, B, C, D, E, F, G, H and I for molecule 1; chain K, L, >>> M, N, O, P, Q, R, and S for molecule 2) >>> >>> There is only one nucleoside-triphosphate and its cognate MG++ in each >>> molecule having alternative conformations (named as conformation A and B). >>> The desired restrains are as follows, >>> >>> In molecule 1, >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name OD2 and chain N and resname ASP and resseq 739 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O3G, B and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,B and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,A and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain N and resname MG and resseq 2004 >>> atom_selection_2 = name O1G,A and chain S and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> In molecule 2, >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name OD2 and chain D and resname ASP and resseq 739 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O3G, B and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,B and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,B and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1B,A and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> atom_selection_1 = name MG,A and chain D and resname MG and resseq 2004 >>> atom_selection_2 = name O1G,A and chain I and resname CMP and resseq >>> 2001 >>> distance_ideal = 2.090000 >>> >>> >>> >>> >>> >>> On Mon, Sep 30, 2013 at 6:31 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov>wrote: >>> >>>> Can you send the residues involved? >>>> >>>> Nigel >>>> >>>> NB. Any files sent to me will be held in strictest confidence. >>>> >>>> >>>> >>>> On Mon, Sep 30, 2013 at 12:51 PM, Zhang yu <phenixzyfish(a)gmail.com>wrote: >>>> >>>>> Hi everyone, >>>>> >>>>> My structure contains a metal coordinating to some residues, one of >>>>> which has alternative conformations. Phenix doesn't pickup the residue with >>>>> alternative conformation when I tried to generate metal restrains using >>>>> ready.set. >>>>> >>>>> Any idea? Thanks >>>>> >>>>> Yu >>>>> >>>>> _______________________________________________ >>>>> phenixbb mailing list >>>>> phenixbb(a)phenix-online.org >>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>> >>>>> >>>> >>>> >>>> -- >>>> Nigel W. Moriarty >>>> Building 64R0246B, Physical Biosciences Division >>>> Lawrence Berkeley National Laboratory >>>> Berkeley, CA 94720-8235 >>>> Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov >>>> Fax : 510-486-5909 Web : CCI.LBL.gov >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> >>> >> >> >> -- >> Nigel W. Moriarty >> Building 64R0246B, Physical Biosciences Division >> Lawrence Berkeley National Laboratory >> Berkeley, CA 94720-8235 >> Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov >> Fax : 510-486-5909 Web : CCI.LBL.gov >> > >

3 4

Refinement going wild in latest versions
by Hugues Nury 04 Oct '13

04 Oct '13

Hello everyone, I am experiencing differences with phenix.refine versions 1.8.3 or 1.8.4 compared to 1.8.2. Performing comparable runs, Rs are rising several percents with the latest versions, while marginally decreasing using version 1.8.2. I am a very recent convert to Phenix, so maybe I'm missing something obvious, but here are the details: Refinement strategy is xyz+real space+tls+individual Bs at 3.5 A, using NCS and secondary structure restraints, and weight optimization. Starting R/Rfree are around 24.5/28.5 Part of the problem seems to come from secondary structure restraints, with (many) messages in the log file of the refinement going wild looking like WARNING: could not process nonbonded pair Original error: cctbx Internal Error: /net/clover/scratch1/phenix/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/pair_tables.h(663): CCTBX_ASSERT(j_sym >= 0) failure. pdb=" N GLN B 130 " segid="B " pdb=" O VAL B 115 " segid="B " In log files of refinement with version 1.8.2, there are no such messages, and in either case the definition of beta strands were done automatically by Phenix But even secondary structure restraints are switched off, it starts ok but goes wrong at the beginning of cycle 2, during local real space refinement start: r_work=0.2271 r_free=0.2785 final: r_work=0.2418 r_free=0.2937 And then continue to worsen. Any help appreciated! Cheers, Hugues -- Hugues Nury Institut de Biologie Structurale 41 rue Jules Horowitz, F-38027 Grenoble Cedex 1, France +33 6 52 45 17 79

3 3

REMARK 3 NCS
by Luca Pellegrini 03 Oct '13

03 Oct '13

Hello, I have noticed that Phenix 1.8.4-1496 (as well as 1.8.3-1479) appears to have stopped writing the REMARK 3 NCS in the PDB header. Is this so? It is useful to have that info when it comes to depositing the coordinates. Many thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

3 3

DEN refinement
by Jan van Agthoven 02 Oct '13

02 Oct '13

Hi everyone, I ran a DEN refinement of my low resolution structure (3.6) to improve my model. I typed in the following command: phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb reference.params with reference.params saying: refinement.reference_model.reference_group { reference = chain A and resseq 1:953 selection = chain A and resseq 1:953 } refinement.reference_model.reference_group { reference = chain B and resseq 1:687 selection = chain B and resseq 1:687 } because the reference file only contains chain A and chain B. Unfortunately I obtained much worse R factors then with a regular refinement: Start R-work = 0.2798, R-free = 0.3176 Final R-work = 0.3733, R-free = 0.4089 Does someone have an idea what could have go wrong? Thanks,

2 2

phaser error
by Alexander Batyuk 02 Oct '13

02 Oct '13

Dear developers, I'm getting the following error while running phaser: ERROR running main function (UNHANDLED): cctbx Error: Lattice type not specified. It comes when I put one placed model (found in a previous run) and search for another. Phenix version 1.8.4, on OSX 10.8.5 Do you have any suggestions? Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

1 0

MR-SAD in phenix
by LISA 01 Oct '13

01 Oct '13

Hi All, If we have partial model we can run MR_SAD by adding a single new keyword to my AutoSol run: input_partpdb_file=MR.pdb But I only have a mtz file not a pdb file in the molecular replacement result with EM map as the model. How can I combine the EM result with SAD to improve the density? I have Ta6Br12 cluster soaked crystal data. How can I define the cluster? How much of F'' and F' of this cluster at the wavelength of 1.254A? Thank you. Lisa

2 1

Plotting disabled
by Luca Pellegrini 01 Oct '13

01 Oct '13

Hello, Phenix.refine (1.8.4-1496) disables plotting in the GUI, complaining that the libpng15.15.dylib is missing (see screen below). The library is actually there, where Phenix says it should be: /opt/X11/lib/libpng15.15.dylib. How do I get Phenix to load it? I am using Mac OSX 10.6.8. Many thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

2 1

metal coordination restrain on alternative conformation
by Zhang yu 30 Sep '13

30 Sep '13

Hi everyone, My structure contains a metal coordinating to some residues, one of which has alternative conformations. Phenix doesn't pickup the residue with alternative conformation when I tried to generate metal restrains using ready.set. Any idea? Thanks Yu

2 1

DEN refinement stuck
by Jan van Agthoven 24 Sep '13

24 Sep '13

Hi, I launched a DEN refinement 4 hours ago, and it remain stuck with the following message: ----------coordinate minimization before annealing---------- Running DEN torsion optimization on 1 processors... Running torsion simulated annealing ...trying gamma 0.0, weight 3.0 Is this normal? Is torsion simulated annealing so long? Thanks,

2 2

Merging two or more dataset
by Singh, Bishal 24 Sep '13

24 Sep '13

Is it possible to merge two or more dataset of same protein of different crystals? If yes, please suggest me the way. I shall be grateful for your help. Bishal Singh PhD student University of Heidelberg, Germany

2 1

Workshop on the PDBx/mmCIF Data Exchange Format For Structural Biology (October 22, 2013) and PSI Workshop on Theoretical Model Archiving and Validation (October 21, 2013)
by Torsten Schwede 24 Sep '13

24 Sep '13

*Workshop on the PDBx/mmCIF Data Exchange Format For Structural Biology* Center For Integrative Proteomics Research Rutgers, The State University of New Jersey Tuesday October 22, 2013 http://www.proteinmodelportal.org/workshop-2013/ The wwPDB has established PDBx/mmCIF as the new standard format for data exchange and archiving in structural biology (http://www.wwpdb.org/news/news_2013.html#22-May-2013). To help facilitate the transition from PDB to PDBx/mmCIF format the wwPDB is organizing a programmer's workshop describing the content and organization of PDBx/mmCIF data, and the available software tools and libraries supporting PDBx/mmCIF (C/C++, Java, and Python). The workshop will be held on Tuesday, October 22, 2013 at Rutgers, The State University of New Jersey (in conjunction with a PSI Workshop on Theoretical Model Archiving and Validation to be held Monday, October 21, 2013): Starting at 9am, the morning session will include presentations from: Paul Adams (Phenix), David Case (AMBER), Tom Goddard (UCSF Chimera), Robert Hanson (JMol), Eugene Krissinel (CCP4/mmdb), Andreas Prilic (BioJava), John Westbrook (RCSB PDB). The afternoon session will offer an opportunity to work hands-on with the presenters and developers in the areas of structural biology and molecular modeling to learn application details and to discuss successful approaches and experiences in adapting software to support PDBx/mmCIF. In addition, the workshop will include a discussion of PDBx/mmCIF extensions required to represent molecular modeling specific information. There is no registration fee, but online registration is required (registration Deadline is October 4). For detailed agenda and online registration: http://www.proteinmodelportal.org/workshop-2013/ Looking forward to welcoming you at the workshop, Andrej Sali, John Westbrook, and Torsten Schwede ---- Prof. Dr. Torsten Schwede Biozentrum Universität Basel & SIB Swiss Institute of Bioinformatics Klingelbergstrasse 50-70 4056 Basel

1 0

define acetyl-methionine for coot and phenix
by Ursula Schulze-Gahmen 23 Sep '13

23 Sep '13

I am trying to include a N-terminal acetylated methionine in my model. I replaced my methionine with a AME residue from the pdb data bank and included a link command to connect the C from AME with the N of the second residue. The AME is defined as HETATM. When I try to regularize this structure in Coot it doesn't recognize that the 1. and 2. residue should stay connected. What or how do I need to define this residue or the connection so that I can model in Coot and refine in Phenix? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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Registration last day: "The Future of Microfocus Protein Crystallography"
by Marjolein Thunnissen 13 Sep '13

13 Sep '13

Dear all, I would like to remind you on a workshop on "The Future of Microfocus Protein Crystallography" which will take place at the MAX IV User meeting on the 24th and the 25th of September, 2013, in Lund, Sweden. Recent developments within protein crystallography methods in combination with the scope offered by the new upcoming synchrotron sources such as the MAX IV 3 GeV storage ring, make exciting new ways of carrying out research within structural biology possible. Small microfocus beamlines with a very high flux and increased coherence will make new types of experimentation feasible. The scientific possibilities will be highlighted through a series of talks by experts showing the impact of the new type of X-ray sources and microfocus beamlines on research within structural biology. The new generation of microfocus beamlines will also set a high demand on instrumentation and suitable software. For example, data collection will potentially be very fast (in milliseconds) and radiation damage will allow only a limited amount of data to be collected from each sample. New technical solutions for sample handling and presentation, data processing methods and more will be needed for these types of experiments, and these will also be presented and discussed at the workshop. Confirmed speakers include David Stuart, Daniel Wacker, Simone Weynand, Jens Preben Morth, Tove Sjögren, Richard Neutze, Janet Smith, Alke Meentz, Alexei Soares, Thomas White, Luca Jovine and Clemens Schulze-Briese The workshop is part of a process to obtain an updated proposal for the possible Phase 2b beam line MicroMAX at the upcoming new 3 GeV storage ring of MAX IV in Lund. This workshop should give the user community an opportunity to explore the scientific possibilities of a new generation of microfocus beam lines, but also it will give them the chance to contribute with specific input on their own experimental demands on the beam line. The workshop is part of the MAX IV laboratory user meeting, but there is no requirement to be a user of the facility and all that are interested are welcome . Registration is through the user meeting website: https://indico.maxlab.lu.se/indico/conferenceDisplay.py?confId=0 . The registration fees are 2000 SEK for academics and 700 SEK for junior scientists such as PhD students and Post-docs. Registration fees include all lunches and the conference dinner. Further information on this workshop can be found at the user meeting websiteand for the MAX IV user meeting at https://www.maxlab.lu.se/um13 . For the organisers, Richard Neutze, Gunter Schneider and Gregers Rom Andersen Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

1 0

Research Assistant Position in Structural Biology of Macromolecular Complexes
by Sebastian Klinge 11 Sep '13

11 Sep '13

*Research Assistant Position in Structural Biology of Macromolecular Complexes* The Rockefeller University, a premier biomedical research institute, seeks a Research Assistant to join our Laboratory of Protein and Nucleic Acid Chemistry. The successful applicant will be part of a creative and highly motivated team of biochemists and structural biologists, which are interested in the structure and function of multi-protein complexes involved in key steps of the Central Dogma of Molecular Biology. The laboratory houses a state of the art large scale fermenter, tissue culture and crystallization rooms and has access to the Rockefeller Structural Biology Resource Center with liquid handling and crystallization robots (Formulator by Formulatrix and Phoenix by Art Robbins respectively) and a Rigaku/MSC microMax 007 HF X-ray generator. B.S. or M.S. degree with a strong background in biochemistry or molecular biology is required. Experience with protein production in insect cells (preferably MultiBac) and familiarity with molecular biology techniques is essential. The ideal candidate will interact well with other members of the laboratory, be well organized and interested in working in a high quality research environment and collaborate closely with the principal investigator in running the laboratory. Responsibilities will include setting up an insect cell facility as well as general laboratory duties such as inventory, organization and pick-up of supplies and cataloging the laboratory's clone stocks. We offer a competitive salary, comprehensive benefits, and a beautiful working environment. To apply to this job, click the following URL, click on 'staff opportunities' and enter keyword 'IRC14241': http://www.rockefeller.edu/hr/career /The Rockefeller University is an Affirmative Action/Equal Employment Opportunity/VEVRAA employer./

1 0

Autobuild
by Heather L Condurso 06 Sep '13

06 Sep '13

I'm a bit confused about what is going on with my autobuild run. I solved a structure from anomalous data to 2.7A but many loops are missing. I ran phaser with the current model and native data that extends to 2.4A and got a solution and started autobuild from there. I used mostly the default settings and rebuild_in_place=False. After a pretty short time I realized the run was over and at the bottom of the log I see this: Cycle 3 R/Rfree=0.28/0.35 Built=488 Placed=467 AutoBuild_build_cycle AutoBuild Run 162 Fri Sep 6 14:33:39 2013 Deciding if we should continue... Recent R change per cycle: 0.0 Ending these build cycles as the recent change in R per cycle has been 0.0 and the required value of change is -0.005 and the R is somewhat acceptable at 0.276670644792 All done with build cycles in this region AutoBuild_set_up_build AutoBuild Run 162 Fri Sep 6 14:33:40 2013 All omit/non-omit regions completed finished AutoBuild Run 162 Fri Sep 6 14:33:40 2013 Finishing AutoBuild Run 162 Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat AutoBuild Run 162 Summary of model-building for run 162 Fri Sep 6 14:33:40 2013 Files are in the directory: /Users/heather/Desktop/M/AutoBuild_run_162_/ Starting mtz file: /Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz Sequence file: /Users/heather/Desktop/M/m.pir Best solution on cycle: 2 R/Rfree=0.26/0.33 Summary of output files for Solution 1 from rebuild cycle 2 --- Model (PDB file) --- pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb --- Model (CIF file) --- cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif --- Refinement log file --- log_refine: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine --- Model-building log file --- log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log --- Model-map correlation log file --- log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT --- refine_map_coeffs: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- refine_data: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz --- Density-modified map coefficients FWT PHWT --- denmod_map_coeffs: /Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz You might consider making one very good model now with: phenix.autobuild \ data=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz \ model=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \ rebuild_in_place=True \ seq_file=/Users/heather/Desktop/M/m.pir My full sequence is 325 amino acids so only about 75% is build in. I am hoping autobuild can help find at least some of these missing residues. Why would the change in R be zero? What is meant by "You might consider making one very good model now with:"? I tried running autobuild with these new files and rebuild_in_place=true and get the same type of message. Is this the best that autobuild can do? I also ran the phaser solution through refinement and can significantly lower the Rs from 0.26/0.33 to 0.22/0.30. I appreciate any advice on how best to proceed. I am using 1.8.2-1472 if that matters. Thanks, Heather

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Postdoctoral Researcher Opportunity in the application of free-electron lasers to structural biology.
by Edward Snell 06 Sep '13

06 Sep '13

Postdoctoral Researcher in application of free-electron lasers to structural biology. Open from Sept 2013 until filled. Employer: Hauptman Woodward Medical Research Institute (Position is situated in Germany) Outline of Position: This position is supported by a new NSF grant devoted to the application of free-electron X-ray lasers to structural biology. The position will be based in Hamburg, Germany at DESY CFEL, but is supported by a grant at SUNY Buffalo. There will be time for research collaborations in addition to support duties. The ideal candidate will hold a PhD in experimental Biophysics or similar. Major Responsibilities: 1) Application of X-ray free electron laser to structural biology and development of sample-delivery devices. 2) International travel to annual meetings being held in the U.S. 3) Collaboration with partner institutions and labs in the U.S. 4) Interact via web conferencing with the principal investigator and scientific director of the project Please send resume and cover letter to: Jill Szczesek Director of Operations and Academic Affairs Hauptman Woodward Medical Research Institute 700 Ellicott Street Buffalo, New York 14203 phone: 716-898-8597 email: jszczesek(a)hwi.buffalo.edu<mailto:[email protected]> Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Senior Scientist, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here!

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PDBTools and TLS
by Mark Saper 03 Sep '13

03 Sep '13

Hi, I couldn't find the answers to these questions in the documentation. 1. If I am refining TLS and individual isotropic ADPs, does phenix.refine derive iso-ADP from the ANISOU records presently in the file, or does it use the iso-ADP from the ATOM record and recombine it with the TLS values? 2. Consequently if I reset the B's for a range of residues on the ATOM cards only, will they be used rather than the ANISOU record to derive the ADP? Is it better to use PDBTools, specify the iso-ADP and also convert to ANISOU? I am doing this for only a selection of the residues. 3. Should phenix.refine input files retain the header lines containing the previously cycle TLS parameters? If so PDB Tools doesn't save them. PDB Editor does. Which is the preferred tool? 4. If one explicitly changes atom ADPs with Coot using Measures>Residue info... the output file reflects the change only in the ATOM lines, but the ANISOU line retains the previous 6 parameters. It seems as if coot should also change the ANISOU to reflect anisou (last 3 parameters=0). Comments or answers? Many thanks in advance! -Mark _______________________________________________ Mark A. Saper, Ph.D. Department of Biological Chemistry, University of Michigan Medical School 3040 Chemistry Building | saper(a)umich.edu | +1 (734) 764-3353

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Error determining reference matches
by Dan McNamara 31 Aug '13

31 Aug '13

Hi all, I am encountering a strange crash when running phenix.refine through the command line with reference model restraints turned on. The references point to two different PDB files, one labeled as chain A and one labeled as chain B. This error occurs whether I have my refinement model in P1 with 192 chains or P2(1) with 96 chains. The chains are A-EZ (192) or A-BH (96). It appears to fail to align the reference models to the sequences in the refinement model. This error does not occur with other smaller target structures under 25 chains and reference models used with the same installation of phenix. I am hoping for any advice on why this might be happening or how I might get around it. ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (401472 atoms) torsion_angles = False (0 atoms) rigid_body = True (401472 atoms in 192 groups) individual_adp = False (iso = 0 aniso = 0) group_adp = True (201984 atoms in 25824 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False n_use = 401472 n_use_u_iso = 401472 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 401472 *** Adding Reference Model Restraints *** determining reference matches automatically... Traceback (most recent call last): File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/command_line.py", line 92, in run master_params=customized_master_params) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/driver.py", line 501, in __init__ log=self.log) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 147, in __init__ self.get_reference_dihedral_proxies() File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 460, in get_reference_dihedral_proxies log=self.log) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 323, in process_reference_groups moving_chain = mod_h) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/utils.py", line 426, in _ssm_align ssm_alignment = ccp4io_adaptbx.SSMAlignment.residue_groups(match=ssm) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", line 215, in residue_groups return cls( match = match, indexer = indexer ) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", line 176, in __init__ self.pairs.append( ( get( f, indexer1 ), get( s, indexer2 ) ) ) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", line 173, in get assert identifier in indexer, "Id %s missing" % str( identifier ) AssertionError: Id ('A', 1, ' ') missing Best, Dan

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coot and mtz interpretation
by Heather L Condurso 30 Aug '13

30 Aug '13

I'm having an issue that when I launch coot from the phenix refine gui it loads the pdb and mtz fine, but the FoFc map colors are green and royal blue. When I open coot first and then load the pdb and mtz files, the FoFc map colors are green and red, but the blobs that were green in the phenix loaded maps are now red and what was royal blue is now green. Has anyone else had this issue? I am running a mac with OS X 10.6.8 and coot 0.6.1 and phenix 1.8.2-1309. I have an identical mac running all the same versions and everything loads green and red as expected. Is there a parameter file somewhere that tells coot how to display the phenix maps that may provide a clue as to what is going on? I appreciate any suggestions, Heather

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a question on NAG-ASN cif file
by fn1＠rice.edu 29 Aug '13

29 Aug '13

Hi Nigel, I tried your nag_asn.cif file. I did not include hydrogen in the refinement, so i always get the error message that NAG-ASN could not be applied. So i remark the angle definition that contains hydrogen and the same for the plane definition, as follows, #NAG-ASN 1 C1 2 ND2 2 HD2 119.000 3.000 #NAG-ASN plane1 2 HD21 .020 by doing this, the program could run through. However, when i check the geometry output .geo file, only the added plane information is seen, no chirality of C1 in NAG is seen. Did i do something wrong? Thank you! Fengyun

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a question on NAG-ASN cif file
by fn1＠rice.edu 29 Aug '13

29 Aug '13

Hi everyone, I am refining a glycoprotein model, and I have applied NAG-ASN link to the ASN. But the beta-conformation of NAG could not be retained after refinement for some sites. I read the cif file and find that there are only angle definitions for NAG-ASN. The dihedral and charility information are missing. Is there a way that I could retain the charility of C1 of NAG? Thank you! Fengyun

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ALS Call for General User Proposals - DEADLINE SEPTEMBER 4 , 2013
by Banumathi Sankaran 28 Aug '13

28 Aug '13

> > The deadline for Jan/July 2014 Collaborative > Crystallography proposals will be *Sep 4, 2013. * > > ---------------------------------------------------------------------------------------- > 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: > > Please follow the instructions for proposal submission at: > http://www-als.lbl.gov/index.php/user-information/user-guide/58.html > Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" > and click on "New Proposal." Enter your proposal information. > > > > Regards, > Banumathi Sankaran >

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processor usage controlin DEN
by miyatake 25 Aug '13

25 Aug '13

Dear phenixbb, Hello, I run DEN refinements using GUI (dev-1439). I wonder whether I can control the number of the processor used during the DEN refinement. I know that we can use nproc in command line, but I'd like use it in GUI. Best regards, H. Miyatake

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phenix.real_space_refine
by Heather L Condurso 23 Aug '13

23 Aug '13

I tried to run the phenix.real_space_refine that was discussed in the CCN but I get the following error. import mmtbx.refinement.real_space.driver ImportError: No module named driver I downloaded the latest nightly build dev-1463. Even when asking for the help I get the same error. I did however successfully create some FEMs which look lovely. Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

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Post-doc position for SAXS at the MAX IV Laboratory
by Marjolein Thunnissen 23 Aug '13

23 Aug '13

The MAX IV laboratory in Lund has opened a position for a Postdoctoral fellow to strengthen the biological SAXS environment at the current SAXS beam line at the MAX-II ring. The position will be for two years and is embedded in the BIOSTRUCT-X EU program. Full information of the position is available at: http://admin.lu.se/o.o.i.s?id=22598&Dnr=554436&Type=E. More information can be obtained from Tomás Plivelic (tomas.plivelic(a)maxlab.lu.se<mailto:[email protected]>). Information about the MAX IV laboratory can be obtained at the homepage www.maxlab.lu.se<http://www.maxlab.lu.se> . best regards Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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Find peaks and holes documentation
by Morten Grøftehauge 22 Aug '13

22 Aug '13

Hi, I wanted to try phenix.find_peaks_holes with anomalous structure factors from XPREP but I ran into a few problems. And then I tried to fix them by reading the manual and that was really hard too. So first the missing manual. If I google it I get this page http://www.phenix-online.org/documentation/find_peaks_holes.htm which is for the GUI. When I go back to the documentation http://www.phenix-online.org/documentation/phenix_documentation.html I can't find the link for it (which is also why I was using Google to find it in the first place). I also checked the source to see if the link was somehow misnamed. Anyway, running it from the command line with default settings is not hard. phenix.find_peaks_holes model.pdb reflections.hkl but I run into this error message Sorry: Unresolved amplitude/intensity ambiguity: /path/path/path/reflections.hkl SHELX reflection files may contain amplitudes or intensities. Please append =amplitudes or =hklf3 or =intensities or =hklf4 to the file name argument or parameter to resolve the ambiguity. and I don't how to do that. If I add .hklf3 at the end of the file name I get the same error. If I go reflections.hkl=hklf3 I just get a message that I need to supply a reflection file. What is the syntax? Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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coot add residue issue
by Heather L Condurso 21 Aug '13

21 Aug '13

Dear all, I have been trying to add a residue to my model in coot for hours now. The add terminal residue function adds a residue far from the end of my chain and I've tried moving it manually and it keeps going back and it never makes a bond between the two amino acids. Is there a trick in coot or a better way to do this in phenix? Thanks, Heather Condurso UF-Department of Chemistry

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peptide ligand refinement problems
by Mengbin Chen 20 Aug '13

20 Aug '13

Dear Phenix Users, My colleague has got into trouble when he was refining a peptide ligand with a coumarin ring attached via a peptide bond. The peptide part is composed of natural amino acids, which does not require a cif file. On the other hand, a cif file has been created for the coumarin ring. Unfortuantely, after the refinement run, the peptide and the coumarin ring fell apart, and we could not figure out why this is happening. We are using the Phenix-dev-1370 version. Any help would be appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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Re: [phenixbb] HKL2000 behaved weirdly
by Mengbin Chen 20 Aug '13

20 Aug '13

Sorry for being late in replying, but thank you all for your suggestions! The resolution is ~3 angstroms, so it was quite easy to pick more than 100 peaks for indexing. So I tried to index ~5-6 images at the same time as you suggested, the Bravais Lattice window appeared (and I reset the beam center too), but the unit cell dimensions were ~10 angstroms along one axis, which was not appropriate since the protein is around 40 kDa. I tried to manually pick peaks for indexing, still cell dimensions were too small to be properly assigned. I feel the crystal has got severe problems of multiple lattices and high mosaicity at the same time, which made it hard to index. I am still playing around with the dataset to see if I can get any luck with it, so I'll let you know if I can work this out. Mengbin On Fri, Aug 16, 2013 at 12:18 PM, Noinaj, Nicholas (NIH/NIDDK) [F] < noinajn(a)niddk.nih.gov> wrote: > Mengbin, > > > This happens in HKL2000 with tough datasets. The data can sometime appear > to be very nice, possibly some high mosaicity, but still not process > properly. I have seen this many times. As mentioned already, the next > step is to start trying different things to get the data to process. > WIthout knowing more about resolution, etc, here is a few things to try. > > 1- Check and the double check the beam center. Then, check it again! > With troublesome datasets, this is EXTREMELY important. In HKL2000, > everytime you hit Abort Refinement, you have to reset the beamcenter again. > SO monitor the beam center and everytime it gets too far away from the > actual numbers, reset it. > > 2- you want to try to have roughly 100 peaks for indexing at minimum (if > possible), so change the resolution limits to 15 ang - 4 ang, then retry > indexing. IF this does not work, try 15-5ang, then 12-5, then 10-5, etc. > > 3- If #2 doesn't work, then you can alway try indexing using multiple > frames, esp if you don't have a enough peaks on the first frame. To do > this, please see the HKL2000 manual, or let me know, i can send you some > screenshots or give you a call to guide you via phone. here, you can use > 5-10 frames for indexing if needed. > > 4- as a last option, you can always manually select your peaks. i have had > this work nicely in the past, but again, last option. > > 5- you could try other data processing programs too such as MoSFLM, XDS, > Xia2, etc. > > If you still don't get it working, i am more than happy to take a quick > look. Just send me one of your frames to analyse. Of course, everything > will be strictly confidential. Thanks in advance and good luck! > > > > > Cheers, > Nick > > > > ________________________________ > From: Mengbin Chen [mengbinc(a)sas.upenn.edu] > Sent: Thursday, August 15, 2013 3:12 PM > To: PHENIX user mailing list > Subject: [phenixbb] HKL2000 behaved weirdly > > Dear All, > > I used HKL2000 to index my data, but weird things happened: after I hit > peak search, the data were selected to index, and I chose primitive > triclinic to continue. After I hit refine, the circles for peak search > disappeared, and if I hit "Bravais Lattice", the table would not show up, > which meant that I could not proceed to refine in the potentially correct > Bravais Lattice. I don't know if anyone else has encountered this problem > before, so any suggestions would be greatly appreciated! > > Thank you in advance, > Mengbin > > -- > Mengbin Chen > Department of Chemistry > University of Pennsylvania > -- Mengbin Chen Department of Chemistry University of Pennsylvania

1 0

Preferred treatment of residues with no electron density
by Mark Saper 20 Aug '13

20 Aug '13

What is the preferred method for handling missing residues or residues with zero occupancy, in terms of PBD submission? I see three options: Remove them from the model set occupancy=0 and flag in REMARKs 475 and 480 keep occupancy=1 and allow the temperature factors to climb I have a disordered region in my molecule which I am restraining to a portion of a structure in which that region is well resolved. There are several residues that have no density in the current refinement, yet I want to keep them in the model. Suggestions? Mark _______________________________________________ Mark A. Saper, Ph.D. Department of Biological Chemistry, University of Michigan Medical School 3040 Chemistry Building | saper(a)umich.edu | +1 (734) 764-3353

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a question on LSTc refinement
by fn1＠rice.edu 19 Aug '13

19 Aug '13

Hi all, I read some previous post on LSTc [SIA(alpha2-6)GAL(beta1-4)NAG] refinement, but i still cannot figure out how to refine it in PHENIX. In the current version of phenix, i still could not find the ALPHA2-6 link. Does anybody have such experience? Another question is that, sialic acid (SIA) is in the monomer library of phenix. But when i run on the pdb directly, it will give the error information like, "unknown bond type for O1A and O1B". Though this error could be solved by provided the cif file generated by phenix.elbow. Thank you very much! Fengyun

3 2

Ensemble refinement, starting water structure and alternative conformations
by Joseph Noel 19 Aug '13

19 Aug '13

Is it important (or at least useful) to remove any waters before initiating ensemble refinement wherein the waters are located in what is obvious electron density for alternative conformations of side chains? Would the presence of such waters possibly result in ensemble refinement NOT modeling the alternative conformations? ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Density modification using partial model phase
by Yi xing 17 Aug '13

17 Aug '13

Does mtz file from phenix.refine report FOM? If not, is there a way to have FOM listed in the mtz file. I am trying to use the mtz from the phenix refined model as the input of the ccp4 density modification (DM) or Dmmulti. For example, mtz file from Phaser molecular replacement has all the columns to run the DM. Many thanks for any help or comments! Best, yi

3 2

HKL2000 behaved weirdly
by Mengbin Chen 15 Aug '13

15 Aug '13

Dear All, I used HKL2000 to index my data, but weird things happened: after I hit peak search, the data were selected to index, and I chose primitive triclinic to continue. After I hit refine, the circles for peak search disappeared, and if I hit "Bravais Lattice", the table would not show up, which meant that I could not proceed to refine in the potentially correct Bravais Lattice. I don't know if anyone else has encountered this problem before, so any suggestions would be greatly appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

2 1