- phenixbb - phenix-online.org

Real Space Refinement with marginal data
by Schubert, Carsten [PRDUS] 14 Apr '10

14 Apr '10

Hi, I was wondering if anyone had experience/advice for real space refinement with phenix using marginal data to 3A. I just did a run (SA, real-space refinement against diff_map, 2 fold NCS, grouped APD, fix_rotamers enabled) were the resulting structure showed lots of disconnected sidechains and some broken main chains. I am just repeating the run w/o real space refinement, may be the combination of SA and real space refinement was a bit harsh, but am wondering what kind of parameters make most sense to tweak in order to avoid having the molecules fall apart. Cheers Carsten

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Autobuild
by sbiswas2＠ncsu.edu 13 Apr '10

13 Apr '10

Hi all, I was wondering if you are required to delete the tmp.dat file everytime you run autobuild. What is the imporatnce of this file? I tried to run autobuild from the same folder but it did not allow me to run until I deleted this file. Thanks Shya

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xtriage and anomalous difference assessment
by Francis E Reyes 13 Apr '10

13 Apr '10

Hi all Is xtriage's assessment of anomalous signal depend on the space group chosen? (i.e. measuring genuine I+/I- or I+/I- related by symmetry operation) ? Thanks F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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SAD Phasing
by Rajagopalan, Senapathy 12 Apr '10

12 Apr '10

Hi Everyone, I have been trying to solve a structure of a protein-DNA complex using SAD data, but am running into problems and have some questions on how phenix solves it. From Mathews coefficient calculation, I know that my protein binds to the DNA as a dimer in the asymmetric unit. And when I use this information to specify the the number of heavy atoms to look for, I always get more (1.5-2X, depending on what resolution cutoff I use) in the final heavy atom sites pdb file. More importantly, the map looks 'incomplete' in the sense that part of one of the strands in the double stranded DNA is missing. My question is if this is the result of phenix using some incorrect sites (such as with low occupancy) while phasing. If so, then how can I fix it. I have tried deleting the low occupancy sites and reading the edited heavy atom sites file explicitly using sites_file=ha.pdb, but it doesn't seem to help. Also, if I just use solve to find the heavy atom sites, those tend to be different too... Any suggestions here would be appreciated. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Group ADP syntax question
by Peter Grey 12 Apr '10

12 Apr '10

Hi Phenix people, Is it possible to have One B-factor per residue for one part of the structure and for other parts to use One isotropic B per selected group of atoms. For example to have one B-factor for the entire chain A and have One B-factor per each residue in chain B ? Thanks, -- Peter

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sculpt program
by sbiswas2＠ncsu.edu 12 Apr '10

12 Apr '10

Dear all, I was trying to generate a model using the sculpt program in phenix. when I run it with both alignment file and pdb file I get the following message: Processing PDB... Next model: ''... Next chain 'A'... No matching alignment for chain 'A'; delete PDB output requested Executing design... Everything is deleted; output file empty Any help with this... thanks, Shya

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assert n_ncs > 0
by Robert Ng 11 Apr '10

11 Apr '10

Hi again, How about this one ... Traceback (most recent call last): File "/usr/local/phenix-1.6.1-348/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/command_line.py", line 71, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 413, in __init__ self.process_ncs_restraint_groups() File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 672, in process_ncs_restraint_groups log = log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 306, in from_atom_selections log=log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 219, in __init__ assert n_ncs > 0 AssertionError Thanks again, Robert

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Optimization of the mask parameters in PHENIX
by Pascal Egea 11 Apr '10

11 Apr '10

Dear All, I am using the latest Phenix version (356) with the GUI and I would like to see the effect of optimization of the mask parameters. How can I do this with the GUI in the latest version ( I am also using the secondary structure restraints) in the manual I can see the command line phenix.refine model.pdb data.mtz optimize_mask=true however I don't see such option in the GUI (I can't see it listed in the whole list of commands) Thanks in advance -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pegea(a)mednet.ucla.edu

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Superimposing homologues
by Young-Jin Cho 09 Apr '10

09 Apr '10

Hi Phenix users, I am wondering if phenix or other program provide superimposing pdb files as best as possible(!) I used Superpose in CCP4 but only worked for same sequence of pdb files. So my first question is how I can superimpose more than two different pdb files that are homologues (including water or not). Of course you can do similar thing in coot or pymol, but I wonder if we have better ways to do this kind of job. Secondly, if things working, to do better superimposition, is it possible to input core domain residues information vs. flexible residues information while superimposing. Thirdly, if I have 10 different structures, is there any way to superimpose into such as a calculated average structure of them and fit others into this averaged structure for better comparison? As always, thanks in advance, Young-Jin

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fix rotamers
by Robert Ng 09 Apr '10

09 Apr '10

Dear all, I want to do fix rotamers with the phenix with my 3A resolution virus data. Just do some try out. But I got the memory error listed below: Traceback (most recent call last): File "/usr/local/phenix-1.6.1-348/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 1170, in run call_back_handler = call_back_handler) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/strategies.py", line 570, in refinement_machine params = params.fit_side_chains) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/refinement/fit_rotamers.py", line 779, in run map_sel = flex.abs(residual_map_data) < params.filter_residual_map_value MemoryError Does anybody has this problem before ? and know how to fix this ? Robert

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applying B_factor and scale correction to an MTZ
by Francois Berenger 08 Apr '10

08 Apr '10

Hello, Is there a tool to apply both the scale and overall B-factor correction found by the wilson plot to a given MTZ file? After applying these corrections, is there another way than redoing wilson to check that the output MTZ is on absolute scale? Thanks a lot, Francois.

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Re: [phenixbb] Superimposing homologues
by Thomas C. Terwilliger 08 Apr '10

08 Apr '10

Hi Young-Jin, phenix.superpose_pdbs fixed.pdb moving.pdb will do all these things for you except making the average structure. All the best, Tom T >> Hi Phenix users, >> I am wondering if phenix or other program provide superimposing pdb files >> as best as possible(!) >> I used Superpose in CCP4 but only worked for same sequence of pdb files. >> >> So my first question is how I can superimpose more than two different pdb >> files that are homologues (including water or not). Of course you can do >> similar thing in coot or pymol, but I wonder if we have better ways to do >> this kind of job. >> Secondly, if things working, to do better superimposition, is it possible >> to input core domain residues information vs. flexible residues >> information while superimposing. >> Thirdly, if I have 10 different structures, is there any way to >> superimpose into such as a calculated average structure of them and fit >> others into this averaged structure for better comparison? >> >> As always, thanks in advance, >> >> Young-Jin >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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OpenMP incompatible with Phenix GUI?
by Donnie Berkholz 07 Apr '10

07 Apr '10

Dear developers, I would really like to use OpenMP parallelization and also use the Phenix GUI. When I attempted a source build with OpenMP support, I was informed that the two were incompatible. My understanding is that this used to work fine with the old wizards. Would it be possible to fix this? -- Thanks, Donnie Donald S. Berkholz, Postdoctoral research fellow James R. Thompson lab, Physiology & Biomedical Engineering Grazia Isaya lab, Pediatric & Adolescent Medicine Medical Sciences 2-66 Mayo Clinic College of Medicine 200 First Street SW Rochester, MN 55905 612-991-1321

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Re: [phenixbb] phenixbb posting
by Leonid Flaks 07 Apr '10

07 Apr '10

Nathaniel Echols wrote: > The server bounced your message - are you subscribed to the list? > FYI, I'm not sure why firefox won't start here; sometimes it gets > confused by Phenix's copy of GTK, but that's not what the error > message looks like. You can try opening the Preferences in Phenix, > select the "File handling" parameters, and check "Reset > LD_LIBRARY_PATH for external apps". Let me know if that doesn't fix > the problem. > > thanks, > Nat > > ---------- Forwarded message ---------- > From: Leonid Flaks <flaks(a)bnl.gov <mailto:[email protected]>> > To: phenixbb(a)phenix-online.org <mailto:[email protected]> > Date: Wed, 07 Apr 2010 15:51:11 -0400 > Subject: problem with firefox and phenix-1.6.1-357 > I installed phenix-1.6.1-357 on Fedora-12. If I click on the question > mark in the GUI, I see the following: > > Using browser /usr/bin/firefox > /usr/lib/firefox-3.5.9/firefox: symbol lookup error: > /usr/lib/libgnome-2.so.0: undefined symbol: g_dgettext > > > and firefox would not start. I saw similar errors reported more then a > year ago, but that is a new fedora-12 installation. > > Any ideas? > > > Thanks, > > Leon > > Yes, I realized that I need to subscribe first, which I did after sending my message ;-) I tried to follow your advice - checked the box, but nothing changed. Same error message. -- Leon

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individual_sites_real_space?
by Francis E Reyes 07 Apr '10

07 Apr '10

Phenixer's I just upgraded from 1.4-87 and noticed that there's individual_sites_real_space now. The documentation (http://www.phenix-online.org/documentation/refinement.htm ) just shows that it's a parameter phenix.refine. What is this and when is it helpful (bad resolution/ bad model? or high resolution/ good model? or high resolution/bad model?) Thx F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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LSTc refinement in phenix.refine
by JXQI 07 Apr '10

07 Apr '10

Dear all, I am refining a structure complexed with LSTc (alpha 2,6-linked galactose,i.e. SIA-GAL-NAG-GAL).I know that the BETA1-4 or BETA1-3 in the mon-lib could restrain the bond distance,but I could not find the links between the SIA and GAL......any suggestions are appreciated. Best regards Janxon

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polygon and membrane proteins
by Pascal Egea 06 Apr '10

06 Apr '10

Dear Developers, I wonder if there would be a simple way to get the Polygon program implemented in Phenix to use only membrane protein deposited structures as the reference data set. I understand that the reference set is much smaller than the whole menagerie of available structures but it represents an homogenous class of protein (crystallized in detergent). Do you think that this would be meaningful and useful? Thanks in advance, -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pegea(a)mednet.ucla.edu

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Re Double stranded DNA restraints?
by Thomas C. Terwilliger 06 Apr '10

06 Apr '10

Hi Sena, I would add this command helices_strands_only=True to force autobuild to just try and build helical segments. This probably won't fix the lack of connectivity however. All the best, Tom T Hi Everyone, Is there a way to force phenix (autobuild) into building a contiguous double stranded DNA. Currently, when I am solving a protein-DNA complex using SAD data: 1) its not recognizing that DNA needs to be double stranded, so it is fitting one of the strands correctly (at least part of it), but the other strand is in the protein density region. 2) It breaks down each of the strand. So it is not fitting as a contiguous 30 mer but instead a 10 mer, two 6 mers and a 8 mer. Thanks Sena

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PPC binaries?
by Marcelo Carlos Sousa 05 Apr '10

05 Apr '10

Is Phenix no longer supported on Mac PPC? ____________________________________________ Marcelo C. Sousa, Ph.D. Department of Chemistry and Biochemistry Cristol Chemistry Building. Room 100 215 UCB University of Colorado at Boulder Boulder, CO 80309 Phone: (303) 735 4341 Fax: (303) 492 5894

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(no subject)
by Prof Jennifer Martin (IMB) 04 Apr '10

04 Apr '10

The protein crystal structure I am refining has a redox modification: cysteine sulfenic acid (S-hydroxy cysteine). How do I go about including parameters for this modification in phenix refine? I have found parameters on HIC-UP (under CSO) but these are for XPLOR/ CNS. Many thanks in advance for suggestions, Jenny Martin University of Queensland

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Torsion angels refinement question
by Peter Grey 03 Apr '10

03 Apr '10

Dear Phenix users, I try to refine a big complex at low resolution. I am a little confused about the syntax of using torsion angels gradient-driven refinement. Is it now the default for individual sites refinement instead of cartesian ? If not, should I add : sites.Torsion_angles=all for example ? Could you shed some light on this, Thank you, -- Peter

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Optimizing the Geometry Weight for a 2.76 A structure
by Sam Stampfer 02 Apr '10

02 Apr '10

Hi, I'm refining a 2.76 A structure and need help optimizing the refinement weight on geometry. When I refine at the default refinement weight (wxc = 0.5), phenix seems to generate a much poorer structure (both geometrically AND by Rfree value) relative to lower wxc values which put a stronger weight on geometry. I am trying to pick the best structure to use for my next round of rebuilding. The R-stats and condensed molprobity stats are listed below (at the end of this email). I have a few questions regarding this structure and those stats: 1. What is the relevance of having a LOW difference between Rfree and Rwork? My structure seems to have a higher than expected Rwork value relative to Rfree (aren't they supposed to differ by 0.05 or so, instead of the 0.03 observed in my structure?) Additionally, as I refine at lower wxc values (more weight on geometry) I get an increased Rwork value with an equal or decreased Rfree (relative to the refinement at a higher wxc value). Does that mean my structure is better or worse? 2. How can I judge the output from my refinement? I have looked at Rwork, Rfree, and the molprobity clashscore and overall score values. I included them below, at the end of this email. How do I tell which the best refinement is? Which one would you suggest? I thought the best was wxc = 0.1 since the R-work and Rfree aren't changed much from the start values but the geometry is far better. 3. How do I optimize the weight on geometry in refinement? My PI said that phenix can do it but not for twinned structures (my structure is twinned). Can the new version of phenix do weight optimization for twinned structures? How? If not, what's the best way for me to do it manually? As always, thanks immensely for all your help! -Sam All have the same values for: Start R-work = 0.2002, R-free = 0.2376 *wxc = 0.01 *Final R-work = 0.2104, R-free = 0.2378 Molprobity Clashscore: 19.46 Molprobity Score: 2.29 *wxc = 0.05 *Final R-work = 0.2049, R-free = 0.2377 Molprobity Clashscore: 20.96 Molprobity Score: 2.38 *wxc = 0.1 *Final R-work = 0.2010, R-free = 0.2388 Molprobity Clashscore: 23.50 Molprobity Score: 2.54 *wxc = 0.2 *Final R-work = 0.1969, R-free = 0.2399 Molprobity Clashscore: 27.15 Molprobity Score: 2.79 *wxc = 0.3 *Final R-work = 0.1945, R-free = 0.2411 Molprobity Clashscore: 30.76 Molprobity Score: 2.97 *wxc = 0.4 *Final R-work = 0.1930, R-free = 0.2420 Molprobity Clashscore: 34.54 Molprobity Score: 3.11 *wxc = default (0.5) *Final R-work = 0.1918, R-free = 0.2429 Molprobity Clashscore: 37.73 Molprobity Score: 3.22

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Re: [phenixbb] Optimizing the Geometry Weight for a 2.76 A structure
by det102＠uoxray.uoregon.edu 02 Apr '10

02 Apr '10

Dear Phil, I don't have access to vol 277 of Met Enz here, which is sad since I wrote a chapter in the thing, so I can't comment on Axel's exact words. I agree that the uncertainty in the ability of the free R estimate based on a subset of reflections to predict the mean of the free R calculated from all possible test sets of that size is proportional to 1/N. My point is that the pdf of the difference of two random variables is not the same as the pdf of either of them. You have to know the coupling between them to decide if the difference between them has greater or less precision than the individual variable. For example, let's assume two measurements with a precision of 1% but the difference in the two measurements is 0.5%. This small difference can be significant if the causes of the uncertainties are systematic. The "errors" would cancel out. I believe the fluctuations in free R estimate due to the small size of the test set are due to the particular indices in the test set and therefore mainly systematic. The intensities of some reflections may have been measured better than others and your test set may happen to be more enriched with those, resulting is a slightly lower free R estimate. Since the test set is always the same during refinement the benefit of this enrichment (or detriment if you were unlucky) will be subtracted out when you compare the two free R estimates during your optimization. I expect the difference between two free R estimates (using the same test set) will be a more precise indicator of the true change in free R than either estimate is in predicting the free R itself. Dale Phil Jeffrey wrote: > Although I am totally unclear why the form of the equation, which is > just counting/Poisson statistics, doesn't also apply to the uncertainty > of calculating the average percentage deviation over a test set of size > N. For example a test set of N=1000 could be regarded as 100 different > test sets of size N=10, and I think it's likely that the distribution of > R-free for these 100 mini test sets would be Poisson in form centered > around the R-free for the superset N=1000. > > So, since the change in |Fo-Fc| for each reflection doesn't simply scale > with wxc in structure refinement nor does it inevitably decrease for > every reflection on structure improvement, the change in R-free for any > given change in structure should be related to N in the form of the > equation given, so does reflect the s.d. of R-free as an estimate for > structure improvement. > > No ? > > If not, then I misinterpreted what Brunger mean on p.394 of his 1997 Met > Enz paper because that's certainly what it read like. > > Phil > > det102(a)uoxray.uoregon.edu wrote: >> >> That uncertainty is not quite the same thing. What you describe >> is the uncertainty in the free R due to the small sampling size of >> the test set. It is the spread of free R's obtained when different >> test sets are chosen for the same project and circumstances, and is >> useful when comparing free R's calculated using different test sets, >> or, heaven forbid, trying to compare free R's from different crystals.

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map grid size
by Sean Gay 02 Apr '10

02 Apr '10

Does anyone know if there is a way to increase the map sampling rate for Phenix fofc and 2fofc maps? I want to make a figure for publication in PyMOL and the map_double command helps a bit, but i'd still like more points on the map grids. Sean Sean C. Gay, PhD Postdoctoral Scholar Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego 9500 Gilman Dr. #0703 La Jolla, CA 92093 Tel. (858)822-7804 Fax. (858)246-0089 Email. scgay(a)ucsd.edu

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Double stranded DNA restraints?
by Rajagopalan, Senapathy 02 Apr '10

02 Apr '10

Hi Everyone, Is there a way to force phenix (autobuild) into building a contiguous double stranded DNA. Currently, when I am solving a protein-DNA complex using SAD data: 1) its not recognizing that DNA needs to be double stranded, so it is fitting one of the strands correctly (at least part of it), but the other strand is in the protein density region. 2) It breaks down each of the strand. So it is not fitting as a contiguous 30 mer but instead a 10 mer, two 6 mers and a 8 mer. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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