- phenixbb - phenix-online.org

Fo-Fc omit map for ligand in the protein-ligand structure
by Wei Shi 20 Sep '14

20 Sep '14

Hi all, I am working with a protein dimer-ligand structure (resolution: 2.8Å) and am going to make a figure showing the bound ligand superimposed with the electron density (Fo-Fc) map obtained after omit refinement. What I did is to make the ligand-free structure model and then use Phenix.refine using the following parameters plus simulated annealing (torsion angle) or (Cartesian): Default: XYZ coordinates + Real-space+ Individual B factors + Occupancies. Also click: Optimize X-ray/stereochemistry weight + Optimize X-ray/ADP weight + Secondary structure restraints + NCS. Contoured at 2σ, the Fo-Fc map generated show green density for most part of the ligand, but for several atoms in the middle of the ligand, the green density is missing... It's like this: some atoms have green density and the next few no green density and then a couple few has green density and then a couple more no green denisty.... The missing green density usually means that part is disordered in the structure, right? I am not sure why the density is missing for some atoms in the middle of the ligand. It would makes more sense if the missing green density is at the end of the ligand... Does anyone happen to have any clue about what it means for the green density missing in my case? Also, I am not sure whether I did the omit refinement right: (1). For simulated annealing, it has two options, one is Cartesian and the other is Torsion angle, and it's said that torsion angle is more suitable of low resolution data. Is there any difference about which one to choose in my case? (2). Is it Okay to run the omit refinement in the presence of the following parameters as I did: Optimize X-ray/stereochemistry weight + Optimize X-ray/ADP weight + Secondary structure restraints + NCS. Thank you so much! Best, Wei

5 24

Increase in R/R(free) after phenix.real_space_refine
by George Devaniranjan 19 Sep '14

19 Sep '14

Hi, I refined (phenix.refine) a 1.0Å structure but it had a few CB outliers and some rotamer outliers. I decided to try real_space_refine, to check if they could be fixed (given that it has a higher radius of convergence). (using run=local_grid_search+minimization_global in real_space_refine) But, the R/R(free) increased from 11.39/13.24( for the refine model) to 16.51/17.55 (real_space_refine model). It seemed a big increase, when I looked at the map against the structure the protein itself seemed fine. The rotamers outliers had decreased, the CB outliers were fixed..etc The solvent fit to the density had worsened in COOT. What am I doing wrong? Any suggestions, advice would be much appreciated. Thank you, George

3 2

RMS angles and comprehensive validation in phenix
by C 19 Sep '14

19 Sep '14

5 6

Problems getting rigid and tls to run
by David Shin 19 Sep '14

19 Sep '14

Hi - Running versions: Version: 1.9.1692 mac-intel-osx-x86_64 osx-10.6.8 Version: 1.9.1692 intel-linux-2.6-x86_64 redhat-e5.10 In both cases, I can run an input model I used previously and get rigid and tls to work. With a newer model, I cannot get either to work (and yes, there was a reason I tested rigid on a model that was refined once). Weirder is I have gone from gui on mac to produce an .eff file to transfer to linux - in the .eff file I get: strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous despite having checked the rigid and tls boxes Weirder yet, is I hand edit the file to add *rigid *tls and run on the linux machine, and both still get turned off. I diff the input refine.eff files between using the older model and newer, and nothing appears very different. The only thing I can think of is that there could be some legacy .hidden files in the working directory that change something, but it makes no sense once I port everything to a different computer. Anyone have this trouble? Thanks, Dave

1 0

Refining structure with overlapping conformations of different residues
by Igor Petrik 19 Sep '14

19 Sep '14

Hi, I am trying to refine a structure in which there are two sets of linked conformations of two residues. Around half of the occupancy (altloc A) corresponds to the sidechain of residue 29 pointing into the pocket and residue 65 pointing out and the other conformation (altloc B) has the side chain of residue 65 in the pocket (where residue 29 is in altloc A) and residue 29 pointing out of the pocket. I am refining them by using occupancy refinement groups in, but phenix refine seems to think that altloc A of residue 29 and altloc B of residue 65 may exist at the same time and pushes them apart to avoid clashes. Is there any way around this? - Igor

2 1

calculate TLS contribution to total B-factor
by Michael Thompson 19 Sep '14

19 Sep '14

Hello All, I have a structure that was refined with phenix.refine using TLS, so my PDB file contains B-total in the isotropic B-factor column as well as ANISOU lines. For the sake of analysis, I am interested in determining the TLS contribution to these total B-factors. How can I split B-total into isotropic and TLS contributions? I'm fairly certain this is possible, as it is the inverse of what one would do after refining a structure with TLS in Refmac, which requires that the isotropic and TLS components be added together prior to deposition. I feel like perhaps there has been some discussion of this in the past, but I'm not able to dig anything up from the bb archives. Any help would be much appreciated. Thanks, Mike

2 1

Problem finding and running iotbx.explore_metric_symmetry
by Arka Chakraborty 17 Sep '14

17 Sep '14

Dear BB members, I am having a problem finding and running the iotbx.explore_metric_symmetry program. I have tried accessing it from the phenix cctbx directory and also from a separate installation of cctbx but could not locate the program. Could anyone point out how exactly to access it?. Thanks a lot in advance, Best regards, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*

2 1

Immediately available: Postdoctoral position in Computational Structural Biology
by David Sivak 17 Sep '14

17 Sep '14

Dear colleagues, This fall I start my own research group in the Physics Department at Simon Fraser University in Vancouver, British Columbia. In the near future, I hope to hire an exceptional, highly-motivated postdoctoral fellow to work on computational structural biology. Please forward this announcement to any interested parties. My group combines approaches from physics, information theory, and statistics to study the fundamental principles of biomolecular function under strong fluctuations. The postdoctoral position will focus on the development of model comparison methods to understand the conformational heterogeneity revealed by structural biology experiments, especially X-ray crystallography. Within this broad research thrust there is ample freedom to pursue particular areas of personal scientific interest. Our theoretical flights of fancy are tethered to reality through a close collaboration with the experimental group of Jaime Fraser at UC San Francisco. Postdoctoral fellows in my group will work in the intellectually-stimulating and interactive biophysics community within SFU Physics, with close ties to the Molecular Biology/Biochemistry department, home to several top-notch structural biology groups. In my own (possibly biased) opinion, the endless all-season outdoors opportunities, mind-blowing food from all ethnicities, and mild weather make Vancouver an enviable place to call home; slightly more objectively, it makes every official top 5 list of most livable cities in the world. The ideal candidate would have experience with computer programming, biomolecular modeling and statistics, and a PhD in a relevant field (broadly construed: physics, biophysics, chemistry, bio- or chemical-engineering, molecular biology, or relevant areas of statistics, computer science, applied math, etc). But most important is intellectual curiosity, enthusiasm for research in this area, and an excellent track record in whatever field they have pursued. Interested candidates should send me a cover letter and CV (including publication list and contact information for 2-3 references). Further information is available at: http://davidsivak.com/ Thank you in advance! David -- David Sivak Asst. Prof., Dept. of Physics, Simon Fraser U david.sivak(a)gmail.com davidsivak.com 778-928-7995

1 0

phenix.merging_statistics and resolution shells
by Murpholino Peligro 17 Sep '14

17 Sep '14

can I specify the ranges of the resolution shells in phenix.merging_statistics? (something like "XSCALE-word" RESOLUTION_SHELLS=) and how many resolution shells are ok? 10, 15, 20?

2 1

LABELIT and MOSFLM version
by Ngoc Anh Thu Ho 16 Sep '14

16 Sep '14

Hello, labelit.index command cannot start Mosflm and gives an error, which reads: "MosflmVersionError: mosflm versions after 7.0.9 not supported” Other than that, indexing seems to be working fine. Can this be fixed or updated somehow? I’m using the latest Phenix 1.9-1692 and Mosflm 7.1.0 (with iMosflm 7.1.1). Best regards, Thu

2 2

calculate CC*
by wei xia 15 Sep '14

15 Sep '14

Hi all:I have a set of data indexed with XDS (space group P222). When I use phaser, the MR solution was in space group P212121.I then changed the space group of mtz file to P212121 using phenix Reflection file editor and did the refinement. Now I use phenix to calculate CC*, in which I input unmerged data (from xds, P222) and merged data (mtz file, P212121) and final pdb file.It turned out to be "incompatible symmetry" error. Are there any easy ways to get the calculate CC* running?Thanks! Wei Xia

2 1

Re: [phenixbb] [ccp4bb] Autobuild in specific area
by Terwilliger, Thomas Charles 14 Sep '14

14 Sep '14

Hi Foggy, This is a situation that autobuild does not address very well yet. Yes, you want rebuild_in_place=False. And yes, if you do that it will remove your model and rebuild it. It will also try to build into the remainder of the map. In practice, you already have pretty much the best that autobuild is going to produce. Delete the protein A chains that autobuild built, and put in your original protein A. Now you have your original model plus whatever autobuild was able to build. An alternative is: select "consider_main_chain_list=True" . This will take your input model A and at each step it will check to see if parts of that model are better than any other model that it has built. This can help for keeping the input model that you put in. All the best, Tom T ________________________________ From: CCP4 bulletin board [CCP4BB(a)JISCMAIL.AC.UK] on behalf of Zhang Foggy [foggyccp4(a)GMAIL.COM] Sent: Saturday, September 13, 2014 10:40 AM To: CCP4BB(a)JISCMAIL.AC.UK Subject: [ccp4bb] Autobuild in specific area Hi, All, I am trying to use Autobuild to build a protein-protein complex model. I obtained partial phase solution (protein-A) through MR, and can see some density of protein-B near protein-A. I would like to use Autobuild to build protein-B model into this area. I load data file, initial density map file, sequence file (both of protein A and B), and protein A model, and run Autobuild. However, The "rebuild-in-place" function confused me a lot, no matter I set it to True or False. When I set to True, it only rebuilt protein A model without adding any additional residues; while I set it to False, it deleted the input protein-A model, and rebuilt a new one... Could somebody tell me how to build the protein B model with keeping the input protein A model in Autobuild? Thanks. [https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif] Foggy

3 3

Autobuild in specific area
by Zhang Foggy 13 Sep '14

13 Sep '14

Hi, All, I am trying to use Autobuild to build a protein-protein complex model. I obtained partial phase solution (protein-A) through MR, and can see some density of protein-B near protein-A. I would like to use Autobuild to build protein-B model into this area. I load data file, initial density map file, sequence file (both of protein A and B), and protein A model, and run Autobuild. However, The "rebuild-in-place" function confused me a lot, no matter I set it to True or False. When I set to True, it only rebuilt protein A model without adding any additional residues; while I set it to False, it deleted the input protein-A model, and rebuilt a new one... Could somebody tell me how to build the protein B model with keeping the input protein A model in Autobuild? Thanks. Foggy

1 0

phenix rosetta installation
by Dan Lin 13 Sep '14

13 Sep '14

Hi all: This is kind of a silly problem, but I'm trying to get phenix.rosetta_refine running on my computer and I am having some difficulty getting rosetta.build_phenix_interface to run. I'm getting a permission denied error in the os.symlink(python_lib, lib_link_name) line in rosetta_build_phenix_interface.py script and presumably I could fix this by changing the write permissions to wherever this points to, but I don't know where. Could anybody point me towards the folder that needs to fixed? Thanks, Dan

2 1

restraints for dna planarity
by John Lee 13 Sep '14

13 Sep '14

Hi, I'm refining a low resolution structure of a dna-protein complex (3.7A) & wondering if someone could help me with setting restraints in Phenix to maintain the base-pair planarity of the dna? With the restraints I have, even with a reference model, I'm getting 'puckering' of the base-pairs. Although the h-bonding distances seem to hold over time, I can't seem to find a way to keep the planarity intact. Thanks in advance for your help. -John

3 2

Phenix-Rosetta integration tests fail with Rosetta MPI on RHEL 6.3
by Sina Masoud-Ansari 12 Sep '14

12 Sep '14

Hi there, I'm wondering anyone has managed to successfully run Phenix with Rosetta MPI on Red Hat Enterprise Linux 6.3 or similar? I currently have a non-MPI build of Rosetta that passes all of the tests in phenix_regression.wizards.test_command_line_rosetta_quick However when running these tests with the MPI build of Rosetta the following tests fail: Running test_relax ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax/test_relax.log test_relax/test_relax_current.log ================================================================= Running test_relax_double ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax_double/test_relax_double.log test_relax_double/test_relax_double_current.log ================================================================= Running test_relax_no_sol ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax_no_sol/test_relax_no_sol.log test_relax_no_sol/test_relax_no_sol_current.log I have attempted to attach an archive of the logs. I'm working with Rosetta 3.5, more recent versions of Rosetta fail other tests in phenix_regression.wizards.test_command_line_rosetta_quick , please see https://www.rosettacommons.org/node/3721 for details. Rosetta 3.5 was compiled with GCC 4.4.6 using OpenMPI 1.6.4 Any help or advice is appreciated. -- Sina Masoud-Ansari Centre for eResearch 409.G21 24 Symonds Street University of Auckland e: s.ansari(a)auckland.ac.nz p: +64 9 3737599 ext 89369 w: http://www.eresearch.auckland.ac.nz

3 4

phenix refine geometry restraints
by George Devaniranjan 12 Sep '14

12 Sep '14

Hi, I was trying to restrain the N-CA-C angle to 110.0 I updated the .def file as follows: angle { action = *add atom_selection_1 = name N atom_selection_2 = name CA atom_selection_3 = name C angle_ideal = 110.0 sigma = 2 I got the following: Sorry: More than one atom selected: "name N" Number of selected atoms: 86 I tried using N in quotes and it doesn't work either but the example in the website had this(below), what am I doing wrong? resname ALA and (name ca or name c or name n or name o) Thank you

2 1

refinement for non-standard DNA base
by John Cheong 11 Sep '14

11 Sep '14

Hi, I have 5-fluoro-Uracil in my DNA:protein complex. I modeled 5-F-dU into the map, ran eLBOW for geometry file and did refinement. After the refinement, 5-F-dU is not connected to the neighboring nucleotides and the phosphate oxygens are rotated to wrong positions. Can anyone teach me how to refine with non-standard DNA base ? Any help or advice would be appreciated. John

2 1

Occupancy refinement of anomalous scatters
by Chen Zhao 09 Sep '14

09 Sep '14

Hi all, I have a question about the occupancy refinement of the anomalous scatters. This is because when I went through all the HA sites, I found that some of them has too high B factor and too high occ. I manually adjusted the occ and fed the model into refinement, but the B factor and occ came back to around their original level again. It seems that those have a stronger peak in the anomalous difference Fourier map has a higher occupancy after refinement, but this does not necessarily equals to a strong density peak in 2Fo-Fc map (some of them even disappear after refinement), and this might be related to their high B factor. Am I doing something wrong in the refinement? I am basically using phenix.refine default setting, but with TLS+isotropic B factor refinement and occupancy refinement of a small region (5-8 residues). The resolution is 3 A, and the refinement is already at the final stage. I am still at the learning stage and your input will be greatly appreciated. Thank you! Sincerely, Chen

2 1

Refinement and Density modification
by Ashu S 09 Sep '14

09 Sep '14

Dear all, I am working on a 3.6A Se SAD data. Autosol followed by autobuild gave a decent map (as expected at this resolution) with a moderate trace. After building poly ala trace and assigning few resides in and around Se positions when I refine the model, all the sharp features of the electron density map are lost. For example, a nice looking helical density becomes a tube. I presume that this happens because wilson B is high (~110 A2) and the map requires modification, sharpening etc. Is there a way to get the map with similar sharp features after model building and refinement as auto build gives? How could I follow exactly the same steps of density modification etc which auto build does? Thanks, Ashu

2 1

Refinement and Density Modification
by Ashu S 08 Sep '14

08 Sep '14

Dear all, I am working on a 3.6A Se SAD data. Autosol followed by autobuild gave a decent map (as expected at this resolution) with a moderate trace. After building poly ala trace and assigning few resides in and around Se positions when I refine the model, all the sharp features of the electron density map are lost. For example, a nice looking helical density becomes a tube. I presume that this happens because wilson B is high (~110 A2) and the map requires modification, sharpening etc. Is there a way to get the map with similar sharp features after model building and refinement as auto build gives? How could I follow exactly the same steps of density modification etc which auto build does? Thanks, Ashu

1 0

refine anomalous
by Andreas Förster 08 Sep '14

08 Sep '14

Dear all, I've solved a structure from a SAD dataset collected at 1.54 Å. The structure contains a good number of sulfurs and also what I think is a potassium ion. To verify, I chose a refinement strategy including "Anomalous groups". This worked well in an important way - R values down by 2 percentage points - but the refined f' and f" values are way off. I start out with these parameters in *.eff: anomalous_scatterers { group { selection = (name SD or name SG) f_prime = 0.319342 f_double_prime = 0.557592 refine = *f_prime *f_double_prime } group { selection = name K f_prime = 0.365562 f_double_prime = 1.06736 refine = *f_prime *f_double_prime } } What I get back is: Anomalous scatterer group: Selection: "(name SD or name SG)" Number of selected scatterers: 15 f_prime: -1.15797 f_double_prime: 0.00577091 refine: f_prime f_double_prime Anomalous scatterer group: Selection: "name K" Number of selected scatterers: 1 f_prime: -4.41689 f_double_prime: 0.00271946 refine: f_prime f_double_prime I thought I'd get close to the book values for S and would be able to identify the other anomalous scatterer by the refined f'/f" values. Naiveté or stupidity? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

2 1

Fwd: Re: Sculptor
by Gabor Bunkoczi 08 Sep '14

08 Sep '14

Apologies, this was meant for the BB. -------- Original Message -------- Subject: Re: [phenixbb] Sculptor Date: 2014-09-08 10:41 From: Gabor Bunkoczi <gb360(a)cam.ac.uk> To: Marie Elizabeth Fraser <frasm(a)ucalgary.ca> Hi Marie, please check the extension of your alignment. If it is .pir, the second line is supposed to be a comment line, and it is therefore ignored. You can either change the extension to .ali, or insert an empty line after the ones starting with ">". If this is not the problem, then this is not supposed to happen. Please send me the logfile in the first instance, although I may need the actual alignment and the PDB file as well (you can delete the target sequence if you wish, an alignment with a single sequence is perfectly valid). BW, Gabor On 2014-09-08 01:22, Marie Elizabeth Fraser wrote: > Hello, > I'm running Sculptor from the Phenix GUI, trying to improve a > molecular replacement model. I've given the pdb file and a sequence > alignment. Sculptor does not appear to accept the first residues > aligned in the sequence alignment. In the alignment, these residues > are residue numbers 42 to 60, so they are on the second line of the > fasta file (the first line after the title) and Sculptor starts at > residue 61 (the subsequent line). Residues 42 to 60 of the target are > to match the first residues of the pdb model, so in the alignment, > there are 41 dashes before the beginning of the sequence for the pdb > file. Am I giving an incorrectly formatted sequence alignment, > misinterpreting what Sculptor does or is Sculptor supposed to do this? > Thank you, Marie > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

1 0

Sculptor
by Marie Elizabeth Fraser 08 Sep '14

08 Sep '14

Hello, I'm running Sculptor from the Phenix GUI, trying to improve a molecular replacement model. I've given the pdb file and a sequence alignment. Sculptor does not appear to accept the first residues aligned in the sequence alignment. In the alignment, these residues are residue numbers 42 to 60, so they are on the second line of the fasta file (the first line after the title) and Sculptor starts at residue 61 (the subsequent line). Residues 42 to 60 of the target are to match the first residues of the pdb model, so in the alignment, there are 41 dashes before the beginning of the sequence for the pdb file. Am I giving an incorrectly formatted sequence alignment, misinterpreting what Sculptor does or is Sculptor supposed to do this? Thank you, Marie

1 0

refine structure with mtz file in P212121 or P222?
by Wei Shi 05 Sep '14

05 Sep '14

Hi all, I am working with a protein-ligand complex structure. The data was indexed with XDS and mtz file is generated using Phenix---Reflection tools---Reflection file editor. The space group used was P222. Then, I used the Phenix---Molecular replacement to find a solution (try all possible in same pointgroup), and the MR solution was in space group P212121. And then, I reindexed the data in XDS using space group P212121 and then generate the mtz file in space group P212121. So, I have two mtz file, in space group P212121 and P222. When I refine the MR solution with the different mtz files, the map generated is not same for the ligand. The statisitcs is better with P222 mtz file than P212121 mtz file. I am wondering why the density for the ligand and the statistics is different using mtz file in different space groups and which mtz file should I use to get the final structure model. Thank you so much! Best, Wei

2 3