August 2015 - phenixbb - phenix-online.org

on b factor refine for phenix.real_space_refine
by Smith Lee 13 Aug '15

13 Aug '15

Dear All, I first run a default phenix.real_space_refine with the map and initial model, with the model got, I run phenix.real_space_refine with run=adp, I find for the second phenix.real_space_refine step with run=adp, it can gives a reasonable value of b-factors for each residues in the model, and it cannot modify the coordinates of any atoms in the model (in comparison with the model got by the default phenix.real_space_refine in the first step). I just read a Nature paper from David Baker group "Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement", it says "Because cryo-EM maps are frequently better in resolution in some regions than others, atomic B factors are fit against cryo-EM density data to maximize the real-space correlation between model and map". For Real-space B-factor refinement, the math functions used by that Nature paper include, ( f is a scattering factor fit to each element) My question is, does b-factor refine only give a reasonable b-factor to each atom or residue in the model (so that we know the displacement of each atom or residue), or besides giving reasonable b-factor, it can also change and optimize the x y z coordinates of each atom in the model, and the phenomenon I observed in phenix.real_space_refine on that it only gives reasonable b-factor without modification of the x y z coordinates was only limited to the case I see in phenix.real_space_refine? Best regards. Smith

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Strong anomalous signal but AutoSol fails
by mohamed noor 11 Aug '15

11 Aug '15

Dear developers I have a low resolution anomalous dataset which Aimless suggests has an effective resolution to 3.3 A and anomalous signal to 3.5 A. However, SAD phasing with AutoSol is not successful with the final R factor around 50 %. I also have another dataset collected at a remote wavelength without anomalous signal to 3 A but they are not isomorphous (> 2 A difference in c axis). The anomalous signal comes from the ligand heme c, which is bound covalently to the protein, so its occupancy should be 1. The protein is quite small with about 120 residues. Xtriage suggests an NCS of 6 to 20 with most likely number to be 13. Is there any reason why a reasonable solution cannot be found? There is no twinning. I am using the latest nightly 1.10 pre2124. Thanks.

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ligand refinement
by xinghuaqin＠126.com 11 Aug '15

11 Aug '15

Hi everyone, I am refining a structure of protein/ligand complex (2.75 Å) almost to the last stage. However, I found that some atoms of the ligand is too close to the protein (1.2 or 1.3 Å) after refinement. How should I avoid this? Should I use the "nonbonded_distance_cutoff" parameter? What the value should be set to? Another question is that at this resolution is it possible for me to refine the occupancy? Any suggestion is appreciated. Best Xinghua Xinghua Qin Ph.D Department of Physiology The Fourth Military Medical University 169# Changlexi Road Xi'an 710032, China Tel. 86-29-84772779 E-mail: xinghuaqin(a)126.com

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Re: [phenixbb] anomalous difference map calculation
by Ashok Nayak 10 Aug '15

10 Aug '15

Alexandra Marques <at.marques(a)fct.unl.pt> wrote: >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb >Unsubscribe: phenixbb-leave(a)phenix-online.org

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Failed ADP refinement with active TLS and weight optimization
by Schubert, Carsten [JRDUS] 10 Aug '15

10 Aug '15

Hi, I am running into some strange issues with regards to ADP refinement especially when I am putting final touches on a structure for PDB submission. The problem manifests itself most prominent in the B-factor refinement of solvent, but also maps are affected and are becoming noisier, so I assume this problem affects the protein as well. I checked this against the current release 1.9 and the latest pre1.10 dev version, both versions show the issue. Refinement protocol includes individual_xyz, individual_adp, TLS and weight optimization. The problem I am running into is that the ADP of waters only changes by a global offset. The problem is tricky to spot but more evident when looking at solvent placed in coot with the default ADP (30). The ADP changes only by a global offset, no individual refinement takes place. Since the protein is refined by TLS the problem is not as evident, but as mentioned the fofc maps get noisier from cycle to cycle even though no manual change to the geometry was performed. To me an indicator that the B-factors are not refined properly. The problem can be circumvented by reverting back to isotropic B-factors and then refine with weight refinement for 5-10 cycles. After that TLS can be switched back on for a final polishing cycle. In stubborn cases I had to randomly assign B-factors close to Wilson-B and refine for more cycles to get out of the hole I refined myself into. Another indicator that something went awry is the weight refinement for the B-factors: ----------Individual ADP refinement---------- R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS work free delta data restr 20.66 26.39 5.73 5.712 67.871 2.160 5.225 20.66 26.38 5.73 5.712 67.871 0.030 5.225 20.66 26.38 5.73 5.712 67.871 0.125 5.225 20.66 26.38 5.73 5.712 67.871 0.500 5.225 20.66 26.38 5.73 5.712 67.871 1.000 5.225 20.66 26.38 5.73 5.712 67.871 1.500 5.225 20.66 26.38 5.73 5.712 67.871 2.000 5.225 20.66 26.38 5.73 5.712 67.871 2.500 5.225 20.66 26.38 5.73 5.712 67.871 3.000 5.225 20.66 26.38 5.73 5.712 67.871 3.500 5.225 20.66 26.38 5.73 5.712 67.871 4.000 5.225 20.66 26.38 5.73 5.712 67.871 4.500 5.225 20.66 26.38 5.73 5.712 67.871 5.000 5.225 Essentially there is no change in R/Rfree with regards to different weights. I have not figured out the exact time point when this happens during the course of the refinement but it seems to be coupled to using TLS in combination with ADP refinement and during the final stages of the refinement. I can provide data offline to reproduce the issue Cheers, Carsten

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Sulfur SAD
by mohamed noor 06 Aug '15

06 Aug '15

Dear all Would you have some tips on collecting datasets for S-SAD at a 'normal' beamline (tunable from 0.5-2.5 A)? How helpful/important is it to use mini kappa? Thanks.

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fedora 22 phenix 1.9 installation
by Agnieszka Kiliszek 06 Aug '15

06 Aug '15

Dear All, I want to install new phenix 1.9 but I got error: ========================================================================= PHENIX Installation version: 1.9 release tag: 1692 machine type: intel-linux-4.1.3-200.fc22.x86_64-x86_64 source machine type: intel-linux-4.1.3-200.fc22.x86_64-x86_64 OS version: linux user shell: /bin/bash destination: /usr/local ========================================================================= =============================== ERROR =================================== intel-linux-4.1.3-200.fc22.x86_64-x86_64 is not a supported platform, installation aborted use the --try-unsupported option to attempt installation on this platform use the --no-gui option for a core PHENIX installation =============================== ERROR ======================= It looks like I have double x86_64 in the machine type and it doesn't want to install phenix. Using --try-unsupported gives me these: ~/phenix-installer-1.9-1692/bundles/bundle-1.9-1692-intel-linux-4.1.3-200.fc22.x86_64-x86_64.tar.gz neither source nor binary available, exiting installation. In these folder I have file bundle-1.9-1692-intel-linux-4.1.3-200.fc22.x86_64.tar.gz so I have changed name to bundle-1.9-1692-intel-linux-4.1.3-200.fc22.x86_64-x86_64.tar.gz but again got error finding installed versions finding binary versions cat: build/intel-linux-4.1.3-200.fc22.x86_64-x86_64/version: No such file or directory no pre-existing binary components detected installing new binary package configuring PHENIX components I checked log and got these: /home/gusia/programy/phenix-installer-1.9-1692/bin/install-from-binary: line 359: /usr/local/phenix-1.9-1692/build/intel-linux-4.1.3-200.fc22.x86_64-x86_64/base/bin/python: No such file or directory What can I do to install phenix? Agnieszka

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R vs Geometry (branched off from: [ccp4bb] Rfree at low resolution: how reliable is it, really?)
by Keller, Jacob 03 Aug '15

03 Aug '15

Dear Crystallographers, In following the thread on Rfree reliability, and in the context of a structure I am currently polishing, I have started to wonder what is the ideal way to weight geometry versus R values. I had always thought the rationalization for using geometric restraints was actually to help R values to decrease eventually, since the truth about one’s protein structure is much more likely to agree with the thousands of molecules already solved than with the particularities of the model one has built or the reflection data under consideration. What happens, though, when one’s R values are, say, 2% or even 5% lower with less weight on geometry? It seems to me that this is a gray area, and it would be great to have some sort of general rule. I know that Phenix has a weight-optimization protocol which uses parallel runs with different weights, but I am curious what method is used to decide which one was best? There may not, however, be such a general rule, since I suppose this question is one we always encounter in science. For example, in fitting a few data points, when does one abandon the use of a linear model in favor of something more sophisticated? Or maybe, indeed, someone *has* discovered some reasonable way of approaching this? All the best, Jacob Keller

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symmetry file for Phenix merging statistics
by Xiao Lei 03 Aug '15

03 Aug '15

Hi Phenixbb members, I am trying to use "phenix merging statistics" tool, and I have an unmerged sca file from HKL2000, because the unmerged HKL2000 output does not have unit cell information, so I also need to input a symmetry file, how can I find the symmetry file? Is there a way to generate a symmetry file? Thanks ahead. Xiao

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Anisotropic B-factors with Trucated Data
by Keller, Jacob 01 Aug '15

01 Aug '15

Dear Crystallographers, I have a dataset which was artificially truncated at 1.7 Ang by the limitations of our setup, but the resolution is probably 1.5 Ang or so. I would like to try running anisotropic B refinement in Phenix, but am not sure how to tweak to get this to happen. I know about the parameter:measurement ratio concept, but I think it may still be better than isotropic. NB the dataset is also 42% twinned. All the best, Jacob Keller ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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