- phenixbb - phenix-online.org

Re: [phenixbb] phenixbb Digest, Vol 117, Issue 9
by Cesar Santiago 27 Aug '15

27 Aug '15

Hi Mark! Anybody for the 24th trip to Alba? I'll be away from the 1st - 16th of September but I can still arrange the trip before leaving. César. ------------------------------------------------------------------ Cesar Santiago, Ph. D. Dept. of Macromolecules Structure at CNB, CSIC. X-ray Crystallography Facility. Campus Universidad Autónoma. Madrid, 28049 csantiag(a)cnb.csic.es On Aug 27, 2015, at 6:42 AM, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: phenix.refine automatic linking options (Engin ?zkan) > 2. external passive 3D monitor with macbook pro or imac for coot > and pymol stereo view (Xiao Lei) > 3. Rank-scaled map (Jianghai Zhu) > 4. Re: Rank-scaled map (Pavel Afonine) > 5. Re: on the starting mtz file for phenix refine (Pavel Afonine) > 6. Ligand addition in COOT for later refinement in Phenix.refine > (Manoj saxena) > 7. Re: Ligand addition in COOT for later refinement in > Phenix.refine (Oleg Sobolev) > 8. Computational Crystallography Newsletter - Volume 6, Number 2 > (Nigel Moriarty) > 9. Starting structure as reference model - crashing in 1.10-2142 > (Tristan Croll) > 10. Re: Starting structure as reference model - crashing in > 1.10-2142 (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 Aug 2015 15:41:31 -0500 > From: Engin ?zkan <eozkan(a)uchicago.edu> > To: Billy Poon <bkpoon(a)lbl.gov> > Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] phenix.refine automatic linking options > Message-ID: <55D63B7B.6000707(a)uchicago.edu> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Dear Billy and Nigel, > > Thank you. Phenix.refine GUI in the latest nightly/release candidate no > longer has the master enable/disable button, and so the problem is resolved. > > Engin > > On 8/13/15 11:28 AM, Billy Poon wrote: >> Hi Engin, >> >> Thanks! We updated that part of the GUI so that it should be more >> intuitive. There is now a button that lets you apply automatic linking >> to all the components and a button that disables all automatic >> linking. You can, of course, still pick which components to enable by >> checking the specific boxes. >> >> On Tue, Aug 11, 2015 at 7:40 AM, Engin ?zkan <eozkan(a)uchicago.edu >> <mailto:[email protected]>> wrote: >> >> Dear Developers, >> >> Using the latest phenix nightly, I observed something odd in the >> phenix.refine UI, and I thought I should report it. If one >> unchecks Automatic ligand linking, this seems to not override its >> options, as the instructions in the Options window suggest. >> Specifically, if "Automatic Ligand Linking" is unchecked, but the >> "Link metals" is checked within its Options window, metal link >> restraints are still created. >> >> I checked the .geo file to confirm this. >> >> Thanks, >> Engin >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> <mailto:[email protected]> >> >> >> > >

1 0

Starting structure as reference model - crashing in 1.10-2142
by Tristan Croll 26 Aug '15

26 Aug '15

Hi, When I attempt to run a refinement in Phenix 1.10-2142 using the starting structure as a reference model, it crashes with the complaint that the reference (actually, the error states NCS - despite no NCS being present or enabled. I guess internally it's using the same code?) is too dissimilar to the model, and a calculated RMSD of >90 (degrees? I'm using torsion-angle restraints in any case). The same settings work without complaint on the same structure in dev-2006. I'm running from the GUI, checking "Reference model restraints" in the main phenix.refine window, and then "use starting model as reference" under "All parameters... Reference model restraints...". Thanks, Tristan

2 1

Computational Crystallography Newsletter - Volume 6, Number 2
by Nigel Moriarty 25 Aug '15

25 Aug '15

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. July 2015 <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf> Articles - A context-sensitive guide to RNA & DNA base-pair & base-stack geometry <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=22> Short Communications - New Phaser-MR search panel in Phenix <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=7> - Quantum chemical techniques for minimising ligand geometries in the active site <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=10> - 13 typical occupancy refinement scenarios and available options in *phenix.refine* <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12> Fitting tips #10 – How do your base pairs touch and twist? <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=3> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, 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

1 0

Ligand addition in COOT for later refinement in Phenix.refine
by Manoj saxena 24 Aug '15

24 Aug '15

Greetings I am trying to place a ligand (CIT) in a protein model that already have some citrate ligands placed. I am doing this using Coot's option "get monomer", and after the fitting of ligand in the density I tried to refine the model using the ligand and the protein pdb as input models. Refinement did not start and I got an error message in Phenix- "Number of groups of duplicate atom labels:....." Could someone please explain how could I get past this error message and what is the correct way to add a ligand to a model that already has some of the ligands of the same type. Many thanks in advance Regards Manoj Saxena

2 1

on the starting mtz file for phenix refine
by Smith Lee 21 Aug '15

21 Aug '15

Dear All, In the on-line phenix document, there is, "Should I use the MTZ file output by phenix.refine as input for the next round of refinement? The only time this is necessary is when you refined against a dataset that did not include R-free flags, and let phenix.refine generate a new test set. In this case, you should use the file ending in "_data.mtz" for all future rounds of refinement. You do not need to update the input file in each round, as the actual raw data (and R-free flags) are not modified". When we have phenic adding R-free flgas in the first time we process the mtz data by phenix.refine, besides the *data.mtz, phenix also create a *.mtz. In the future phenix.refine, can I refine by always using the *.mtz created in the R-free flag adding step, rather than refine by always using the *data.mtz created in the R-free flag adding step? What is the difference between that *data.mtz and that *.mtz? And what is the side-effect if in the future steps I refine by always using the *.mtz created in the R-free flag adding step? Best regards. Smith

2 1

Rank-scaled map
by Jianghai Zhu 21 Aug '15

21 Aug '15

Hi, I know PHENIX can calculate a rank-scaled density map. Could anyone inform me which program in PHENIX actually does this? Thanks. Best, --Jianghai

2 1

external passive 3D monitor with macbook pro or imac for coot and pymol stereo view
by Xiao Lei 21 Aug '15

21 Aug '15

Dear phenixbb members, I'm thinking to view stereo 3D structure on coot and pymol with passive 3D monitor, does anyone have experience of doing this with a macbook pro or imac and a external passive 3D monitor connected using HDMI port? If mac does not support this, should I buy a PC and a passive 3D monitor to do it? Thanks ahead. Xiao

1 0

phenix.refine automatic linking options
by Engin Özkan 20 Aug '15

20 Aug '15

Dear Developers, Using the latest phenix nightly, I observed something odd in the phenix.refine UI, and I thought I should report it. If one unchecks Automatic ligand linking, this seems to not override its options, as the instructions in the Options window suggest. Specifically, if "Automatic Ligand Linking" is unchecked, but the "Link metals" is checked within its Options window, metal link restraints are still created. I checked the .geo file to confirm this. Thanks, Engin

2 2

Phenix on Mageia
by Marie Elizabeth Fraser 19 Aug '15

19 Aug '15

Hello, We are having a problem getting the display of the cycles of Phenix running on our Linux machines. I am running Mageia 4, but the problem first appeared when I added a new student and he started to run Phenix on Mandriva. When I changed to Mageia 4, I had to do a clean install, so everyone got new home directories. Then the problem appeared for all of us. This has gone in as a bug report (and I can send the message if that would help). The response was that we were using a character like “é” in the filename or directory. I do not think that we are. However, at the bottom of the bug report it does say "LATIN CAPITAL LETTER A WITH RING ABOVE = Ã…”, which sounds like the symbol for Angstrom. Has anyone else seen a similar problem and been able to fix it? Thank you, Marie

1 0

planarity between atoms of neighboring residues
by Agnieszka Kiliszek 19 Aug '15

19 Aug '15

Dear All, I would like to add restrains between two residues. I was trying to use geometry restrains planarity but I don't know how to select atoms from two different residues. I mean, I have: chain A resid 1 atoms: C5' C' and O1' chain A resid 2 atom: N1' I would like all 4 atoms to be planar. I found example only for atoms from the same residue. Can you help me? Agnieszka

2 1

Re: [phenixbb] Different cell content than expected in Xtriage
by Singh, Bishal 19 Aug '15

19 Aug '15

Dear Folmer, Thank you very much for your words. Yes! I refined the model after molecular replacement. Electron density is nicely defined for all residues including their side chains. There is no extra electron density. All refinement parameters are fine. Rwork and Rfree are around 22% and 25%, respectively. The model that I used for phaser was a homology model generated from a structure with 60 % sequence identity to my protein. I prefer to use homology model than providing sequence identity in phaser because I think that the local structural errors are more precisely defined in homology models. Thanking you again! Kind regards, Bishal From: Folmer Fredslund <folmerf(a)gmail.com<mailto:[email protected]>> Date: Tue, 18 Aug 2015 15:34:23 +0200 To: noro <b.singh(a)dkfz-heidelberg.de<mailto:[email protected]>> Subject: Re: [phenixbb] Different cell content than expected in Xtriage Hi Bishal, Did you try to refine the model from phaser? Did you check the packing of the 2 molecules? Did you look at the electron density from phaser and see if some of it could look like an extra molecule? It is not impossible to have 70% solvent content, so I don't think you should be too worried, just investigate the result. You probably have another molecule there, phaser was just not able to find it, but you should be able to manually fit it easily. Btw, how similar is your model to your own protein? Hope this helps Folmer Fredslund 2015-08-18 15:02 GMT+02:00 Singh, Bishal <b.singh(a)dkfz-heidelberg.de<mailto:[email protected]>>: Dear all, I am solving crystal structure of a protein of size 33.7kDa in space group P 43 21 2 at 2.25 Å resolution. Unit cells constants are 121.51 121.51 156.6 90 90 90. The cell content analysis in Xtriage showed 1050 residues (~ 3X 33.7 kDa) per ASU with 50 % solvent content, whereas the molecular replacement in mr-phaser produced a dimer (2X 33.7 kDa). When we consider a dimer per ASU, it should have approximately 70 % solvent content. Please suggest me whether solution is right or not. I shall appreciate your opinions. Kind regards, Bishal _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]> -- Folmer Fredslund

2 1

Coot mutation of Asp residue to isoAsp residue
by Xiao Lei 19 Aug '15

19 Aug '15

Dear Phenixbb members, I suspect one Asp residue in my model may be an isoAsp (isomerization of Asp). I am asking if there is way to mutate Asp residue to isoAsp(isoaspartic acid) residue in coot GUI (I'm using coot 0.8.1 EL in Mac OS X10.10.5)? I know there is a mutation button on coot, but the mutated aa lists are all natural amino acids. If I have to delete the Asp residue first and then build isoAsp into the density map, is there a way in coot to build an isoAsp residue in map? Thanks ahead. Xiao

2 5

Different cell content than expected in Xtriage
by Singh, Bishal 18 Aug '15

18 Aug '15

Dear all, I am solving crystal structure of a protein of size 33.7kDa in space group P 43 21 2 at 2.25 Å resolution. Unit cells constants are 121.51 121.51 156.6 90 90 90. The cell content analysis in Xtriage showed 1050 residues (~ 3X 33.7 kDa) per ASU with 50 % solvent content, whereas the molecular replacement in mr-phaser produced a dimer (2X 33.7 kDa). When we consider a dimer per ASU, it should have approximately 70 % solvent content. Please suggest me whether solution is right or not. I shall appreciate your opinions. Kind regards, Bishal

3 2

"Table 1" wavelength
by mohamed noor 16 Aug '15

16 Aug '15

Dear all A trivial question but just to be sure: For a structure phased and built using MR-SAD with a dataset collected at one wavelength and refined with a higher-resolution dataset at a different wavelength, how should the wavelength be reported in "Table 1"? And what if the higher-resolution dataset is not isomorphous to the anomalous dataset? Is it sensible to do MR-SAD first, redo MR with the better dataset against the MR-SAD model and then refine at the higher resolution (about 0.8 A better)? Thanks.

2 1

Post-doctoral position in Structural Biology at the Goethe-University Frankfurt, Germany
by Maike Bublitz 14 Aug '15

14 Aug '15

Dear all, please find below a job announcement posted on behalf of my colleague Jun. Prof. Inga Hänelt at the Goethe-University Frankfurt: The Structural Biology of Membrane Transporters group of Inga Hänelt, Institute of Biochemistry at the Goethe University in Frankfurt am Main invites a post-doctoral researcher to join the Emmy Noether project “Determinants of ion channel versus transporter mechanism in the K(+) transporter superfamily“. The project is in need of a candidate with strong biochemical skills for membrane protein purification and/or experience in protein crystallization. If you are interested in further information please follow the link below. http://biochem.uni-frankfurt.de/fileadmin/user_upload/MechanismsMembraneTra… <http://biochem.uni-frankfurt.de/fileadmin/user_upload/MechanismsMembraneTra…> Contact Information for this post: Dr. Inga Hänelt Juniorprofessor for Biochemistry Institute of Biochemistry, Biocenter N220/1.03 Goethe-University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Phone: 0049-69-798-29261 Fax: 0049-69-798-29495 Email: Haenelt(a)biochem.uni-frankfurt.de <mailto:[email protected]> -- Dr. Maike Bublitz Department of Biochemistry, Biocenter Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany phone: +49 (0)69 798 29274 bublitz(a)em.uni-frankfurt.de <mailto:[email protected]>

1 0

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

2 1

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.

3 10

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

2 1

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

1 0

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

2 1

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.

3 2

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

2 2

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

1 0

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

2 3

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 *******************************************

3 7