- phenixbb - phenix-online.org

R factor
by zhangh1＠umbc.edu 19 Sep '10

19 Sep '10

Hi, I want to calculate Fc based on the PDB file and reproduce the R factor in it. I first tried phenix.model_vs_data. It optimized ksol bsol and b_cart, and the output R factor (0.2143) is close enough to that in PDB (0.215). However, it didn't generate mtz files containing the calculated Fc. Then, I take the optimized ksol bsol and b_cart as the input and tried phenix.fmodel. I wrote my own code to calcuate the R factor. However, I got a lower R factor (0.2078). I think the reason might be my R calculation formula (sigma(fo-fc)/sigma(fo)) is wrong; or model_vs_data did more than just did flat solvent correction and anisotropic scaling. So, I am wondering whether phenix can: (1) Do the similar thing as model_vs_data (hope can be somehow faster:), but generate Fc-containing mtz file; (2) Do a simple R factor calculate to see whether my code is wrong (maybe answered already:) Thanks! Best Regards, Hailiang

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generate Rfree flag for twinned crystals with 3 twin fractions
by Zheng Zhou 19 Sep '10

19 Sep '10

Dear all After reading the informative posts in mailing list, I started to deal with my first twinning dataset. The space group is P3. Xtriage found 3 twin laws. R vs R statistics indicated perfect twinning for two twin laws and one is twin with RPS. I realize that twin-related reflections should be in the same work or free group. Could phenix handle the Rfree flag correctly for me when there are more than one twin fraction identified? By applying one twin law, the Rfree dropped from 37% to 28% using phenix. When I use Refmac, the twin fractions are refined and the Rfree is down to 26%. I copied the Rfree flag from phenix to the ccp4 in this case. When I let ccp4 generate Rfree flag automatically, the Rfree is refined to 26% too. Should I label the Rfree at a higher space group? Thanks for your advice Best, Zheng (Joe) Zhou

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Resolve NCS masks
by Florian Schmitzberger 18 Sep '10

18 Sep '10

Dear All, I would have a question regarding the use of masks in Resolve in Phenix for density modification: Is it possible to output the NCS and/or solvent masks Resolve is using during the Autosol run (similar as the options from the stand alone Resolve version) such as: mask_as_mtz ncs_mask_file mask.mtz protein_mask_file What are the best criteria (other than the final maps of course) within the output from Phenix.resolve to judge if the NCS (and/or solvent) mask was chosen adequately? (NCS_overlap?) I am mostly concerned if the masks chosen do include some of the more peripheral parts of my protein molecule and do not flatten these regions. Secondly, it is possible within Phenix Autosol wizard to supply a pdb file (with dummy atoms) for the mask for Resolve to construct the NCS mask? i.e. similar to set mask_pdb file= dummyatom.pdb Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

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Ligand restraints editing with REEL
by Joseph Brock 18 Sep '10

18 Sep '10

Hi all, I'm working on a 1.5A structure that contains a novel ligand within the active site, which is an Arsenic derivative of Glutathione, using the Phenix GUI, version 1.6.4-486. I have been using the 'Molinspiration' webpage (http://www.molinspiration.com/docu/webme/) to generate a smiles string, which I then feed into ELBOW. Although the structure/chemical restraints of Glutathione should be unchanged by the covalent linkage to arsenic through the cysteinyl sulfur, the resulting restraints file consistently restricts one of the dihedrals to a value that is incompatible with the (quite clear) electron density. This occurs regardless of wether i use AM1 optimization, and is unresponsive to using native Glutathione (which refines into the corresponding density extremely well) as an input geometry file with any of the available 'Use geometry for' options (final geometry, initial geometry, etc). I then tried opening the output file in REEL and manually changing the corresponding dihedrals to those of glutathione, however after running simple optimization, the resulting restraints file has the same problem, and upon choosing the 'transer geometry and restraints' option (or any option) midway through running the 'eLBOW optimization' or 'AM1 optimization' options, Phenix consistently crashes. Any advice on how to transfer the origional geometry of native Glutathione to my new ligand effectively would be greatly appreciated. I'm a little confused as to the abilities of REEL, and how to affect them. Thanks so much in advance. Cheers, -Joe.

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autobuild : MSE's keep coming back
by Lepore, Bryan 17 Sep '10

17 Sep '10

i used "semet=False" the .pdb has MET the .seq has M the output models, however, keep getting MSE's in them, complete with selenium. am i missing something? -bryan

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Re: [phenixbb] Something that came up on the CCP4 list...
by Simon Kolstoe 16 Sep '10

16 Sep '10

Just for the record I've had it make a big difference a number of times as well with both refmac & shelx. I was under the impression that phenix.refine was "cleverly" allowing me to use that trick by just starring the add riding hydrogens in the def file however it seems not - something worth knowing! Simon On 16 Sep 2010, at 20:01, Phil Jeffrey wrote: > I've had it make a big difference in certain circumstances. And in > other circumstances not so much. Definitely worth a try. I do not > use the technique routinely. > > Phil Jeffrey > Princeton > > > > On 9/16/10 11:49 AM, Simon Kolstoe wrote: >> So just to clarify further - if i am having problems with the final >> geometry of a model (eg clashscore as reported by molprobity), is >> it an >> appropriate trick to add hydrogens and then refine in phenix.refine >> using the riding hydrogens option, or does this not really change >> anything? >> >> Simon >> >> On 16 Sep 2010, at 14:26, Pavel Afonine wrote: >> >>> Hi Simon, >>> >>>> Could I just seek some clarification? I was under the impression >>>> that >>>> phenix.refine calculated riding hydrogens by default and took these >>>> into account as a restraint on the geometry? >>> >>> if you want hydrogen atoms to be used in refinement (as "riding >>> model" >>> or explicit) your need to make sure the PDB file that you give to >>> phenix.refine contains H atoms. That is you need to add them using >>> programs like phenix.reduce or phenix.ready_set or using >>> corresponding >>> functionality in the GUI. >>> >>> phenix.refine will not add them internally as part of refinement IF >>> hydrogen atoms are NOT present in input PDB file. >>> >>> Adding hydrogen atoms as 'riding model' does not add any refinable >>> parameters, but the scattering contribution from them is included >>> most >>> of the time. This is why we do not use H atoms silently but require >>> them to be in input PDB file - simply to make sure the reported >>> statistics (such as R-factors) is easily reproducible. >>> >>> All the best! >>> Pavel. >>> _______________________________________________ >>> 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 >

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LABIN labels for Autosol/resolve NCS scores
by Florian Schmitzberger 16 Sep '10

16 Sep '10

Dear All, I would have a number of Phenix related questions: Firstly, I used the anisotropy server ( to anisotropically truncate my mtz file with anomalous signal (SAD data). My question is if the labels (for F+/F- and SIGF+/SIGF- are correctly recognized by Phenix (Autosol). The columns labels are: F_ref for FP; QSIGF_ref for SIGFP; GF(+)pk for F(+); LSIGF(+)pk for SIGF(+), GF(-)pk for F(-); LSIGF(-)pk for SIGF(-). It seems QSIGF and GF(+)pk/LSIGF(+)pk etc. are , but I am uncertain if it recognizes F_ref, because for the LABIN INPUT LABELS it says "NONE" for"F". Phenix does not seem to detect the anistropy ("Not using aniso- corrected data files as the range of aniso b is only 19.52 and 'correct_aniso' is not set); so I suppose I should use the correct_aniso=True keyword. Secondly, what are good values for the evaluation of the NCS mask and NCS averaging Resolve is using in Phenix; NCS overlap values (e.g. in my case 1.1) and NCS_CORR (in my case 0.52) in the "resolve.scores" file. Does an NCS overlap value of greater than 1 make sense? I am working with a (anisotropic) dataset with 4.1/4.5 A resolution, 78 % solvent content, 2-fold NCS; Perhaps a naive question: It is not possible to use B-factor sharpened maps for autobuilding with Phenix Autobuild is it? Thank you for any comments! Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

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f', f'' of Bromide?
by Tri Ngo 16 Sep '10

16 Sep '10

Dear Phenix-BB members, I am trying to solve the MAD data of one bacteria protein. The crystal was soaked with 1M Sodium Bromide. The data were collected at three different wavelength. I intend to use Autosol to solve this structure, but I am not sure which parameter I should put in the field: f' and f''? I think there is a table in the synchrotron but maybe I didn't notice about that. So now what should I do? Thank you very much for your input! Best wishes, -- * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150

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Intl Conf on Structural Genomics, Toronto, Canada, May 10-14, 2011
by Thomas C. Terwilliger 16 Sep '10

16 Sep '10

Dear Colleagues, We are pleased to let you know about the upcoming International Conference on Structural Genomics 2011, to be held in Toronto, Canada on May 10-14, 2011. This meeting is the 6th in this series of biennial meetings of the International Structural Genomics Organization. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics and structural/chemical biology, and their impact on research in biology, medicine and disease. A limited number of student travel fellowships will be available for travel to this meeting. A substantial number of short talks will be selected from poster abstracts. Please see http://www.icsg2011.org for further details. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

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64-bit Snow Leopard support
by Nathaniel Echols 16 Sep '10

16 Sep '10

Mac users-- The latest nightly version of Phenix (dev-532) is now capable of compiling 64-bit objects on Snow Leopard, which should help those of you working on very large and/or high-resolution structures. You will need to use the source installer for this; it will automatically recognize the machine type as "mac-intel-osx-x86_64" and use the correct sources. There are several things to be aware of before trying this: 1. I had to switch to the development version of wxPython to get the GUI working, and it's both inherently less stable and based on fundamentally different OS libraries, which may cause problems. I've fixed some of the most obvious issues and everything appears to run now, but I expect to find more glitches. (This shouldn't affect command-line users.) 2. We haven't extensively tested 64-bit Phenix on Mac; there may be undiagnosed low-level bugs, even for command-line-only use. This should change soon. 3. For the above reasons, and because source installation is generally difficult to support, we recommend that you continue to use the 32-bit binary installer if you are not experiencing memory problems. (It will figure out what you are trying to do and correct the machine type accordingly.) 4. One side effect of this change is that an installation made on Leopard will not work on Snow Leopard, and vice-versa. I may be able to fix this. Hopefully there will be a binary installer in the near future, if I can ever figure out how to fix NFS on my workstation. -Nat

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Something that came up on the CCP4 list...
by Simon Kolstoe 16 Sep '10

16 Sep '10

In the fascinating current discussion on the ccp4 list Pavel said: >Dear Ed, > >no, if you start with model that has no hydrogens, they will not be generated internally. > >Pavel. > On 9/15/10 2:58 PM, Ed Pozharski wrote: > Sure. But if I start with model that has no hydrogens, they will be > generated but not passed to the output, right. just like refmac. > > On Wed, 2010-09-15 at 14:52 -0700, Pavel Afonine wrote: >> Dear Ed, >> >> On 9/15/10 2:47 PM, Ed Pozharski wrote: >>> On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote: >>>> So the riding hydrogen model is imperfect. At least with >>>> phenix.refine >>>> you can measure it, unlike the default behavior of REFMAC. (But >>>> you >>>> can >>>> tell it to write hydrogens out, I believe). >>>> >>> My impression is that default behavior of phenix.refine is the >>> same - I >>> had to change parameters to include hydrogens in the output. >> No, if your input file contains H atoms, the output file will contain >> them too (in phenix.refine). You don't have to change any >> parameters for >> this. >> >> Pavel. Could I just seek some clarification? I was under the impression that phenix.refine calculated riding hydrogens by default and took these into account as a restraint on the geometry? Simon

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nqh-flip option
by Christian Roth 16 Sep '10

16 Sep '10

Dear all, I put manually in the parameterfile from the gui the option nqh_flips=True. After the run starts, a popup comes up claiming about an invalid unsupported option and the refinement stops without producing any file, even not a log-file. Does the nqh option not longer exists or what happend here? I use at the moment phenix 1.6-289. Thanks for your help. Christian

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Re: [phenixbb] autobuild : MSE's keep coming back
by Thomas C. Terwilliger 16 Sep '10

16 Sep '10

Hi Bryan, Hmmm...I can't seem to make it happen with my standard inputs. Can you possibly send me directly (terwilliger(a)lanl.gov) your AutoBuild_run_1_/autobuild.eff file or better yet that plus your input files and I'll try that out here? Thanks a lot, All the best, Tom T >>> are you using a recent version? >> >> v1.6.4 release tag 486 >> >>> is this rebuild_in_place or not? >> >> well, i did not specify rebuild_in_place, however, i poked around and can >> see that autobuild has switched on rebuild_in_place so i call that a >> "yes". >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Re: [phenixbb] autobuild : MSE's keep coming back
by Lepore, Bryan 15 Sep '10

15 Sep '10

> are you using a recent version? v1.6.4 release tag 486 > is this rebuild_in_place or not? well, i did not specify rebuild_in_place, however, i poked around and can see that autobuild has switched on rebuild_in_place so i call that a "yes". -bryan

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Re: [phenixbb] [ccp4bb] Deposition of riding H
by Dr. Mark Mayer 15 Sep '10

15 Sep '10

>However this thread appears to have reached the point where not much new >ground is being broken. As the person who started this thread I'll second Phil Jeffrey's comment. I chose to continue my depositions with riding H, and the rcsb agreed to accept the coordinates. Its been great hearing the experts weigh in on this. I've learned a lot, and clearly there is no consensus. As one of the vast majority of crystallographers dependent on all the hard work that program developers undertake to support structural biology, I'm happy to follow advice given by the developers of the various programs I use, and for Phenix the current advice is to deposit with riding H. -- Mark

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Re: [phenixbb] [ccp4bb] Deposition of riding H
by Felix Frolow 15 Sep '10

15 Sep '10

Pavel, Shelxl is working in correct coordinates - fractional... Many things are easier in fractional coordinates. Are you sure that Phenix does not go orthogonal -> fractional -> orthogonal in internal calculations? When fixing of parameter is made in fractional coordinates it does not produce confusion. Shelxl also make fractional -> orthogonal (AKA PDB) which is also correct. Constrain is not transferred there. BTW Shelxl knows symmetry very well and will constrain atoms that occupying symmetry elements. Shortly Shelxl knows crystallography best. When you will see number of lines in Shelxl Fortran code ( do not kill Fortran to early) you will be surprised. There are not so many of them. No graphical user interface yet, but COOT is of great help. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfrolow(a)post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 15, 2010, at 19:11 , Pavel Afonine wrote: > Hi Tim, > >> The pdbe.org, for example allows to upload auxiliary files and in my opinion the >> uploading of the final .ins-file (not the .res-file!) should be made mandatory >> in the case of shelxl refinement. >> >> Since coot has now become utterly convenient even for shelxl refinement, there >> is no reason one should not deposit the .ins-file ([flame] and the PDB-file >> probably for legacy reasons [/flame]). > > I was always wondering but never had a good occasion to ask (my Shelxl knowledge is limited and may be outdated so I apology in advance if my questions are too dummy; also I realize that I'm asking a non-CCP4 question on CCP4bb for which I apology again): > > - how .ins file encodes the information about NCS groups used in refinement (atom selection for NCS groups, restraint weights for different groups, etc? > > - how .ins file encodes the information about TLS (again, atom selections for TLS groups, TLS matrices, etc)? Related, does it have a concept of having TLS and other components to the total atomic displacement parameter (ADP)? > > - If I recall it correctly, to fix (=not refine) a certain parameter (say occupancy or B-factor) in Shelxl you need to add a number 10 to it. Is it true? IMHO, this might lead to confusion if such a file gets deposited to PDB. > > All the best! > Pavel.

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How does phenix.fmodel treat isotropic and anisotropic B?
by zhangh1＠umbc.edu 15 Sep '10

15 Sep '10

Hi, I am doing a phenix.fmodel calculation for a PDB structure containing anisotroipc B. If I understand it correctly, the B factor is composed of both the isotropic B for ATOM line (Biso) and the anisotropic B from ANISOU line (Uani): Fc=sigma ( fi * exp (-Biso*s*s) * exp (-st*Uani*s) * exp (i*r*s) ) Please correct me if the above equation is wrong. I also noticed that in PDB, the Uani (after scaling by 10^-4) is generally much smaller than Biso. So I assume that Biso has a much bigger contribution than Uani, the latter only implying the vibrational anisotropicity. However, I did a test calculation by setting all Bio to 0 whereas keeping Uani unchanged. Due to the above assumption, I expected the results should be very different from the native structure; however, coot told me they were just so close... Maybe I am wrong somewhere... Best Regards, Hailiang

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Sep 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 Sep '10

14 Sep '10

Dear Users, The deadline for Nov/Dec 2010 Collaborative Crystallography proposals will be *Sep 15, 2010. * ---------------------------------------------------------------------------------------- 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: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for Nov/Dec 2010 allocation period, proposals must be submitted by *Sep 15, 2010.* The deadline for CC proposals for the time period Jan/Feb 2010 will be Nov 15, 2010. Regards, Banumathi Sankaran

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Reproducibility of R-factors
by miket＠chem.ucla.edu 14 Sep '10

14 Sep '10

Hi All, I recently used phenix.model_vs_data to evaluate a structure that was refined using Refmac. The R_work and R_free calculated by refmac are 0.18 and 0.20, while model_vs_data calculates them as 0.20 and 0.22. Should I be concerned about this discrepancy? Is it typical for different programs to calculate different values for R-factors using the same data, and if so what is the source of this difference? Seems to me like there shouldn't be much of a difference (at least not 2%). Maybe I'm wrong. Any insight/advice would be appreciated. Thanks, Mike Thompson -- Michael C. Thompson Graduate Student Yeates Lab Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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Deposition of riding H
by Dr. Mark Mayer 14 Sep '10

14 Sep '10

Here's one for the community, which I'll post to both Phenix and CCP4 BBs. Where does the crystallographic community stand on deposition of coordinates with riding hydrogens? Explicit H are required for calculating all atom clash scores with Molprobity, and their use frequently gives better geometry (especially at low resolution). Phenix uses explicit riding H for refinement, and outputs these in the refined PDB. Refmac also uses riding H but does not output H coordinates. While depositing a series of structures refined at 1.4 - 2.75 A with Phenix got the following email from the RCSB, who asked I resupply coordinates without H for two of the structures. Since we can't see H even at 1.4 Å I don't understand why an arbitrary cut off of 1.5 Å was chosen, and also why explicit H atoms used in refinement and geometry validation should be stripped from the file. FROM RCSB We encourage depositors not to use hydrogens in the final PDB file for the low resolution structures (> 1.5 A). Please provide an updated PDB file. We request you to use processed PDB file as a starting point for making any corrections to the coordinates and/or re-refinement. -- Mark

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Re: [phenixbb] Deposition of riding H
by Jeff Headd 14 Sep '10

14 Sep '10

Hi Mark, If hydrogens are used to arrive at a final refined model (whether riding or not) it is essential for the reproducibility of results that the H atom records be included in the deposited model. How B-factors are specified and some final atomic positions (such as rotatable methyl groups) are difficult or impossible to predict once removed, so without their deposition this information would be lost and any published statistics would not be reproducible as published. This point is illustrated in one of our recent papers: Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Cryst. 2010, 43, 669-67. Further, there is no universal standard currently in use that specifies H bond-lengths (some use electron cloud distances, others neutron distances, some a mixture of both), meaning that without inclusion of H atom records (or at least a reference to which library was used) it is very difficult to know where the H atoms were placed. Thanks, Jeff On Tue, Sep 14, 2010 at 10:32 AM, Dr. Mark Mayer <mayerm(a)mail.nih.gov> wrote: > Here's one for the community, which I'll post to both Phenix and CCP4 BBs. > > Where does the crystallographic community stand on deposition of coordinates > with riding hydrogens? > Explicit H are required for calculating all atom clash scores with > Molprobity, and their use frequently gives better geometry (especially at > low resolution). Phenix uses explicit riding H for refinement, and outputs > these in the refined PDB. Refmac also uses riding H but does not output H > coordinates. > > While depositing a series of structures refined at 1.4 - 2.75 A with Phenix > got the following email from the RCSB, who asked I resupply coordinates > without H for two of the structures. Since we can't see H even at 1.4 Å I > don't understand why an arbitrary cut off of 1.5 Å was chosen, and also why > explicit H atoms used in refinement and geometry validation should be > stripped from the file. > > FROM RCSB > > We encourage depositors not to use hydrogens in the final PDB file for > the low resolution structures (> 1.5 A). Please provide an updated PDB > file. We request you to use processed PDB file as a starting point for > making any corrections to the coordinates and/or re-refinement. > -- > > Mark > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

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Re: [phenixbb] autobuild : change reflection file mid-job?
by Thomas C. Terwilliger 14 Sep '10

14 Sep '10

Hi Bryan, Yes, I think to change the reflections file you will have to rerun the job as the reflections are read once in autobuild and propagated from there out. All the best, Tom T >> [it was inevitable..] >> >> if i swap the reflection file mid-job - THAT sounds like catastrophe : >> >> so does autobuild determine the format *only* from the .sca, .mtz affix? >> >> and it looks like reflections are read once at startup, and propagated >> from there out? >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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autobuild : change reflection file mid-job?
by Lepore, Bryan 14 Sep '10

14 Sep '10

[it was inevitable..] if i swap the reflection file mid-job - THAT sounds like catastrophe : so does autobuild determine the format *only* from the .sca, .mtz affix? and it looks like reflections are read once at startup, and propagated from there out? -bryan

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Palestrant, Deborah is out of the office.
by deborah.palestrant＠novartis.com 14 Sep '10

14 Sep '10

I will be out of the office starting 09/13/2010 and will not return until 09/15/2010. I have limited access to email and will respond to your message when I return.

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Re: [phenixbb] autobuild : change .seq mid-job?
by Thomas C. Terwilliger 13 Sep '10

13 Sep '10

Hi Bryan, I think that you can do this, though I have not tried it. You need to replace two files: 1. your original sequence file wherever it is "/wherever/.../myseq.dat 2 a file with the same name "myseq.dat" or whatever, in the directory AutoBuild_run_1_/TEMP0 I would expect all model-building after that to have the new sequence. (Note that runs that are already going as sub-processes will keep their sequences). Now if this is rebuild_in_place, this would not be a good idea. I am assuming it is rebuild_in_place=False, and so it should work... Let me know how it turns out, -Tom T >> i have a long autobuild job going. i'd like to change the .seq files as >> its going - if i keep residue 1 numbered, could this still be a >> catastrophe? >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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