Search results for "look through"

Re: [phenixbb] Autobuild

by Heather L Condurso

Tom, First, I had refine input model before rebuilding turned off. I thought this meant whether it would refine before doing anything else which I didn't really think was necessary but maybe I was wrong. I found an autobuild.eff file and it looks like all that was different in my refinement was that I hadn't selected simulated annealing in autobuild and had in refine. I can run it again with these adjusted parameters to see if I get a better result. As for the maps, the refine maps are definitely better than the autobuild maps but not by all that much. These missing regions are pretty long so fit_loops hasn't been too helpful. I also had the problem that once I ran fit_loops, I would get an error if I tried to put the new pdb file through refinement. Something about missing fields but it had only added a residue here and there across many monomers so I gave up. I guess what would be helpful to me is how best to use my computing time to try to get autobuild to get me the best possible model it can. I can input my refined structure but what parameters will make autobuild focus on extending the model to build in the missing regions instead of continually trying to rebuild a model that is already at a CC=0.90 around the built atoms? Thanks, Heather On Fri, Sep 6, 2013 at 6:32 PM, Terwilliger, Thomas C <terwilliger(a)lanl.gov>wrote: > Hi Heather, > > Hmm... a little hard to tell what the problem is. > > So first: autobuild should have refined this model as one of the first > things it did. Did it get about the same R that you got when refining it > directly with phenix.refine? If no, then have a look at the refinement > .eff files (the autobuild one is in AutoBuild_run_1_/TEMP0 unless that was > cleaned up) and see what is different. > > Next....what happens if you just run phenix.refine to get a map, also > take the map from this autobuild run, and look at them along with your > model. Is one a lot better than the other? > > If you take your best working map and run phenix.fit_loops with this > model...how does that do? > > All the best, > Tom T > > ------------------------------ > *From:* phenixbb-bounces(a)phenix-online.org [ > phenixbb-bounces(a)phenix-online.org] on behalf of Heather L Condurso [ > condurso(a)bc.edu] > *Sent:* Friday, September 06, 2013 3:54 PM > *To:* PHENIX user mailing list > *Subject:* [phenixbb] Autobuild > > I'm a bit confused about what is going on with my autobuild run. I > solved a structure from anomalous data to 2.7A but many loops are missing. > I ran phaser with the current model and native data that extends to 2.4A > and got a solution and started autobuild from there. I used mostly the > default settings and rebuild_in_place=False. After a pretty short time I > realized the run was over and at the bottom of the log I see this: > > Cycle 3 R/Rfree=0.28/0.35 Built=488 Placed=467 > > > AutoBuild_build_cycle AutoBuild Run 162 Fri Sep 6 14:33:39 2013 > > > > Deciding if we should continue... > > Recent R change per cycle: 0.0 > > > Ending these build cycles as the recent change in R per cycle has been > > 0.0 and the required value of change is -0.005 > > and the R is somewhat acceptable at 0.276670644792 > > All done with build cycles in this region > > > AutoBuild_set_up_build AutoBuild Run 162 Fri Sep 6 14:33:40 2013 > > > All omit/non-omit regions completed > > > finished AutoBuild Run 162 Fri Sep 6 14:33:40 2013 > > > Finishing AutoBuild Run 162 > > Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat > > AutoBuild Run 162 > > > Summary of model-building for run 162 Fri Sep 6 14:33:40 2013 > > Files are in the directory: /Users/heather/Desktop/M/AutoBuild_run_162_/ > > > > Starting mtz file: > /Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz > > Sequence file: /Users/heather/Desktop/M/m.pir > > > Best solution on cycle: 2 R/Rfree=0.26/0.33 > > > Summary of output files for Solution 1 from rebuild cycle 2 > > > --- Model (PDB file) --- > > pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb > > > --- Model (CIF file) --- > > cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif > > > --- Refinement log file --- > > log_refine: > /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine > > > --- Model-building log file --- > > log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log > > > --- Model-map correlation log file --- > > log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval > > > --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT > FOFCWT PHFOFCWT --- > > refine_map_coeffs: > /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz > > > --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM > FreeR_flag --- > > refine_data: > /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz > > > --- Density-modified map coefficients FWT PHWT --- > > denmod_map_coeffs: > /Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz > > > > You might consider making one very good model now with: > > > phenix.autobuild \ > > data=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz > \ > > model=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \ > > rebuild_in_place=True \ > > seq_file=/Users/heather/Desktop/M/m.pir > > > My full sequence is 325 amino acids so only about 75% is build in. I am > hoping autobuild can help find at least some of these missing residues. > Why would the change in R be zero? What is meant by "You might consider > making one very good model now with:"? I tried running autobuild with > these new files and rebuild_in_place=true and get the same type of message. > Is this the best that autobuild can do? I also ran the phaser solution > through refinement and can significantly lower the Rs from 0.26/0.33 to > 0.22/0.30. I appreciate any advice on how best to proceed. > > I am using 1.8.2-1472 if that matters. > > > Thanks, > Heather > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

12 years, 5 months

Re: [cctbxbb] some thoughts on cctbx and pip

by Graeme.Winter＠Diamond.ac.uk

Hi Aaron Re: talk about if interest I think it would be very useful to have a roadmap of where this is going, the intentions and how we expect it to play with other cctbx-dependent projects - have I missed this? Having it somewhere e.g. on the wiki would be a big help Thanks Graeme On 17 Aug 2019, at 00:36, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: Hi Luc, thanks. I did recall someone working on this a while back. For conda, there are a couple more things to finish and then we hope to have cctbx available through conda. 1) There is work being done in a branch to make cctbx use boost in standard locations (e.g. the system boost, or a conda boost). That will allow us to use install boost by conda and not build it ourselves. (https://github.com/cctbx/cctbx_project/tree/conda_boost). Also, newer versions of boost are being tested (up through 1.70). (This will also enable python 3.7 support.) 2) We need to work on getting a make install step in place so that we can build the conda package and upload it. 3) We want to split the dependencies up by builder (cctbx, cctbx-lite, dials, phenix, etc.) into meta packages and their associated manifests. I can talk more about this if there is interest. Thanks, -Aaron On Fri, Aug 16, 2019 at 1:48 PM Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: Hi, I did look into that many years ago, and even toyed with building a pip installer. What stopped me is the exact conclusion you reached too: the user would not have the pip experience he expects. You are right that it is a lot of effort but is it worth it? Considering that remark, I don’t think so. Now, Conda was created specifically to go beyond pip pure-python-only support. Since cctbx has garnered support for Conda, the best avenue imho is to go the extra length to have a package on Anaconda.org<http://anaconda.org/>, and then to advertise it hard to every potential user out there. Best wishes, Luc On 16 Aug 2019, at 21:45, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: Hi, to avoid clouding Dorothee's documentation email thread, which I think is a highly useful enterprise, here's some thoughts about putting cctbx into pip. Pip doesn't install non-python dependencies well. I don't think boost is available as a package on pip (at least the package version we use). wxPython4 isn't portable through pip (https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). MPI libraries are system dependent. If cctbx were a pure python package, pip would be fine, but cctbx is not. All that said, we could build a manylinux1 version of cctbx and upload it to PyPi (I'm just learning about this). For a pip package to be portable (which is a requirement for cctbx), it needs to conform to PEP513, the manylinux1 standard (https://www.python.org/dev/peps/pep-0513/). For example, numpy is built according to this standard (see https://pypi.org/project/numpy/#files, where you'll see the manylinux1 wheel). Note, the manylinux1 standard is built with Centos 5.11 which we no longer support. There is also a manylinux2010 standard, which is based on Centos 6 (https://www.python.org/dev/peps/pep-0571/). This is likely a more attainable target (note though by default C++11 is not supported on Centos 6). If we built a manylinuxX version of cctbx and uploaded it to PyPi, the user would need all the non-python dependencies. There's no way to specify these in pip. For example, cctbx requires boost 1.63 or better. The user will need to have it in a place their python can find it, or we could package it ourselves and supply it, similar to how the pip h5py package now comes with an hd5f library, or how the pip numpy package includes an openblas library. We'd have to do the same for any packages we depend on that aren't on pip using the manylinux standards, such as wxPython4. Further, we need to think about how dials and other cctbx-based packages interact. If pip install cctbx is set up, how does pip install dials work, such that any dials shared libraries can find the cctbx libraries? Can shared libraries from one pip package link against libraries in another pip package? Would each package need to supply its own boost? Possibly this is well understood in the pip field, but not by me :) Finally, there's the option of providing a source pip package. This would require the full compiler toolchain for any given platform (macOS, linux, windows). These are likely available for developers, but not for general users. Anyway, these are some of the obstacles. Not saying it isn't possible, it's just a lot of effort. Thanks, -Aaron _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

6 years, 5 months

Re: [phenixbb] Phenix.refine on coordinate-optimised structures

by Pavel Afonine

Hi Joey, your question can accommodate multiple interpretations and thus multiple answers as result. Dorothee's was one. Here is another one. First off, what's the goal? Do you want to get a better model of your crystal structure or lowest possible R- factors? Besides, depending on the data quality (resolution, completeness, etc) you'd need to choose a good parameterization of ADPs (individual anisotropic for all but H if resolution is sub-angstrom, isotropic plus TLS at medium to low, etc). Then also depending on data quality, you might be able to observe and model static (space) disorder using alternative locations. If that's the case you will want to refine occupancy factors of such partially occupied sites. If the resolution is not low, are you sure you placed all convincing water? If not, you may want to let phenix.refine to do this for you automatically. And then towards the end make sure to check them in Coot. There is a lot of choices and possibilities in-between, as one can imagine. If you have more questions or need more help, we can possibly do it more efficiently by chatting over Zoom, let me know and I will set up a call. Pavel On 8/7/20 19:22, Dorothee Liebschner wrote: > Hi, > > The strategy depends also on the resolution of the data, so if you > could tell us that, we can give suggestions. Also the type of data, I > guess X-ray diffraction? > > Out of curiosity, how do model quality metrics look like (clashscore, > ramachandran, etc) at this point? If you keep coordinates fixed, they > won't improve in refinement. > > Best wishes, > > Dorothee > > On Fri, Aug 7, 2020 at 2:52 PM Joey Farrell <jpfarrell(a)uchicago.edu > <mailto:[email protected]>> wrote: > > Hello, > > I am trying to design a set of input parameters that I will be > passing through the phenix.refine function. The structures > > that I am working with have already had their X,Y, and Z > orthogonal Å coordinates optimised via separate protocol. > > I am looking for advice on which strategies and parameter values > to use with phenix.refine to improve the crystallographic R-factors > > of such structures while preserving their earlier optimisation in > real space. > > I have been having some success using “strategy = > tls+individual_adp+occupancies” (where tls = “chain A”, tls = > “chain B”, etc.) as > > well as adjusting the wxu_scale value until R-work and R-free are > minimised. Are there other strategies or phenix.refine > functionalities > > that may also prove helpful with this end in mind? I believe there > may be ways to further improve R-work and R-free with this software > > that I am not yet aware of. > > Thank you for your help! > > Best, > > Joey > > _______________________________________________ > 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]> > > > > -- > Project Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org <https://phenix-online.org/> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

5 years, 6 months

Re: [phenixbb] High B-factors after Phenix restrained refinement -- peptide building

by Tom Terwilliger

Hi Dialing, You should be able to build the peptide in either of 2 ways: 1. Cut out the density for the peptide with phenix.cut_out_density and build into cutout.mtz with phenix.build_one_model, supplying the sequence of the peptide, and not refining the model. This will just build the peptide. Then you can translate the model that is built back using phenix.cut_out_density. 2. Alternatively, you can put your data file and your map coefficients, and complete sequence file including the peptide into phenix.autobuild and it should try to build the peptide in addition to the rest of your model. You can also include your working model to speed it up. All the best, Tom T On Dec 16, 2011, at 1:04 AM, Dialing Pretty wrote: > Hi Nat, > > I have a protein-peptide complex crystal, and I got the 3-D structure of the protein part in the complex by rigid body refinement with isomophous crystal crystal structure as the search model, and I got the peptide structure by Coot peptide building, then I refine the whole protein-peptide complex. > > Will you please tell me which Phenix program can be used to build the peptide as I mentioned in the situation above? I want to get a Coot alternative for the peptide building. > > I am looking forward to getting your reply. > > Cheers, > > Dialing > > From: Nathaniel Echols <nechols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Sent: Friday, 16 December 2011 3:31 PM > Subject: Re: [phenixbb] High B-factors after Phenix restrained refinement > > On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13(a)queensu.ca> wrote: > > I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of > > rigidbody refinement with Phenix Refine I proceeded to restrained > > refinement. The R/Rfree from the refinement decreased nicely as expected but > > the B average is at ~100 (using Group B factor refinement option). I took > > the same model and mtz through Refmac and the B average is about ~40. Has > > anyone experienced this before? I am almost positive it maybe a setting > > issue in Phenix Refine that i should be looking at to get the B factors to > > refine correctly. > > How are you calculating the average B? Refmac prints "residual" > B-factors in the B column of ATOM records - these do not include the > contribution from TLS and Ucryst (an overall B-factor for the entire > crystal). In Phenix, the ATOM records always have the total isotropic > B-factor, and this will always be higher than the equivalent in > Refmac. So it's quite likely that both programs are correct, they're > just reporting very different things. (And for what it's worth, a > mean B-factor of 100 is totally normal at 3.3A resolution.) > > -Nat > _______________________________________________ > 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 Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

14 years, 1 month

[phenixbb] Re: inconsistency of Molprobity results between RealSpaceRefine and ValidationCryoEM

by Kevin M Jude

Thanks Nigel! From: Nigel Moriarty <nwmoriarty(a)lbl.gov> Date: Thursday, September 25, 2025 at 11:37 AM To: Kevin M Jude <kjude(a)stanford.edu> Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] inconsistency of Molprobity results between RealSpaceRefine and ValidationCryoEM Kevin All of this arises from a simple miscommunication. The default restraints for refinement in Phenix is the Conformation Dependent Library. It basically changes the ideal values for the protein backbone based on the phi/psi.angles. While Moprobity in Phenix uses the same libraries, it appears the communication has broken so it's not using the CDL but rather the single value restraints. As a result, .geo file (which is the gold standard) is correct and the Molprobity is slightly wrong. As a power user (you look in the .geo file), I suggest you check the .geo file until I correct this. Cheers Nigel --- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov<http://CCI.LBL.gov> ORCID : orcid.org/0000-0001-8857-9464<https://orcid.org/0000-0001-8857-9464> On Tue, Sep 23, 2025 at 12:20 PM Kevin M Jude <kjude(a)stanford.edu<mailto:[email protected]>> wrote: I notice inconsistencies in the Molprobity results reported for the same structure from RealSpaceRefine and from ValidationCryoEM. As an example, for bond angle restraints, RSR reports that there are four >4sigma outliers (but does not list the outliers), while ValidationCryoEM reports 0. RSR CryoEMValidation Number of restraints 13228 13228 RMS(deviation) 0.509 0.51 Max. deviation 9.997 9.998 Min. deviation 0 0 Number of outliers > 4sigma 4 0 Browsing through the .geo file, I don’t see any >4 sigma deviations among the highest residual angles, so I think this is an error. I also see small discrepancies in Ramachandran favored, rotamer outliers, and clash score which seem to come down to minuscule differences in measurements at the margins. This is for Phenix 1.21.2-5419. Happy to share files offline. -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org<mailto:[email protected]> To unsubscribe send an email to phenixbb-leave(a)phenix-online.org<mailto:[email protected]> Unsubscribe: phenixbb-leave@%(host_name)s

4 months, 2 weeks

[phenixbb] Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)

by Bjørn Panyella Pedersen

Dear colleagues, We have an open postdoc position. 3 days left before deadline. Come joint us. Great working environment, World-class science. Good work/life balance. /Bjørn ----------------------------------- Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. online posting: https://tinyurl.com/MBGpostdoc We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021.

4 years, 11 months

Re: [phenixbb] Coot mutation of Asp residue to isoAsp residue

by Zhijie Li

Hi Xiao, IsoAsp is essentially an L-Asp linked with next aa through its side chain (beta) carboxyl. So the mutation button won’t help you. You need to build in a new L-ASP, which is treated as a covalently linked ligand (HETATM records), instead of a standard residue (ATOM records) of the protein chain. A practical method might be: 1) delete the original Asp, 2) import a free L-Asp using “get monomer”, delete its hydrogen atoms and drag it into the density, delete one oxygen atom on the beta-carboxyl and change the residue’s numbering and chain id to fit it into the sequence, 3) edit the PDB, if necessary, to turn the ASP into a ligand (a HETATM record inside the chain). For step 3, you may need to rename the ASP to something else (IAS was used for isoASP in older pdb, so I would go with IAS ) so that coot won’t try to make a regular peptide bond using its main chain carboxyl during real space refinement. Of course you will need to make a cif file for the “new” compound too. I guess you can make a copy of ASP.cif from the monomer library and change everything in it to IAS. I think if you have placed the IAS to the right location and its ends are in bonding distance with the neighbouring aa residues you may not need to do anything for refmac. For phenix.refine you will need to add a bond description to the .edit file for each linkage the IAS makes to the neighboring aas. You may take a look at the structure 1AT6 and its PDB file. The residue IAS 101 is an example of isoASP. Note that the IAS atoms are HETATM in the chain and there are two LINK records in the header to indicate its linkage to neighbouring aas (LINK records are normally not generated or needed during refinement using refmac or phenix.refine). Zhijie From: Xiao Lei Sent: Monday, August 17, 2015 6:50 PM To: PHENIX user mailing list Subject: [phenixbb] Coot mutation of Asp residue to isoAsp residue 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 -------------------------------------------------------------------------------- _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

10 years, 5 months

Re: [phenixbb] Phaser SAD question

by Randy J. Read

Dear Peter, I'm interested in your observation that you get better signal from an anomalous difference map computed with density-modified phases than you get with an LLG map using the MR model. Presumably the density modification just started from the model phases as well? We've never tried that, so we'll have to look into that. Unfortunately, you can't at the moment start the LLG completion with a "model" specified through structure factors, though this is on our to-do list. With the MR+SAD option, because it is iterative, there are sites found in subsequent cycles (where the information from some of the anomalous scatterers has become available) and you end up with a set of reliable sites that can be significantly larger than the set obtained from the first LLG map. Does your anomalous difference Fourier with density modified phases give you a larger apparently reliable substructure than the iterative completion? You could use phenix.emma to compare the two substructures and see how much they have in common. You can indeed give Phaser the set of sites that you got from the anomalous difference map. One way to choose the cutoff would be to see how deep the deepest hole is (i.e. how many standard deviations the map goes in the negative direction), and choose a larger number in the positive direction. Or you could just use the peaks above 6-7 sigma. I'd be interested in hearing how you get on with this approach, off-line if you prefer. Good luck and Happy Christmas! Randy Read On Dec 24 2009, Peter Grey wrote: >Dear Phenix Experts, > >I use the SAD+MR option in Phenix. The ASU is huge and the number of >scatterres is in the few hundreds range. I try to minimize the number of >runs of Phaser SAD+MR since they take long time on my computer and would >appreciate your insight regarding the following : > > - I noticed that I get much higher signal and much larger number of sites > if I use density modified phases to calculate the anomalous difference > map. Is it possible to input these phases instead of the model to Phaser > ? > > - If not, do you recommend providing Phaser with the list of sites found > in this difference anomalous map. Should such a list include only the > sites you can be sure of (say above 7 sigma) or all possible sites (say > above 5 sigma) ? > > - Should I use the (peak height)/(sigma of map) as the first estimate of > occupancy ? if so do I have to normalize it (strongest site has occupancy > of 1) or can I leave the height/sigma values as they are ? > > >Many thanks, > >Peter. >

16 years, 1 month

Re: [phenixbb] phenix gui freezes

by hari jayaram

Hello John, I have seen exactly this problem after running phenix.validate . Not only does the GUI freeze , but it seems to take the windowing system down with it. The window manager gets unresponsive. Remote shelling into the system was possible , but there was no active python process that I could kill to get control back. In the end I had to restart-X to log back in loosing what I was doing in other windows. I have seen this at-least 2 or 3 times on two 64 bit ubuntu hardy running machines with phenix 1.6.289. Both boxes have 4 to 8 cores and 8 to 16 GB of ram. On mac OSX running 10.6.2 , on a core duo , so probably everything is running in 32 bit mode . Things are relatively very stable. Other than a few times where phenix said it was launching coot and just sat there, I have been using it without incident, so much so I have switched to using my slow laptop because of something I thought was wrong at my end. Looking forward to troubleshooting instructions . Thanks Hari On Thu, Mar 11, 2010 at 7:28 AM, John Berrisford <jmb(a)mrc-mbu.cam.ac.uk>wrote: > Dear All > > A little while ago I posted a message about the GUI freezing on linux > systems, either run remotely (centos) or locally (ubuntu system). I never > received a solution and I'm still having this problem despite upgrading to > version 1.6. > > On my ubuntu system the GUI seems to freeze either when the screen saver > comes on (set to turn the screen off) or I switch desktop - although not > everytime I do this. > The freezing GUI means that I have to force quit phenix after every > refinement run (I haven't tried other tasks) and that the freeR is not > reported to the GUI (not a major problem). Thankfully in version 1.6 the > configuration and results for each refinement run are recorded and I can > retrieve this information by loading a job through job history - a big > improvement over version 1.5. > > Anyone else having this problem and does anyone know a solution? > > Thanks > > John > > -- > John Berrisford > > Medical Research Council > Mitochondrial Biology Unit > Wellcome Trust / MRC Building > Hills Road > Cambridge > CB2 0XY > WEB: www.mrc-mbu.cam.ac.uk > TEL: +44 (01223) 252918 > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

15 years, 11 months

Re: [phenixbb] calculate Fc for the whole unit cell from a Fc of a single symmetric unit.

by zhangh1＠umbc.edu

Sorry I haven't got a chance to check my email recently. Yes, I meant expansion to P1. The thing is cctbx relies on the atomic model I think, but I only have model Fc available. Hailiang > I suspect what Hailang means is expansion into P1. > > I am sure this can be accomplished through some either existing or > easily coded cctbx tool. However, when I looked into a different task > recently that included P1 expansion as a step, I learned that SFTOOLs > can do this, albeit there was a bug there which caused trouble in > certain space groups (may be fixed by now so check if there is an > update). > > Hailang - if P1 expansion is what you need, I could share my own code as > well, let me know if that is something you want to try. > > Cheers, > > Ed. > > On Fri, 2011-07-08 at 14:44 -0700, Ralf Grosse-Kunstleve wrote: >> Did you get responses already? >> If not, could you explain your situation some more? >> We have algorithms that do the symmetry summation in reciprocal space. >> The input is a list of Fc in P1, based on the unit cell of the >> crystal. Is that what you have? >> Ralf >> >> On Wed, Jul 6, 2011 at 1:38 PM, <zhangh1(a)umbc.edu> wrote: >> Hi, >> >> I am wondering if I only have structure factors calculated >> from a single >> symmetric unit, is there any phenix utility which can >> calculate the >> structure factor for the whole unit cell given the symmetric >> operation or >> space group and crystal parameters? Note I don't have an >> atomic model and >> only have Fc. >> >> Thanks! >> >> Hailiang >> >> _______________________________________________ >> 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 > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

14 years, 7 months

Search results for query "look through"