Search results for "look through"

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

4 years, 10 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

13 years, 6 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

9 years, 10 months

[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, 4 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. >

15 years, 6 months

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, 3 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 > >

13 years, 11 months

Re: [cctbxbb] bz2 support on Ubuntu

by David Waterman

Thanks, I did this, currently churning through the base build. Checking the latest Python_install_log I see hopeful-looking things like "building 'bz2' extension". I can only assume I've installed a few more packages since I did the original build. Will report back if there are any new problems, otherwise I think this might be fixed :) Cheers -- David On 8 June 2017 at 13:08, <markus.gerstel(a)diamond.ac.uk> wrote: > Hi David, > > > > You’ll have to look into the python setup.py script to figure that one out. > > https://github.com/python/cpython/blob/2.7/setup.py#L1463 > > Python expects the library to be in some fixed place, and If it’s not > there support is disabled. > > > > Regarding your rebuild question. I would keep the base_tmp directory, you > then don’t have to redownload and recompile everything. Stuff should still > recompile if anything changed, and if versions are updated etc. > > If you definitely want to recompile everything you can still save time by > running this **in the base_tmp directory**: > > find . -maxdepth 1 -mindepth 1 -type d -print0 | xargs -0 -n 1 -- rm > –rf > > This removes all subdirectories, leaving the files intact, so you don’t > have to redownload everything. > > > > I would expect the steps *export, rm -rf base, python bootstrap.py base, > cd build, setpaths, libtbx.configure, make* to suffice. > > > > -Markus > > > > *From:* cctbxbb-bounces(a)phenix-online.org [mailto:cctbxbb-bounces@ > phenix-online.org] *On Behalf Of *David Waterman > *Sent:* 08 June 2017 12:58 > *To:* cctbx mailing list <cctbxbb(a)phenix-online.org> > *Subject:* [cctbxbb] bz2 support on Ubuntu > > > > Hi folks, > > > > My bootstrap build of cctbx/DIALS on Ubuntu 16.04.2 LTS produces a base > Python that does not have bz2 support. This is despite the fact that the > package "libbz2-dev is already the newest version (1.0.6-8)." Looking in > Python_install_log I see > > > > Python build finished, but the necessary bits to build these modules were > not found: > > _bsddb _curses _curses_panel > > _sqlite3 _tkinter bsddb185 > > bz2 dbm dl > > gdbm imageop readline > > sunaudiodev > > > > Has anyone got any ideas? Anyone done a boostrap build on Ubuntu where bz2 > can be imported in Python? > > > > Also, what's the procedure to rebuild from base, recovering all the > currently configured modules? My guess is that something like this would do > it, but is there a better way? > > > > export MYMODULES=$(libtbx.list_modules | tr '\n' ' ') > > rm -rf base_tmp/ base/ build/ > > python bootstrap.py --builder=dials base > > python bootstrap.py --builder=dials build > > cd build > > source setpaths.sh > > libtbx.configure $MYMODULES > > make > > > > Cheers > > > -- David > > > > -- > > 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 > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > >

8 years

Re: [phenixbb] red blobs (Andrea Smith)

by Pavel Afonine

Hi Andrea, here is what you can do today.. phenix.mosaic model.pdb data.mtz (yes, command line only, so far). This will take a minute or less (or more if the model is very large) and create model_mosaic.mtz file that contains the following Fourier map coefficients for mFo-DFc and 2mFo-DFc kind of maps: mFo-DFc_whole mFo-DFc_main mFo-DFc_mosaic 2mFo-DFc_whole 2mFo-DFc_main 2mFo-DFc_mosaic (you can see the MTZ file content by using this command: phenix.mtz.dump model_mosaic.mtz) The suffixes 'whole', 'main' and 'mosaic' refer to the types of masks used in calculation of each map and are explained in the paper: https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909 To reiterate: 'whole' refers to the standard default bulk-solvent mask; 'main' refers to the largest part of the standard default bulk-solvent mask (small mask droplets inside protein region are removed); 'mosaic' refers to the mosaic mask, which is essentially the 'main' mask plus only those smaller masks that contain measurable amounts of the bulk-solvent (the rest, empty ones, that are responsible for 'red blobs' are removed). Next, you load these maps and your atomic model into Coot and inspect. Artifacts such as 'red blobs' you reported earlier should be absent in 'mFo-DFc_mosaic' map. This may lead to improvement of corresponding '2mFo-DFc_mosaic' map. Now, as you can see, this is separate from refinement. Here is what you should be able to do tomorrow.. Today I will add a parameter to phenix.refine (main.mosaic=True/False), which means if you get and install tomorrow's nightly build of Phenix (dev-5285 and up) the mosaic maps, both mFo-DFc_main and 2mFo-DFc_mosaic, will be present in the MTZ file created by phenix.refine (which is available in both CL and GUI). Let me know if you have any questions! Good luck! Pavel On 3/28/24 06:24, Andrea Smith wrote: > Hi all, > > can anyone please tell me how to use the mosaic model? I went through > the phenix documentation and didn't find anything about how to use it. > > Thank you, > Andrea > > > > On Friday, March 15, 2024 22:14 CET, "Andrea Smith" > <andrea.smith(a)uochb.cas.cz> wrote: >> Hi, >> >> I went through the paper quickly during the day thinking I will have >> a thorough look at home only to realize I don't have acces to it. >> >> From the quick look it seemed that my biological background will not >> be enough to understand all of it, but I remember that it said at the >> end that the mosaic model is implemented in phenix. However, I don't >> know where. I went through the parameters in GUI and didn't find >> anything that seemed to fit the description. >> >> Could you please explain what setting I need to use in the refinement? >> >> Thank you, best, >> Andrea >> >> On Friday, March 15, 2024 16:16 CET, Pavel Afonine <pafonine(a)lbl.gov> >> wrote: >>> Hi All, >>> >>> The explanation of the reason for these blobs and the solution is both >>> detailed in depth in this paper: >>> >>> https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909 >>> >>> Quick facts are: >>> >>> - These blobs are artifacts of bulk-solvent modeling. >>> - You can efficiently deal with them in Phenix. >>> - In some cases (which I witnessed myself), it is important to deal with >>> them for map improvements elsewhere (for example, in regions of >>> interest, such as ligands). >>> >>> Let me know if you have any questions! >>> >>> All the best, >>> Pavel >>> >>> >>> On 3/15/24 07:39, Mitchell D. Miller wrote: >>> > Hi Andrea, >>> > >>> > You can also put a few zero occupancy atoms in the negative >>> > density to force phenix.refine to exclude the region >>> > from the bulk solvent mask. >>> > >>> > (You may also need to set >>> > refinement.mask.ignore_zero_occupancy_atoms = False >>> > so that the zero occupancy atoms are included in the mask) >>> > >>> > Regards, >>> > Mitch >>> > >>> > >>> > >>> > Quoting Kay Diederichs <kay.diederichs(a)uni-konstanz.de>: >>> > >>> >> Hi Andrea, >>> >> >>> >> hmm, did phenix.refine actually use optimize_mask=true ? >>> >> >>> >> If you compare the logfiles of phenix.refine (for the default run >>> >> with opimize_mask=false, and the new run with optimize_mask=true) >>> >> side-by-side with xxdiff or vimdiff (yes this needs to be run from a >>> >> command-line) then there should be a difference. >>> >> >>> >> Making peace with the red blobs is somewhat unsatisfactory from a >>> >> technical viewpoint, but probably not relevant from a biological one. >>> >> >>> >> I'd guess that the authors of >>> >> https://journals.iucr.org/a/issues/2024/02/00/pl5035/index.html would >>> >> be interested to look at your case ... >>> >> >>> >> Best wishes, >>> >> Kay >>> >> >>> >> >>> >> Am 15.03.24 um 08:27 schrieb Andrea Smith: >>> >>> Hi Kay, >>> >>> >>> >>> I tried the mask optimization and there is no change in how the >>> >>> final map looks like. >>> >>> >>> >>> Should I just make peace with it? >>> >>> >>> >>> Best, >>> >>> Andrea >>> >>> >>> >>> On Thursday, March 14, 2024 23:11 CET, Kay Diederichs >>> >>> <kay.diederichs(a)uni-konstanz.de> wrote: >>> >>>> Hi Andrea, >>> >>>> >>> >>>> in your case, phenix.refine seems to fill bulk solvent into volumes >>> >>>> that >>> >>>> are not actually filled by solvent. >>> >>>> It might help to optimize the mask, see >>> >>>> >>> https://phenix-online.org/documentation/reference/refinement.html#bulk-solv… >>> >>>> >>> >>>> "6. Mask parameters". >>> >>>> >>> >>>> Best, >>> >>>> Kay >>> >>>> -- >>> >>>> Kay Diederichs http://strucbio.biologie.uni-konstanz.de >>> >>>> email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 >>> >>>> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 >>> Konstanz >>> >>>> >>> >>>> This e-mail is digitally signed. If your e-mail client does not >>> >>>> have the >>> >>>> necessary capabilities, just ignore the attached signature >>> >>>> "smime.p7s". >>> >>>> _______________________________________________ >>> >>>> phenixbb mailing list >>> >>>> phenixbb(a)phenix-online.org >>> >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>>> Unsubscribe: phenixbb-leave(a)phenix-online.org >>> >> >>> >> -- >>> >> Kay Diederichs http://strucbio.biologie.uni-konstanz.de >>> >> email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 >>> 4049 >>> >> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 >>> Konstanz >>> >> >>> >> This e-mail is digitally signed. If your e-mail client does not >>> have the >>> >> necessary capabilities, just ignore the attached signature >>> "smime.p7s". >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > phenixbb mailing list >>> > phenixbb(a)phenix-online.org >>> > http://phenix-online.org/mailman/listinfo/phenixbb >>> > Unsubscribe: phenixbb-leave(a)phenix-online.org

1 year, 3 months

Re: [phenixbb] Sharing a Phenix project via Dropbox

by Sebastiano Pasqualato

Hi Derek, I didn't have this kind of problem, and could easily install Google Drive by defining " /Google Drive " as default path. Maybe I created the directory beforehand, and then selected it while installing Google Drive, but honestly I don't remember. I think I can easily create a directory in / Best, Sebastiano > On 19/mag/2014, at 09:10, Derek Logan <derek.logan(a)biochemistry.lu.se> wrote: > > Hi Sebastian, > > Instinctively this sounded like the easiest solution of all those suggested. However when I try to do this for Dropbox through the Preferences it says "Can't create a Dropbox folder in the requested location", so it looks like it's hard-wired to use locations in my home directory. Has anyone else succeeded in moving a Dropbox folder to / ? It doesn't work for Google Drive either - it says the location is not writeable. I have administrator privileges on my Mac. Do I have to change permissions on / manually? > > Best wishes > Derek > >> On 16 May 2014, at 15:56, Sebastiano Pasqualato <sebastiano.pasqualato(a)GMAIL.COM> wrote: >> >> >> Hi Derek, >> >> the way I work with Google Drive is installing its folder (you can choose where to put it) directly into / (that is /Google Drive - unfortunately you cannot change its name and have to live with the space). >> If you and your collaborators all do that in your Macs, Phenix will find always the same path and work with no hassles. >> >> HTH, >> ciao, >> Sebastiano >> >> >>> On 16 May 2014, at 15:49, Derek Logan <derek.logan(a)biochemistry.lu.se> wrote: >>> >>> Hi Nat, >>> >>> Thanks for your reply. However could it be that it works for you because you have the same user name on each Mac, so that your home directory is always /Users/nat (or whatever)?. Thus the hard-wiring of full paths into the Phenix files would not be a problem for you? In our case there are at least 3 users with different names (in different countries!) who might want to access the same project. Otherwise I would think that Google Drive should behave just like Dropbox? >>> >>> I'm sure Jürgen's idea would work but it would be nice if possible to avoid creating a separate common user. I don't remember having done this since we had a "data processing account" on our microVAXes for integrating film data at Oxford in the early 1990s :-) Any other ideas? >>> >>> /Derek >>> >>>> On 16 May 2014, at 14:47, nathanielclar5 . <nathanielclar5(a)GMAIL.COM> wrote: >>>> >>>> Do you have the dropbox app on every computer, so that the files can be accessed through finder? I use Google Drive to sync phenix project directories between my 3 Macs, and usually it works perfectly. If I run a job on one computer, I can open a phenix gui on another, and it will show the intact job history, including jobs run on a different computer. Sometimes I get a error that 'this is not a valid phenix project directory' when I attempt to import a job folder created on a different computer. When that happens, I just make a new sub-folder within it, make that the new project folder, and move on...so maybe I'm running into the same problem as you and ignoring it. Usually it's problem free however. >>>> >>>> Nat >>>> >>>> >>>> >>>>> On Fri, May 16, 2014 at 5:03 AM, Derek Logan <derek.logan(a)biochemistry.lu.se> wrote: >>>>> Hi, >>>>> >>>>> Has anyone ever successfully shared a Phenix project through Dropbox? I tried Googling for info on this without success. I have tried sharing but it doesn't work because Phenix uses the full path to the project, e.g. /Users/derek/Dropbox/project rather than ~/Dropbox/project, which would work for all users sharing the project. I tried manually editing project.phil in the .phenix directory, but at the end of a run of phenix.refine it was overwritten again. Is there somewhere (job_history.phil?) I can replace /Users/derek with ~ so that it the change will be permanent? I think that this would be a very effective way for me to set up a project being run by one of my PhD students involving people from at least 3 labs that could have opinions on the refinement! >>>>> >>>>> /Derek >>>>> >>>>> P.S. We are all using Macs. >>>>> >>>>> _______________________________________________ >>>>> 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 >> >> -- >> Sebastiano Pasqualato, PhD >> Crystallography Unit >> Department of Experimental Oncology >> European Institute of Oncology >> IFOM-IEO Campus >> via Adamello, 16 >> 20139 - Milano >> Italy >> >> tel +39 02 9437 5167 >> fax +39 02 9437 5990 >> web http://is.gd/IEO_XtalUnit >

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