Search results for "look through"

Re: [phenixbb] Joint X-ray / neutron refinement

by Kristoffer Lundgren

Hello phenixbb, When trying to do joint refinement in phenix.refine 1.21-5207 using the suggested joint_xn.eff file found at https://phenix-online.org/documentation/reference/refinement.html#neutron-a… as a template I get some error messages (running phenix.refine from the command line): Unrecognized PHIL parameters: ----------------------------- xray.refinement.refine.strategy (file "joint_xn.eff", line 33) xray.refinement.main.simulated_annealing (file "joint_xn.eff", line 36) xray.refinement.main.ordered_solvent (file "joint_xn.eff", line 37) xray.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 38) neutron.refinement.refine.strategy (file "joint_xn.eff", line 45) neutron.refinement.main.simulated_annealing (file "joint_xn.eff", line 48) neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line 49) neutron.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 50) Can you please advice on how to proceed? It looks like the options supplied are not recognized at all by phenix.refine. Best regards Kristoffer From: <phenixbb-bounces(a)phenix-online.org> on behalf of Derek Logan <derek.logan(a)biochemistry.lu.se> Date: Monday, 22 January 2024 at 09:39 To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Ulf Ryde <ulf.ryde(a)compchem.lu.se>, "esko.oksanen_ess.eu" <esko.oksanen(a)ess.eu> Subject: ***SPAM*** [phenixbb] Joint X-ray / neutron refinement Hi phenixbb, I'm trying to understand the current status of joint X-ray/neutron refinement in phenix.refine. The announcement of the latest release mentions a change in the algorithm as described in the recent publication. In the documentation: Structure refinement in PHENIX<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> phenix-online.org<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> [AURqZhI53yp3gAAAABJRU5ErkJggg==]<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> it's described how you can run joint refinement using a parameter file. Does this mean that it is *only* possible in this way and not through the GUI? The GUI was very useful in the past as it automatically opened Coot with the maps for both X-rays and neutrons, and the refinement statistics for both were displayed in the GUI. As far as I can see joint refinement via the GUI last worked in version 1.19.2-4148 from 2021. Best regards Derek

1 year, 4 months

Re: [phenixbb] TLS makes my r-factors shoot through the roof

by Pavel Afonine

Hi Morten, sorry for the trouble once again. Hm.. this seems like a case where I need the data to be able to reproduce the problem myself and fix it. Could you please send me all inputs so I can do it? I'll need data and model, and tell what exactly did you do, or just .eff file. Please send files off-list: directly to my email. I'm traveling right now so I might not be able to look right away, though I will do my best to address this problem asap (once I get the files). Thanks, Pavel On 5/29/12 7:39 AM, Morten Groftehauge wrote: > I like the new version but it does not seem to have helped much. > Before it shot up by 3%, this time by 2.5%. > > > > On 29 May 2012 12:23, Pavel Afonine <pafonine(a)lbl.gov > <mailto:[email protected]>> wrote: > > Hi Morten, > > I'm sorry about the problem. > > Are you using the latest Phenix? There was a bug in > phenix.refine that I fixed a while ago, and the bug behavior > was very similar to what I see happening in your case. > > Could you please try the latest version and see if the problem > goes away? Please let me know. > > Pavel > > > On 5/29/12 3:56 AM, Morten Groftehauge wrote: > > Hi Phenixbb, > > 3.2A data, 110 Wilson B, I41, twinned. Imperfect inverted > repeat dsDNA with 4 protein monomers, NCS not used in > refinement. > If I don't include TLS I get a nice stable R-factor while > RMS goes down. > If I include TLS (whether as one group per chain or as > chosen by Phenix) this happens: > > > > Density disappears around some of the DNA bases as an > obvious difference. If I run Refmac with TLS it just never > finishes. > > While I could just refine without TLS this does make me > worried that there is something wrong with my model or my > data (besides being terrible). > > Cheers, > Morten >

13 years, 1 month

[phenixbb] GRC on Diffraction Methods: end July 2014

by Anastassis Perrakis

Dear all, We are getting closer and closer to the 2014 edition of my favorite Gordon Research Conference (https://www.grc.org/programs.aspx?year=2014&program=diffrac ) on Diffraction Methods in Structural Biology "Faster, Smaller, Better: Novel Technologies for Diffraction Experiments in Molecular Biology and Drug Discovery" , which this year will also feature before it starts the Gordon Research Seminars "Towards Integrative Structural Biology" (https://www.grc.org/programs.aspx?year=2014&program=grs_diff), targeting young scientists! Thanks to INSTRUCT (http://www.structuralbiology.eu) there will be four fellowships for young European researchers coming originally from an INSTRUCT member country or working in an INSTRUCT member country (http://www.structuralbiology.eu/resources/countries). Each fellowship will amount to 750 Euro, covering registration for both the GRC and the GRS, and all local expenses. It is a condition that you have to attend both the GRS and the GRC and submit a poster for both events. If you want to apply for such a fellowship, please send me an email reply (maintain the subject line please), including a single-page PDF file, a very short CV, an equally short abstract of your research, and a motivation statement explaining why you think this event is crucial for your career. Please include the email of your direct supervisor in the end of this letter, and a statement that she/he has agreed to cover the travel expenses for you to attend, if your fellowship application comes through. The deadline for receiving these letters is Wednesday 16 April at 12:CET (yes, thats less than a week from now! get writing!). The letters will be reviewed by an INSTRUCT panel, and the chosen four candidates will get a notification by the 8th of May! And, of course, I do take this opportunity to remind to everyone that the (almost) final program is on-line, we have an absolutely amazing group of speakers lined up, and the available places are filling up fast! So please remember to register on time! Looking forward to see you all at Bates College for what I trust you can make an exciting and memorable meeting! Best regards, Tassos PS If the file is not PDF, if its more than one page, if the characters you use are too small to read, etc etc, don't be too surprised if you do not get the travel fellowship award! Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

11 years, 2 months

Re: [cctbxbb] cif parser & ccp4 mon_lib incompatibility

by James Stroud

On Apr 10, 2013, at 11:46 PM, Nathaniel Echols wrote: > On Wed, Apr 10, 2013 at 3:58 PM, James Stroud <xtald00d(a)gmail.com> wrote: > Thanks for tracking this down. The installer I used was double-clickable black-box "foolproof" no-thinking point-and-click: ccp4-6.3.0.2-arp.dmg > > Well, for what it's worth, I just nuked my installation and downloaded the same thing minus ARP/wARP, and now I have the same header as you reported. Will continue digging tomorrow, but I suspect that either the updates will eventually fix the problem, or something has changed in the installer (although using an older version of the monomer library seems like a weird choice). I actually iterated through updates until I there were no more. I think I over-shot the sweet spot, though: chernev 13% setenv MMTBX_CCP4_MONOMER_LIB /usr/local/ccp4-6.3.0/lib/data/monomers/ chernev 14% cctbx.python ./tst_sa.py Traceback (most recent call last): File "./tst_sa.py", line 267, in <module> exercise_1() File "./tst_sa.py", line 122, in exercise_1 pi = get_pdb_inputs(pdb_str=pdb_str_1) File "./tst_sa.py", line 108, in get_pdb_inputs rama_potential=None, log = None) File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object mon_lib_srv = mmtbx.monomer_library.server.server() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__ geostd_list_cif_obj = geostd_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON > Also note that you can download the monomer library as a separate package from Garib Murshudov's home page: > > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ [ click "software" --> "Refmac5" --> "Dictionary of ligands" ] > > and this looks like it is formatted correctly. I'll give this one a try. James > > -Nat

12 years, 2 months

Re: [phenixbb] Completeness issue by phenix

by Engin Ozkan

I believe the default in scalepack2mtz in ccp4i is Anomalous on. That clearly explains your observations. You should consider Ralf's point that the data might have been converted to mtz with separate Friedel pairs, even though it was scaled initially as not. Engin ----- Original Message ----- From: "Rupert Russell" <rjmr(a)st-andrews.ac.uk> To: "Ralf W. Grosse-Kunstleve" <rwgk(a)cci.lbl.gov>, "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Monday, December 15, 2008 10:44:03 AM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] Completeness issue by phenix Dear Ralf, I too have experienced this issue many times before. My .mtz files were generated through the ccp4i "import merged data" tab (default parameters), after the data were processed with scalepack. Letting phenix use the .sca file instead overcomes this but this is not an ideal situation for cross-compatibility between different programs. Cheers Rupert Russell Ralf W. Grosse-Kunstleve wrote: > Hi YoungJin, > > I suspect phenix.refine decided your mtz file contains anomalous data > when you actually have non-anomalous data. Could you look in the > phenix.refine output for something like this: > > ================================== X-ray data ================================= > > F-obs: > 1yjp.mtz:FOBS_X,SIGFOBS_X > > R-free flags: > 1yjp.mtz:R-free-flags > > Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X > Observation type: xray.amplitude > Type of data: double, size=495 > Type of sigmas: double, size=495 > Number of Miller indices: 495 > Anomalous flag: False > ^^^^^ > in particular here > > If you see "Anomalous flag: True" try adding this to the phenix.refine > command line: > > xray_data.force_anomalous_flag_to_be_equal_to=False > > Let me know if this doesn't help. > If it does help, I'd be interested to know how the .mtz file was > generated. > > Ralf > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

16 years, 6 months

Re: [phenixbb] phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups

by Mayer, Mark (NIH/NICHD) [E]

Great; look forwards to using, A question for those of us who have been using TLSMD for a few years is how the groups differ. You give timing comparisons for GroEL but do not report if the TLS groups differ, and if they do, how much the groups differ: e.g. is it a residue or two at the group ends, or larger differences. Mark ________________________________________ From: Pavel Afonine [pafonine(a)lbl.gov] Sent: Tuesday, December 14, 2010 9:45 PM To: PHENIX user mailing list Subject: [phenixbb] phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups PHENIX users: starting dev-610 (development version of PHENIX) there is a new tool available for completely automated partitioning a model into TLS groups: http://www.phenix-online.org/download/nightly_builds.cgi To run: phenix.find_tls_groups model.pdb or if you have a multiple CPU machine: phenix.find_tls_groups model.pdb nproc=N where N is the number of CPUs available (thanks Nat for parallelization!). There is no parameters that a user is supposed to tweak (except defining the number of CPUs, if desired). The result of running the above command are atom selections that define TLS groups. These atom selections are ready to use in phenix.refine. This is available from PHENIX GUI too, where automatically defined TLS groups can be readily visualized and checked on the graphics (thanks Nat!). The algorithm is fast. For example, for a GroEL structure (3668 residues, 26957 atoms, 7 chains) it takes only 135 seconds using 1 CPU, and 44 seconds using 10 CPUs. Analogous job takes 3630 seconds using TLSMD server. For a lysozime structure it takes 9.5 seconds with one CPU, and 2.5 seconds using 10 CPUs. The timing results may vary depending on the performance of your computer. There is ongoing work that will slightly improve phenix.find_tls_groups within the next few weeks / a month; however the current version is functional and can be tried now. An example of such improvements are analyzing (scoring) user-defined TLS groups (for example, TLS groups from PDB file header), automated combining cross-chain TLS groups (non-contiguous segments) that will be obtained through connectivity analysis, better handling non-protein chains, and more. Integration with phenix.refine is also planned. Any feedback is very much appreciated! Thanks, Pavel. _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

14 years, 6 months

Re: [phenixbb] matplotlib

by Nathaniel Echols

On Thu, Aug 18, 2011 at 10:39 AM, Ed Pozharski <epozh001(a)umaryland.edu>wrote: > In a nutshell, phenix gui may in some circumstances screw up other > programs that use matplotlib. It's not the fault of Phenix; matplotlib is unusually inflexible in how it deals with these cache files, and it is nearly unique among Python modules in its dependence on writing to the user's home directory. This isn't the only problem; another issue is that matplotlib creates these caches, and the maintainers appear to never have considered what would happen if the cached directory were removed. So when you run the GUI in version X of Phenix, then remove version X and install version Y, it will still look for the fonts installed with version X. I complained about this last December, and it remains unsolved in any of the official releases (one of which was this year). The likely cause is that phinix gui calls on bundled matplotlib which is > different from one I have installed (not to mention that I am using > Lucid (because it's LTS) which has python 2.6 and not the 2.7 that is > bundled with phenix). However, it still writes into the same > ~/.matplotlib folder, thus I end up with incompatible data. Certainly, > the problem will be gone when matplotlib gets bumped up to 1.0.1 in next > Ubuntu release. > The issue with removing installations will remain, however. You could avoid the incompatibility problem by running "phenix.wxpython" if you need to use matplotlib. (We're using Python 2.7.2 right now, and generally update to the latest release in the 2.x series shortly after it comes out.) This is yet another example of why the standalone installation approach > is ideologically objectionable on modern Linux. But of course, the > practical advantage gained by not having to package the software for any > possible OS flavor/version users may choose outweighs the lower risks of > package incompatibility and the reduced size of the packaged product. We don't have the resources to support a more ideologically pure distribution mechanism - the installers are maintained by me and Ralf in between other projects. Also, we often depend on new features in the various dependencies that would not be immediately available through the package managers (for instance, we switched to Python 2.6 almost immediately because I needed the multiprocessing module). There are many things in the current installers that I'm unhappy with, but they don't take very much time to maintain, which is essential. -Nat

13 years, 10 months

Re: [phenixbb] phaser MR

by Francis E Reyes

Shya, Did phaser complain that the asymmetric unit was too full? How do the self rotation maps look? Are the crystallographic peaks exact or off by a few degrees (your resolution data may make it difficult to see this)? How do the N(z) cumulative intensity distributions look (make sure to calculate this with thin resolution bins, i.e. increase BINS in Scala I think)? Does your data look sigmoidal on this plot? Perfect twinning or an NCS that's close to a crystallographic axis is difficult to diagnose from merged intensity statistics and even more difficult with resolution worse than 2.5. I recommend Dauter Acta Cryst (2003) D59 2004-2016 for a good discussion of this. Your space group might be too high. See the subgroups of P422 at http://cci.lbl.gov/~phzwart/p422_2.png . Reintegrate and merge the data in each space group, MR a single copy of your model (let phaser complete the ASU) and compare the Rpim's (from scaling/merging) and the Rwork/Rfree from a rigid body refine without NCS, with NCS, with appropriate twin laws, and with twin laws + NCS. No need to do a full refinement just yet. Allow phenix.refine to create the Rfree flags. Choose the space group which gives the best statistics. I recently had a case (Hardin, Reyes, Batey J. Biol. Chem., Vol. 284, Issue 22, 15317-15324, May 29, 2009) of a protein that merged into P422 but was difficult to refine in that space group. I brought it back to P4 and refined with NCS+twin to give more reasonable Rwork/ Rfree (5-7% difference from the P422 to P4). HTH, FR On Jul 23, 2009, at 3:54 PM, sbiswas2(a)ncsu.edu wrote: > Hi Francis, > Thanks for your response. The matthews coefficient suggests two > molecules > in the AU. Phaser also finds two molecules. I ran the dataset through > phenix xtriage it did not indicate twinning though. The molecule also > exists in nature as a monomer. > Shya > > >> Twinning? What's your matthews coefficient say? Do you know if your >> structure is a multimer (biochemistry, etc)? Does it agree with the >> matthews coefficient? >> >> If the unit cell is not big enough to hold all of the contents,then >> this is an indicator for twinning . >> >> FR >> >> On Jul 23, 2009, at 3:09 PM, sbiswas2(a)ncsu.edu wrote: >> >>> Hi all, >>> >>> I was trying to solve a structure by molecular replacement. I scaled >>> the >>> data in P4222 space group (resolution 2.7A) with two molecules in >>> the >>> assymmetric unit (molecule A and B) I ran phaser with my model and >>> got a >>> Zscore of 5.1. When I look at the map that I got from phaser I could >>> easily see good electron density for both molecules, However upon >>> inspection of the electron density map there were considerable >>> interaction >>> or clashes with molecule B and a symmetry atom. Molecule A had no >>> clashes >>> however with the symmetry atoms. I was wondering if anyone knows how >>> to >>> resolve this. Could it be a problem of space group. The statistics >>> are >>> good for space group P4222 and the I/sigI was good till 2.7A. >>> Any advice is appreciated, >>> Shya >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> --------------------------------------------- >> Francis Reyes M.Sc. >> 215 UCB >> University of Colorado at Boulder >> >> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D >> >> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

15 years, 11 months

Re: [phenixbb] Phaser-MR output after each component placement

by Johannes Cramer

Ok, thanks to the both of you. Looks like I will try again, once the new version is out and in cases where I would like to examine the placements, just run it via script. Cheers, Johannes Am Di., 28. Juli 2020 um 10:02 Uhr schrieb Randy Read <rjr27(a)cam.ac.uk>: > Hi Boaz, > > At the moment, that is indeed the only thing you can do with the partial > solution information from the log file. In the CCP4 environment, you can > cut and paste lines from the log file to make a .sol file, and use that to > run something like a refinement job to produce a PDB and MTZ for a partial > solution, but the Phenix environment uses Python pickle files to store the > transformations, so that option doesn’t apply. (Unless you run Phaser from > a script, in which case the Phenix and CCP4 versions work the same.) > > At one point, Phaser was writing out a PDB file for the top solution at > every point in the process, but we felt that led to clutter and that it was > confusing. > > There’s a major rewrite going on at the moment, and the new phasertng will > primarily be run through the phaser.voyager pipeline. One of the design > criteria here was to be able to examine branches that weren’t taken or > intermediate points in the ongoing search, and to be able to work with them > while the overall job is still running. So there will be a better option > in the hopefully not too distant future! > > Best wishes, > > Randy > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building Fax: +44 1223 > 336827 > Hills Road E-mail: > rjr27(a)cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > > On 27 Jul 2020, at 23:02, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > > > Hi, > > The closest option that comes to mind to do what you're looking for is > to take the Euler angles+translations for each of the monomers in the .sol > file (or at the top of the final pdb file) and apply each of them to the > initial model using any transformation program of your choice. > > I am more familiar with running Phaser using the ccp4 gui but it > shouldn't be very different under Phenix. > > Phaser people may well suggest a more elegant option. > > Stay safe, > > Boaz > > > > Boaz Shaanan, Ph.D. > > Department of Life Sciences > > Ben Gurion University of the Negev > > Beer Sheva > > Israel > > > > On Jul 27, 2020 16:02, Johannes Cramer <johannes.cramer(a)gmail.com> > wrote: > > Dear phenix board, > > > > does anyone of you know if there is an option in phaser-MR to output a > pdb after each placed component? > > For example: I suspect there to be 5 molecules in the AU. I start a > replacement with 5 molecules and phaser places 1 (I would like to inspect > that), 2 (again, I would like to look at the e.g. top 10 results), 3 and so > on... > > Is that possible? I couldn't find the option in the gui or in the phenix > documentation, but maybe in the CLI? > > I know I can run one after the other, but that would potentially waste > CPU time until I find time to inspect them. > > > > Cheers, > > Johannes > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > Unsubscribe: phenixbb-leave(a)phenix-online.org > >

4 years, 11 months

Re: [phenixbb] Problem with AutoBuild and Alternative Conformations

by Dale Tronrud

Thanks for the quick response. I have been using the GUI so I'll see if I can figure out what box to put this file in. AutoBuild did do an outstanding job, despite the problem with the Bchl-a's and I'm looking forward to digging into the map, when I get this stuff straightened out. Dale Thomas C. Terwilliger wrote: > Hi again Dale, > > I spoke too quickly...it is not so easy to change the code as I hoped. > > However here is a work-around that may be preferable anyhow: > > 1. Remove your ligand from the PDB file to be rebuilt and put it in "lig.pdb" > > 2. add to your commands for autobuild: > > input_lig_file_list=lig.pdb > > This will put all the contents of lig.pdb at the end of all PDB files just > before refinement. > > All the best, > Tom T > > > Hi Dale, > > Your hypothesis: "I suspect that the coder assumed that all alternative > conformations mutually exclusive and involve the same subset of the > residue." is quite correct. (I am the coder in question). > > I think that I may be able to fix this particular problem and take care of > the cases you have in this structure by simply allowing all conformations > of ligands in the input file to be kept during rebuilding. With luck, > this will work and will be in the final 1.3b version due out very shortly. > > The autobuild wizard still will not know how to build multiple > conformations into a structure. For the time being it will have to stick > with building one conformation. > > Thanks very much for the suggestion! > -Tom T > > > >> Hi, >> >> I desire to resolve a crystal, who's structure factors I've downloaded >> from the PDB, using my new high resolution model of this protein from a > different species. I have decided to use the AutoMR wizard from Phenix > for the chore. The MR seems to work just find, but I've run into a > problem with the follow-up AutoBuild. >> This protein has a peptide chain that I would like rebuilt with the >> proper amino acid sequence and seven Bchl-a molecules that I would like > to be carried through to the end. Since the probe is from a high res > refinement it contains quite a few groups with alternative > conformations. This is not a problem in the protein part as it is being > rebuilt and comes back with a single conformation for each residue. The > Bchl-a molecules, however, are being horribly mutilated. >> In the Bchl-a groups, the "A" conformation is being promoted to >> be the "main" (and only) conformation and the "B", "C", "D", "E", and, > yes, the "F" conformations are lost. A Bchl-a molecule is much larger > than an amino acid so it is quite possible, and reasonable, for one part > to have a "A" and "B" pair of conformations, another part to have a "C" > and "D" pair, and somewhere else for there to be a "E" and "F" pair. > When conformation "C", "D", "E", and "F" are discarded whole sections of > the Bchl-a molecule disappear >> completely. This is bad. >> >> I suspect that the coder assumed that all alternative conformations >> mutually exclusive and involve the same subset of the residue. I would > prefer a more careful analysis to uncover the fact that "A" and "B" go > together, and "C" and "D" go together. If there is a need to reduce the > complexity of the model, (and I would prefer that all the alternatives > make it through to the end) could the program keep "A", "C", and "E", or > whatever makes sense for any particular residue? Better yet, instead of > always keeping the first alternative of a set, could it keep the one > with the highest occupancy? >> I'm using phenix-1.3b-rc6 on a Fedora 6 PC. >> >> Thanks, >> Dale Tronrud >> > >

17 years, 6 months

Search results for query "look through"