Search results for "look through"

Re: [phenixbb] How do I turn off sidechain rotamer fitting?

by Owen Pornillos

I'm now doing paired refinement with and without real space refinement and will send you the files when they are done. Thanks, Owen On Jul 15, 2013, at 3:03 PM, Pavel Afonine wrote: > Hi Owen, > > local real-space refinement will not fit a side-chain into a rotamer > outlier: it uses both, map and rotamer library, and also it uses a > quite > complex logic that aims to find best density fit and at the same time > keep good geometry (no outliers of any sort). That's why I wanted to > look at the files because to me what you described is an indicator > of a > problem somewhere else or a bug.. > > Pavel > > On 7/15/13 11:56 AM, Owen Pornillos wrote: >> Hi Pavel - >> >> Thanks for the reply. >> >> I have a 2.6 A data set that has a dimer in the asymmetric unit, and >> so I'm using NCS. Some of the big sidechain densities (LYS, ARG, >> etc.) >> are not well-defined so I'd like to just restrain them to the other >> chain. The auto rotamer fitting of course tries to fit them, and the >> result is a list of half a dozen or so rotamer violations. I'm going >> through the list to see if the density truly defines different >> conformations. I think this is just a general run of the mill problem >> with fitting/refinement with NCS. >> >> Thanks, >> >> Owen >> >> On Jul 15, 2013, at 1:55 PM, Pavel Afonine wrote: >> >>> Hi Owen, >>> >>> you can disable it by turning of real-space refinement off. >>> >>> I'm interested to know what exactly is not going well: could you >>> please >>> explain this to me off list and send files so I can reproduce the >>> problem? >>> >>> Pavel >>> >>> >>> On 7/15/13 10:46 AM, Owen Pornillos wrote: >>>> I'm using one of the nightlies - dev 1427. It's not doing very >>>> well >>>> in combination with NCS. Or what is the most recent nightly that >>>> does >>>> not have this feature? >>>> >>>> Many thanks, >>>> >>>> Owen >>> >>> _______________________________________________ >>> 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

12 years, 6 months

Re: [phenixbb] Molecular replacement with fixed solution

by Randy Read

Hi, There are two ways to do this, and I’ve just tested them both using the beta-lactamase:BLIP tutorial from the Phenix distribution. 1. The easy way, which is what users are generally meant to do. Define all the necessary background information (data, both ensembles: beta and blip, composition with sequence files). Specify one search for one component, e.g. beta. When this finishes, go to the main “Input and general options” pane of the GUI and, in the “Use partial solution from previous job” pulldown, choose the job that placed the beta component. Now go to the “Search procedure” pane and uncheck “beta” for the search model and check “blip” instead. Run the search, and it will place the blip component in the context of the already placed beta-lactamase component. This could go wrong if the user is obsessively tidy and deletes the definition for the “beta” ensemble between the first and second jobs, because the partial solution information specifies how to place a defined ensemble (which therefore still has to be defined), but it does not store the placed ensemble. 2. The harder way, which is probably what you were trying to do. After placing the first component, define a new ensemble, giving the PDB file from the phaser subdirectory created in the first search (I called this ensemble “beta_placed”). For this one, check the box labelled “Ensemble is fixed partial solution”. Again, in the “Search procedure” pane, uncheck “beta” and check “blip”, then run the search. Note that you’re not specifying any search for the already placed component. This way of doing things was really only created so people could come in halfway through a structure solution with another molecular replacement program, not as the way you would choose to do it with Phaser. Actually, the very easiest way, which I hope most users do by default, is to decide at the beginning what you are hoping to find in the structure solution and specify all the copies of all the components you’re looking for in one job. That approach gives Phaser the most flexibility to use an adaptive search strategy. So, in the tutorial, users are instructed to set up two searches in the one job, searching for both “beta” and “blip”. Let me know if that doesn’t clarify things. Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC 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 16 Jan 2015, at 18:56, Muhammed bashir Khan <muhammad.bashir.khan(a)UNIVIE.AC.AT> wrote: > Hi There; > > I want to solve the structure with molecular replacement using phaser in > phenix GUI. When I get solution from the one, how I can use as it as > already solution using phenix in the next run. I use the "ensamble is > fixed partial solution" but seems its not working. Any suggestion will be > highly appreciated. Thanks > > Regards > > > -- > Muhammad Bashir Khan > ************************************************** > Department for Structural and Computational Biology > Max F. Perutz Laboratories > University of Vienna > Campus Vienna Biocenter 5 > A-1030 Vienna > Austria > > Austria > > Phone: +43(1)427752224 > Fax: +43(1)42779522 > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

11 years

Re: [phenixbb] Using the Same Test Set in AutoBuild and Phenix.Refine

by Dale Tronrud

Requested mtz.dump inserted later in letter. Pavel Afonine wrote: > Hi Dale, > >>> 1) Why you specify reflection MTZ file twice in phenix.refine script? >>> >>> >> I put the mtz in twice because if I put it in once phenix.refine >> complains that I have no free R flags. It seems to want one file with >> the amplitudes and another with the flags. Since I have both in the >> same file I put that file on the line twice and phenix.refine finds >> everything it needs. >> > > phenix.refine looks for free-R flags in your main data file > (1M50-2.mtz). Optionally you can provide a separate file containing > free-R flags (I have to write about this in the manual). However, if > your 1M50-2.mtz contains free-R flags then you don't need to give it > twice. So clearly something is wrong at this step and we need to find > out what is wrong before doing anything else. Could you send the result > of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your > data file? Or I can debug it myself if you send me the data and model. > dale@fluorine [2] phenix.mtz.dump 1M50-2.mtz Processing: 1M50-2.mtz Title: [No title given] Space group symbol from file: P 43 3 2 Space group number from file: 212 Space group from matrices: P 43 3 2 (No. 212) Point group symbol from file: PG432 Number of crystals: 2 Number of Miller indices: 45448 Resolution range: 119.572 2.14861 History: From FREERFLAG 8/12/2007 00:31:08 with fraction 0.050 From f2mtz 8/12/2007 00:31:02 data from CAD on 8/12/07 Crystal 1: Name: HKL_base Project: HKL_base Id: 1 Unit cell: (169.1, 169.1, 169.1, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: HKL_base Id: 0 Wavelength: 0 Number of columns: 4 label #valid %valid min max type H 45448 100.00% 0.00 45.00 H: index h,k,l K 45448 100.00% 1.00 78.00 H: index h,k,l L 45448 100.00% 0.00 55.00 H: index h,k,l FreeR_flag 45448 100.00% 0.00 19.00 I: integer Crystal 2: Name: allen-2002 Project: FMO-ct Id: 2 Unit cell: (169.1, 169.1, 169.1, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: 1 Id: 1 Wavelength: 0 Number of columns: 2 label #valid %valid min max type FP 41607 91.55% 0.00 15171.00 F: amplitude SIGFP 41607 91.55% 0.00 1716.00 Q: standard deviation >> If the MD5 hash of the test set depends on the resolution then certainly >> I could be in trouble. > > No. It must always use the original files before any processing. > >> Does the resolution limit affect the MD5 hash of the test set? >> > > No. If it does then it is a very bad bug. I will play with this myself > later tonight. > >> >>> 3) Does this work: >>> >>> (...) >> I'll try these but it will take a bit of time. >> > > Don't run it until completion. Just make sure it passed through the > processing step. > > Pavel. > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb

18 years, 1 month

Re: [phenixbb] The 5'end guanosine triphosphate is not linked to the rest of RNA model by Phenix refine

by Zixian Li

Hi Nigel, Thanks a lot for your help! The short communication paper you directed to me helps me understand how different visualization programs deal with defined links. The geometry file (.geo) is where one should check whether or not the defined bond is linked. In fact, I found the data_link name "p" is necessary. If without supplying cif_link_GTP-G.params file to Phenix.refine, no linked bond is shown in the .geo file. With the .params file, the linked bond is found in .geo file as below: bond pdb=" O3' GTP C 1 " pdb=" P G C 2 " ideal model delta sigma weight residual 1.600 1.570 0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" O3' GTP D 1 " pdb=" P G D 2 " ideal model delta sigma weight residual 1.600 1.597 0.003 2.00e-02 2.50e+03 1.99e-02 However, the issue of broken O3'-P linker persists in Coot when applying real space refine zone on the RNA model after Phenix refinement. So I sent you a separate email with all necessary files that you can have a look at your convenience. Thank you very much! Zixian Li ________________________________ From: Nigel Moriarty <nwmoriarty(a)lbl.gov> Sent: Tuesday, July 7, 2020 4:38 PM To: Zixian Li <zixian.li(a)mail.mcgill.ca> Cc: phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] The 5'end guanosine triphosphate is not linked to the rest of RNA model by Phenix refine Zixian Li Some things that immediately require comment. 1. Coot is a separate tool from Phenix and it therefore does not know the things that phenix.refine knows. It does not use the automatic linking or restraints that Phenix uses. You need to supply the restraints that you want Coot to use. Unfortunately, it does not read the params files that Phenix uses. It relies on its internal coding to decide what is linked and what is not. Also http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10 2. Using the same data_link name "p" is not necessary so I would avoid it. 3. The only surefire way to know if a link has occurred in the refinement is to look in the .geo file. You may have some info in the log file also. Having said that, I'm happy to look into the problem if it persists and you send me the files. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> On Tue, Jul 7, 2020 at 1:09 PM Zixian Li <zixian.li(a)mail.mcgill.ca<mailto:[email protected]>> wrote: Dear Phenix Community, I'm at beginner level of using Phenix. I have difficulty to refine a protein-RNA complex in Phenix. I refined the protein model without RNA first, then I built the RNA model into the difference density map in Coot through Calculate>Other Modelling Tools>Ideal DNA/RNA, where I input the sequence and fit nucleotides into the density. At the 5' end it's guanosine triphosphate (GTP) but the modeler tool in Coot only generates nucleoside monophosphate. So I built the RNA model from the second nucleotide at 5' end downstream until where RNA density was too poor to model. I did the real space refine zone in Coot to fit this main part of the RNA into its density the best possibly. For the GTP at 5' end, I realized there is GTP.cif restraint file in Phenix monomer library. So I obtained an arbitrary pdb file for GTP using eLBOW and corrected atom names matching the definition in GTP.cif file. Then I can also fit GTP into the RNA density at 5' end using real space refine zone in Coot. Now I have a broken RNA model with GTP unlinked to the ribose-phosphate backbone. For Phenix refinement, I supplied a cif_link_GTP-G.params file to define the linkage for the two RNA chains in the complex: refinement.pdb_interpretation { apply_cif_link { data_link = p residue_selection_1 = chain C and resname GTP and resid 1 residue_selection_2 = chain C and resname G and resid 2 } apply_cif_link { data_link = p residue_selection_1 = chain D and resname GTP and resid 1 residue_selection_2 = chain D and resname G and resid 2 } } After refinement, I noticed O3' of GTP appears connected to P of the following nucleotide G in the refined model in Coot. However, if I do the real space refine zone in Coot, the linkage becomes broken, i.e., I cannot refine the RNA model as a whole: Coot only allows separate real space refine for GTP and the rest. It seems Coot still cannot recognize GTP and the rest as one body. In the refinement settings there is a button for Automatic linking options. Interestingly, I noticed if I leave the automatic covalent linking as default, Phenix writes Link records in the output pdb after refinement. But it also links one of the protein residues to the GTP in chain D. In order to avoid the unwanted intermolecular linkage, I clicked Link none for Automatic linking options, then there is no any link records written in the output pdb despite of the defined linkage in cif_link_GTP-G.params file. So it seems for me Phenix ignores the input cif_link_GTP-G.params file, it writes Link records only if the Automatic linking option is activated. I worried whether it could be due to the syntax of the cif_link_GTP-G.params file. So I tried the following syntax in two separate files, the same issue was observed. cif_link_GTP-G_chC.params refinement.pdb_interpretation.apply_cif_link { data_link = p residue_selection_1 = chain C and resname GTP and resid 1 residue_selection_2 = chain C and resname G and resid 2 } cif_link_GTP-G_chD.params refinement.pdb_interpretation.apply_cif_link { data_link = p residue_selection_1 = chain D and resname GTP and resid 1 residue_selection_2 = chain D and resname G and resid 2 } I also need to point out that p linkage is pre-defined in the list of links (mon_lib_list.cif) in Phenix monomer library. I apologize for this long explanation of the problem. I hope it is clear. I really appreciate your advice in advance. Sincerely, Zixian Li _______________________________________________ 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]>

5 years, 7 months

Re: [phenixbb] SAD related query

by Peter Zwart

Hi Tara, sorry for the late reply. Yesterday was a holiday. I had a look at the mtz file you send me and things are disturbing. The 'strong' data goes to about 3A, which is not too bad. The data complete, but the intensity statistics as given by xtriage look really murky: ------------------------------------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - <I^2>/<I>^2 : 1.649 - <F>^2/<F^2> : 0.862 - <|E^2-1|> : 0.587 - <|L|>, <L^2>: 0.382, 0.211 Multivariate Z score L-test: 13.067 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it. No (pseudo)merohedral twin laws were found. Patterson analyses - Largest peak height : 6.820 (correpsonding p value : 5.346e-01) The largest off-origin peak in the Patterson function is 6.82% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics are significantly different then is expected from good to reasonable, untwinned data. As there are no twin laws possible given the crystal symmetry, there could be a number of reasons for the departure of the intensity statistics from normality. Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems as well as bad data quality might be possible reasons. It could be worthwhile considering reprocessing the data. ------------------------------------------------------------------------------- As your spacegroup is P4322, i suggest you try carefull reprocessing of your data in P43 to check the intensity statistics in that spacegroup. You could have data that is merohedrally twinned and you might have overmerged your data,. This would be possible if twin fraction is relatively close to 50%. Furthermore, are you sure about the P43 bit? What about P41? HTH Peter 2007/9/4, Thomas C. Terwilliger <terwilliger(a)lanl.gov>: > Hi Tara, > > It sounds like autosol was not able to find a very good solution to your > structure. I would not be too optimistic from what you have said so far, > but here is a list of things to check over (from the about-to-be-released > phenix manual...!) > > all the best, > Tom T > > > Autosol SAD tutorial: What to do if I do not get a good solution: > > If you do not obtain a good solution, then it's not time to give up yet. > There are a number of standard things to try that may improve the > structure determination. Here are a few that you should always try: > > * Have a careful look at all the output files. Work your way through > the main log file (e.g., AutoSol_run_1_1.log) and all the other > principal log files in order beginning with scaling > (dataset_1_scale.log), then looking at heavy-atom searching > (p9_se_w2_PHX.sca_ano_1.sca_hyss.log), phasing (e.g., phaser_1.log or > phaser_xx.log depending on which solution xx was the top solution) and > density modification (e.g., resolve_xx.log). Is there anything strange > or unusual in any of them that may give you a clue as to what to try > next? For example did the phasing work well (high figure of merit) yet > the density modification failed? (Perhaps the hand is incorrect). Was > the solvent content estimated correctly? (You can specify it yourself > if you want). What does the xtriage output say? Is there twinning or > strong translational symmetry? Are there problems with reflections > near ice rings? Are there many outlier reflections? > * Try a different resolution cutoff. For example 0.5 A lower > resolution than you tried before. Often the highest-resolution shells > have little useful information for structure solution (though the data > may be useful in refinement and density modification). > * Try a different rejection criterion for outliers. The default is > ratio_out=3.0 (toss reflections with delta F more than 3 times the rms > delta F of all reflections in the shell). Try instead ratio_out=5.0 to > keep almost everything. > * If the heavy-atom substructure search did not yield plausible > solutions, try searching with HYSS using the command-line interface, > and vary the resolution and number of sites you look for. Can you find > a solution that has a higher CC than the one found in AutoSol? If so, > you can read your solution in to AutoSol with sites_file=my_sites.pdb. > * Was an anisotropy correction applied in AutoSol? If there is some > anisotropy but no correction was applied, you can force AutoSol to > apply the correction with correct_aniso=True. > > > > > > Dear all, > > I am a novice user of phenix. I am trying to obtain phases for SAD > > dataset > > collected at 2.5 angs from autosol.But when i give the phases to > > autobuild, > > the R-factor is not decreasing below 49%. Also, in warp, it is unable to > > built with a message "encounterd an unknown element". Can someone suggest > > me > > what could be the problem. > > > > Thanks for any suggestion in advance. > > Tara Kashav > > > > On 9/3/07, phenixbb-request(a)phenix-online.org < > > phenixbb-request(a)phenix-online.org> wrote: > >> > >> Send phenixbb mailing list submissions to > >> phenixbb(a)phenix-online.org > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> http://www.phenix-online.org/mailman/listinfo/phenixbb > >> or, via email, send a message with subject or body 'help' to > >> phenixbb-request(a)phenix-online.org > >> > >> You can reach the person managing the list at > >> phenixbb-owner(a)phenix-online.org > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of phenixbb digest..." > >> > >> > >> Today's Topics: > >> > >> 1. command-line Patterson maps (Bryan W. Lepore) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Sun, 2 Sep 2007 00:07:51 -0500 (CDT) > >> From: "Bryan W. Lepore" <bryanlepore(a)mail.utexas.edu> > >> Subject: [phenixbb] command-line Patterson maps > >> To: phenixbb(a)phenix-online.org > >> Message-ID: > >> < > >> Pine.LNX.4.64.0709020001190.16588(a)cpe-70-116-17-26.austin.res.rr.com> > >> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > >> > >> will phenix calculate Pattersons from trial sites or a reflection file > >> on > >> the command line? i.e. something besides hacking what is already there. > >> > >> e.g. cns has predict_patterson.inp. i can't seem to find a way to do it > >> from the command line - such as `phenix.patterson --sg=94 > >> reflections.mtz`. i saw phenix.maps but that looks like electron > >> density > >> only. > >> > >> -bryan > >> > >> > >> ------------------------------ > >> > >> _______________________________________________ > >> phenixbb mailing list > >> phenixbb(a)phenix-online.org > >> http://www.phenix-online.org/mailman/listinfo/phenixbb > >> > >> > >> End of phenixbb Digest, Vol 22, Issue 1 > >> *************************************** > >> > > > > > > > > -- > > Tara Kashav, > > Dr. S. Gourinath's Lab, > > Lab No 430, > > School of Life Sciences, > > Jawaharlal Nehru University, > > New Delhi - 110067 > > _______________________________________________ > > 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 >

18 years, 5 months

Re: [phenixbb] alternatives to RMSD

by Edward A. Berry

I agree that would be useful as an alternative to RMSD, but if I understand the original post, the problem with RMSD is that the two secondary structure elements are connected by a variable turn so that they cannot be superimposed simultaneously. That could still be a problem, comparing maps. What you can do is report the change in angle between them, and the residues making up the hinge. A program called dyndom (dynamic domains) is good for this, Or you can superimpose each "domain" separately, view the superimposed molecules, and see haw far into the turn from each side thesuperposition is good To get the change in angle between the two parts, first superimpose model A on model B using only residues in domain 1 (say, the helix). Save that reoriented model A, and now superimpose it on model B using only residues in domain 2 (the strand). The angle involved in this second rotation is the chang in interdomain angle. (You could also report RMSD for superposition of the individual domain, but helix-on-helix or strand-on-strand are likely to be pretty good fits and not very informative.) eab On 07/05/2014 10:22 AM, PC wrote: > Hi Pavel, > > Thank you very much, this sounds very interesting. > > I have used ccp4, coot and phenix but I am no expert but I am definitely interested in trying this method if you could give more information. > > Thank you, > Patrick. > > > -----Original Message----- > *From:* pafonine(a)lbl.gov > *Sent:* Fri, 04 Jul 2014 20:34:33 -0700 > *To:* patrick.cossins(a)inbox.com, phenixbb(a)phenix-online.org > *Subject:* Re: [phenixbb] alternatives to RMSD > > Hi Patrick, > > RMSD is a poor measure in this case as it does not account for B-factors, occupancies, alternative conformations and so on information a crystal structure model may make available. Macromolecules are not a bunch of points in space. > > While I'm sure more thorough methods exist, I would vote for the simplest, most direct and obvious one. You can calculate electron density map using a Gaussian approximation from model A and B (yes, electron density map - not a Fourier image of it!). That will naturally account for all: B-factors, occupancies, other disorder. Then you can calculate a map similarity measure, such as map correlation, for instance. After all, why use a cannon to kill a fly?! > > If you are interested to follow this route I can explain the details. > > All the best, > Pavel > >> Hi Phenix users, >> >> I am not a crystallographer but I though you guys might be a good place to ask this question. >> >> I have 2 super secondary structures, A and B and they consist of Helix-turn-Strand >> >> Due to the turn the two structures have a poor RMSD because the two flanking fragments of Helix and Strand are far from each other but when I superimpose the two fragments individually(helixA with helix B and standA with strandB in Pymol they align very well). >> >> Now, is there a way to express this instead of using the RMSD? >> When the two structures align well the RMSD is very good but a slight movement and the RMSD is awful. >> But looking at the two structures I can see they follow the same path through space. >> >> Thank you, >> Patrick > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ > Protect your computer files with professional cloud backup. Get PCRx Backup and upload unlimited files automatically. <http://backup.pcrx.com/mail> > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

11 years, 7 months

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

by Xiao Lei

Hi Zhijie, Thank you very much for the information. For step 1 you mentioned, I can get monomer with L-Asp but it seems I can not drag it (or I do not know how to do) and can not delete or modify it to become isoAsp. I will try play around more though. Xiao On Mon, Aug 17, 2015 at 6:33 PM, Zhijie Li <zhijie.li(a)utoronto.ca> wrote: > 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 <xiaoleiusc(a)gmail.com> > *Sent:* Monday, August 17, 2015 6:50 PM > *To:* PHENIX user mailing list <phenixbb(a)phenix-online.org> > *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] calculate Fc for the whole unit cell from a Fc of a single symmetric unit.

by Ralf Grosse-Kunstleve

We can expand reciprocal-space arrays, too, with the cctbx.miller.array.expand_to_p1() method. You can use it from the command line via phenix.reflection_file_converter --expand-to-p1 ... See also: http://www.phenix-online.org/documentation/reflection_file_tools.htm Ralf On Mon, Jul 11, 2011 at 10:56 AM, <zhangh1(a)umbc.edu> wrote: > 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 > > > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

14 years, 6 months

Re: [cctbxbb] bz2 support on Ubuntu

by David Waterman

Great, all working now. It seemed I didn't need to mess with libtbx.list_modules after all, I could just rebuild the foundations without the house falling down. So, for reference I did this: rm -rf base cd base_tmp find . -maxdepth 1 -mindepth 1 -type d -print0 | xargs -0 -n 1 -- rm -rf cd .. python bootstrap.py --builder=dials base cd build source setpaths.sh make reconf -- David On 8 June 2017 at 14:15, David Waterman <dgwaterman(a)gmail.com> wrote: > 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, 8 months

Re: [phenixbb] The 5'end guanosine triphosphate is not linked to the rest of RNA model by Phenix refine

by Nigel Moriarty

Zixian Li Some things that immediately require comment. 1. Coot is a separate tool from Phenix and it therefore does not know the things that phenix.refine knows. It does not use the automatic linking or restraints that Phenix uses. You need to supply the restraints that you want Coot to use. Unfortunately, it does not read the params files that Phenix uses. It relies on its internal coding to decide what is linked and what is not. Also http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10 2. Using the same data_link name "p" is not necessary so I would avoid it. 3. The only surefire way to know if a link has occurred in the refinement is to look in the .geo file. You may have some info in the log file also. Having said that, I'm happy to look into the problem if it persists and you send me the files. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, Jul 7, 2020 at 1:09 PM Zixian Li <zixian.li(a)mail.mcgill.ca> wrote: > Dear Phenix Community, > > I'm at beginner level of using Phenix. I have difficulty to refine a > protein-RNA complex in Phenix. > > I refined the protein model without RNA first, then I built the RNA model > into the difference density map in Coot through Calculate>Other Modelling > Tools>Ideal DNA/RNA, where I input the sequence and fit nucleotides into > the density. At the 5' end it's guanosine triphosphate (GTP) but the > modeler tool in Coot only generates nucleoside monophosphate. So I built > the RNA model from the second nucleotide at 5' end downstream until where > RNA density was too poor to model. I did the real space refine zone in Coot > to fit this main part of the RNA into its density the best possibly. > > For the GTP at 5' end, I realized there is GTP.cif restraint file in > Phenix monomer library. So I obtained an arbitrary pdb file for GTP using > eLBOW and corrected atom names matching the definition in GTP.cif file. > Then I can also fit GTP into the RNA density at 5' end using real space > refine zone in Coot. Now I have a broken RNA model with GTP unlinked to the > ribose-phosphate backbone. > > For Phenix refinement, I supplied a cif_link_GTP-G.params file to define > the linkage for the two RNA chains in the complex: > > refinement.pdb_interpretation { > apply_cif_link { > data_link = p > residue_selection_1 = chain C and resname GTP and resid 1 > residue_selection_2 = chain C and resname G and resid 2 > } > apply_cif_link { > data_link = p > residue_selection_1 = chain D and resname GTP and resid 1 > residue_selection_2 = chain D and resname G and resid 2 > } > } > > After refinement, I noticed O3' of GTP appears connected to P of the > following nucleotide G in the refined model in Coot. However, if I do the > real space refine zone in Coot, the linkage becomes broken, i.e., I cannot > refine the RNA model as a whole: Coot only allows separate real space > refine for GTP and the rest. It seems Coot still cannot recognize GTP and > the rest as one body. In the refinement settings there is a button for > Automatic linking options. Interestingly, I noticed if I leave the > automatic covalent linking as default, Phenix writes Link records in the > output pdb after refinement. But it also links one of the protein residues > to the GTP in chain D. In order to avoid the unwanted intermolecular > linkage, I clicked Link none for Automatic linking options, then there is > no any link records written in the output pdb despite of the defined > linkage in cif_link_GTP-G.params file. So it seems for me Phenix ignores > the input cif_link_GTP-G.params file, it writes Link records only if the > Automatic linking option is activated. I worried whether it could be due to > the syntax of the cif_link_GTP-G.params file. So I tried the following > syntax in two separate files, the same issue was observed. > > cif_link_GTP-G_chC.params > refinement.pdb_interpretation.apply_cif_link { > data_link = p > residue_selection_1 = chain C and resname GTP and resid 1 > residue_selection_2 = chain C and resname G and resid 2 > } > > cif_link_GTP-G_chD.params > refinement.pdb_interpretation.apply_cif_link { > data_link = p > residue_selection_1 = chain D and resname GTP and resid 1 > residue_selection_2 = chain D and resname G and resid 2 > } > > I also need to point out that p linkage is pre-defined in the list of > links (mon_lib_list.cif) in Phenix monomer library. > > I apologize for this long explanation of the problem. I hope it is clear. > > I really appreciate your advice in advance. > > Sincerely, > Zixian Li > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

5 years, 7 months

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