Search results for "look through"

Re: [phenixbb] red blobs (Andrea Smith)

by Andrea Smith

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, 10 months

Re: [phenixbb] Very poor density, but very important loops

by Pavel Afonine

Hi Andrew, we (Lester and myself) recently implemented a new tool in PHENIX called phenix.grow_density. It is based on the idea published a while ago: Acta Cryst. (1997). D53, 540-543 Local Improvement of Electron-Density Maps A. G. Urzhumtsev We are currently looking for tests cases for this procedure, and I guess your case is just perfect for it! The phenix.grow_density tool is not at that level of automation so you can take it, run it and get the answer, but rather it would require some back-and-forth trials. So, if you would like to give it a try, here is what I suggest: - you send me the data and model and tell what are the loops you would like to improve (of course all data will be kept confidentially); - I run it through phenix.grow_density and hopefully (no promises, we are testing it!) give you back improved maps that you can use to build in your poor loops. - We may need to go through a few iterations of this (or may not if it doesn't work from the start). I will be in travel next week, so if you decide to send the data, I can't promise that I work on it immediately, but I (or Lester) will try. Please let me know what you think. Of course, you can try computing kick maps as well to see if it improves the maps too. Pavel. On 10/23/09 11:57 AM, Waight, Andrew wrote: > Hello All, > > I am putting the finishing touches on my structure, a novel membrane protein channel. The data extends to 2.1A and the R factors are currently at ~17/21. However there is a certain loop/helical region where the density gets pretty poor, Unfortunately this is a relatively important ligand binding site so I would like to extract as much information from my patchy blobs as possible. I am wondering if generating a kick map would be useful in this scenario. If so am I missing something other than setting use_kick_maps = True and adding a couple more map definition labels (as described by Pavel)? Also does anyone have any advanced technique suggestions for this type of circumstance, i.e. would it make sense to combine multiple reflection datasets? Thanks so much for all your help, I am a true phenix enthusiast and feel like I owe quite a bit to all of you who have made this amazing program possible. > > Drew Waight >

16 years, 3 months

Re: [phenixbb] Can I use PHENIX "Find NCS" tool to verify space group ?

by Terwilliger, Thomas Charles

Hi Alex, The notation that This NCS object does not contain point group symmetry This NCS object does not contain helical symmetry. means that the NCS itself is not point-group or helical symmetry (not including any space-group symmetry). For crystallographic data this summary is usually not useful because it doesn't include space-group symmetry in the calculation. You can probably tell if your NCS is similar to the 2-fold axis in P 3(2) 2 1 that goes along (1,1,0) by examining the NCS log file. It will have a summary of point-group symmetry like this: Analysis of NC symmetry using cutoff of 0.10 A as maximum distance between intersecting elements Looking for point-group symmetry among the 2 NC elements that might be members This point group is a rotation about a line going through the point xyz (orthogonal A) = 12.858 -10.339 23.956 xyz (fractional)= 0.224 -0.175 0.213 in the direction of xyz (orthogonal A) = 0.807 0.294 0.513 In your case you are looking for this kind of point-group symmetry where the line goes through something like (0,0,0) or (0,0,0.5) and the direction is something like (0.866,0.50,0), corresponding to a line going half-way between the X and Y axes, where this 2-fold belongs in P 3(2) 2 1. (I could have some angles mixed up here but if you get +-0.866 and +/- 0.5 in some order for x and y and 0 along z it's probably this 2-fold). I'll be happy to look at your log file if you do this. All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org <phenixbb-bounces(a)phenix-online.org> on behalf of Alex Lee <alexlee198609(a)gmail.com> Sent: Saturday, April 22, 2017 5:18 PM To: PHENIX user mailing list Subject: [phenixbb] Can I use PHENIX "Find NCS" tool to verify space group ? Hi All, I have a protein/dna dataset (3A resolution) with space group (SG) ambiguity, it could be P32 with two copies of molecules (one copy of molecule composed of protein homodimer with asymmetric dsDNA) in asymmetric unit (ASU) or P3221 with one copy of molecule in ASU. Both SG can give me MR solutions and after Refmac P32 Rfree is around 31% while P3221 Rfree is around 34% (without any twin refine at this stage). Density maps from both SG makes sense and they are similar by eye inspection. Because of partial twinning of the dataset (estimation twin fraction alpha around 0.22) , which confuse programs of assigning the correct SG. Pointless and Xtriage suggests P6222, which we are sure it's not correct (based on performance on both MR, Refmac and biology sense that dsDNA is asymmetric, and if P6222 is true then based on Mathew coef. there will be a monomer protein with single strand ssDNA in ASU). Zanuda suggests SG P32 in both cases (input experimental data P32 or P3221 along with refined model). However, Zanuda may not work well in twin case. In short, the problem now is to choose one SG from P32 or P3221. There is one suggestion that try SG P32, as there are two copies of molecules in ASU in P32 group, try find the NCS operator in P32 and check if this operator is close to crystallographic symmetry operator or not, if it is, then SG is P3221, if it's not, then SG is P32. I did a few rounds of search in Internet, I found Phenix "Find NCS tool" and input PDB of my refined structures from both P32 and P3221. For both test, Find NCS tool did find NCS operator but in the end of the log file I see the same results as below: This NCS object does not contain point group symmetry This NCS object does not contain helical symmetry. I am asking: 1. does "This NCS object does not contain point group symmetry" from Find NCS tool mean that NCS operator in my PDB is not crystallographic symmetry operator? 2. Is there a tool in Phenix which can find the NCS operator and check if the NCS operator is close to crystallographic symmetry operator or not? Thanks ahead.

8 years, 9 months

[phenixbb] Job opening: Scientist, Computational Chemistry

by Ying Zhang

Dear all, This post is to bring your attention to a job opportunity of a scientist position at Plexxikon Inc. We are looking for a highly motivated, computational chemist with expertise in protein structure predictions/modeling. Experience with small molecule design is a plus, but not required. Please help to distribute this to anyone that might be interested. Plexxikion (https://www.plexxikon.com/) is located in South San Francisco at CA, USA. We only consider candidates based in US. This Scientist will be a critical member of the Structural Chemistry team. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. Plexxikon utilizes its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage compounds in a number of therapeutic areas, including two marketed drug. Zelboraf(tm) (vemurafenib) was the first precision medicine to be approved for the treatment of BRAF-mutant metastatic melanoma; Turalio(tm) (pexidartinib) was the first FDA-approved therapy for tenosynovial giant cell tumor. You can find details about this position at https://careers.jobscore.com/apply_flow/standard_applications/apply?job_id=… Please apply through the link, but not reply to this email. Best Regards, Ying Zhang, Ph.D Sr Director, Research Planning Plexxikon Inc

4 years, 6 months

[phenixbb] Job opening: Scientist/Sr. Scientist, Structural Biology at Plexxikon Inc, South San Francisco, CA, USA

by Ying Zhang

Dear all, This post is to bring your attention to a job opportunity of a scientist/Sr. Sicentist position at Plexxikon Inc. We are looking for a highly motivated, structural biologist with expertise in crystallography. Plexxikon (https://www.plexxikon.com/) is located in South San Francisco at CA, USA. We only consider candidates based in US. This Scientist will be a critical member of the Structural Chemistry team. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. Plexxikon utilizes its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage compounds in a number of therapeutic areas, including two marketed drug. Zelboraf(tm) (vemurafenib) was the first precision medicine to be approved for the treatment of BRAF-mutant metastatic melanoma; Turalio(tm) (pexidartinib) was the first FDA-approved therapy for tenosynovial giant cell tumor. You can find details about this position at https://careers.jobscore.com/careers/plexxikon/jobs/scientist-structural-bi… Please apply through the link. Best Regards, Ying Zhang, Ph.D Sr Director, Research Planning Plexxikon Inc

4 years, 3 months

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

by Nathaniel Echols

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

14 years, 1 month

Re: [phenixbb] sigma cutoff

by Kay Diederichs

> > > Hi, > > According to the Phenix manual, phenix.refine uses no sigma cutoff by > default. Since I haven't changed this manually, why do I see in my pdb > file MIN(FOBS/SIGMA_FOBS) 1.340? > > Thanks for help, > Karolina > > This one I can answer because I asked myself the same question recently. The answer is that Phenix does not impose any sigma cutoff, but rather your data are such that the minimum value of Fobs/Sigma_Fobs is 1.34 . You can verify this for yourself by going through your reflection file, line by line, and calculating Fobs/Sigma_Fobs for each reflection. You will find that all your reflections have a Fobs/Sigma_Fobs larger or equal to 1.34 . So it has nothing to with phenix; phenix just reports a property of your data. An easier way than doing it "manually" is using CCP4 sftools for calculating a new column "ratio", writing out the resulting MTZ file, and looking at this with mtzdmp. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

16 years, 6 months

[phenixbb] Help with custom bond restraints syntax

by Andrew T. Torelli

Hi all, I'm having what I believe is a simple problem defining custom bond restraints between a side chain in my protein model and a ligand (non-covalent bond). Here is a minimal form of my custom bond definition file that suffers from the error: refinement.geometry_restraints.edits { Atom1 = chain F and resid 1 and name FE1 Atom2 = chain A and resid 69 and name SG bond { action = *add atom_selection_1 = Atom1 atom_selection_2 = Atom2 distance_ideal = 2.35 sigma = 0.1 slack = None } } I'm using phenix 1.4-153 and I get the following error: ERROR: Unused parameter definitions: refinement.geometry_restraints.edits.Atom1 (file "/HOME/andrew/PHENIX_paramfiles/test.edits", line 5) refinement.geometry_restraints.edits.Atom2 (file "/HOME/andrew/PHENIX_paramfiles/test.edits", line 6) I've checked through the online manual and I believe my syntax is correct, but I'm not sure why my custom bond restraint is being ignored. A second question is: once I get the custom bond/angle restraints correctly implemented, is there a better or more convenient place to look and confirm that the restraints have been imposed other than the .geo file phenix.refine outputs? Thank you very much for your help, -Andy

16 years, 4 months

Re: [phenixbb] Changing an amino acid to an unusual amino acid

by Kevin Jude

I just went through this with a blue FP. Carsten is correct about how to define the peptide bonds, but an easier way is to use JLigand. The tutorial at http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html#link is helpful. You will have to define the i-1 and i+1 links in separate .cif files if you use JLigand. HTH kmj On Tue, Jun 2, 2015 at 4:40 PM, Schubert, Carsten [JRDUS] < CSCHUBER(a)its.jnj.com> wrote: > Hi Nat, > > > > bonds in COOT do not mean much, as they do not translate into bonded > interactions in the refinement programs. Phenix for instance tries to > figure out the bonding by itself through some distance based heuristics. > However in your case it looks as if the CRO residue may not be defined as a > polymer, i.e. part of a protein chain in the monomer library you are using. > In Windows the monomer library is located in > C:\WinCoot\share\coot\lib\data\monomers. Look at the difference in the > headers for CYS.cif and CRO.cif or PTR.cif (phosphotyrosine). The > aminoacids or modified aminoacids considered part of the peptide chain have > all ‘peptide’ in the header, CRO does not. That is probably the reason why > coot does not make any bonds. This would probably cause problems later on > with Phenix as well. You could pull out the CRO.cif into your directory, > modify it to make it a peptide and read it into coot and phenix during > refinement. I would also run it through REEL to make sure the definitions > are kosher. > > > > HTH > > > > Carsten > > > > > > *From:* Natalia Ketaren [mailto:[email protected] > <nketaren(a)mail.rockefeller.edu>] > *Sent:* Tuesday, June 02, 2015 5:42 PM > *To:* Schubert, Carsten [JRDUS] > *Subject:* Re: Changing an amino acid to an unusual amino acid > > > > Hi Carsten, > > > > Th residue is a part of the correct chain. It just doesn’t make an bonds > with the residues on either side of it. Is this common for unusual amino > acids when adding to the main chain? > > > > Cheers, > > > > Nat > > _____________________________ > > Natalia E. Ketaren, PhD > Postdoctoral Associate > Rout Laboratory > Box 213 > The Rockefeller University > 1230 York Avenue > New York, NY 10065 > > Tel: (212) 327-8136 > Fax: (212) 327-7193 > Natalia.Ketaren(a)rockefeller.edu > website: http://lab.rockefeller.edu/rout/ > NCDIR: http://www.ncdir.org/ > > > > On Jun 2, 2015, at 5:26 PM, Schubert, Carsten [JRDUS] < > CSCHUBER(a)its.jnj.com> wrote: > > > > Hi Natalia, > > > > if the missing/wrong chain IDs are really the problem you can change them > in COOT under Calculate -> Change Chain IDs. The dialog is a bit tricky, > since you probably have to use the correct residue range to change an > individual residue into an existing chain. In your case I would write out > the PDB file and use a text editor to change the chain ID and move the > residue into its correct place in the file. > > > > HTH > > > > Carsten > > > > *From:* phenixbb-bounces(a)phenix-online.org [ > mailto:[email protected] > <phenixbb-bounces(a)phenix-online.org>] *On Behalf Of *Natalia Ketaren > *Sent:* Tuesday, June 02, 2015 5:17 PM > *To:* phenixbb(a)phenix-online.org > *Subject:* [phenixbb] Changing an amino acid to an unusual amino acid > > > > Hello All, > > > > I’m working on a GFP structure and I’m trying to incorporate the CRO > (chromophore) residue into the structure using coot. My process is to use > Extension->Modelling—>Replace residues, where it’s suppose to replace a Tyr > residue. I type the 3 letter code, CRO, the residue appears, I’m able to > real space refine it, but it does not incorporate CRO into the desired > chain. Would someone be able to help me figure out what I’m doing wrong? > And possibly walk me through a solution? > > > > Cheers, > > > > Nat > > _____________________________ > > Natalia E. Ketaren, PhD > Postdoctoral Associate > Rout Laboratory > Box 213 > The Rockefeller University > 1230 York Avenue > New York, NY 10065 > > Tel: (212) 327-8136 > Fax: (212) 327-7193 > Natalia.Ketaren(a)rockefeller.edu > website: http://lab.rockefeller.edu/rout/ > NCDIR: http://www.ncdir.org/ > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org >

10 years, 8 months

Re: [phenixbb] alternatives to RMSD

by Dmytro Guzenko

Hi Patrick Take a look at the Binet-Cauchy kernel, e.g. here: http://bioinformatics.oxfordjournals.org/content/30/6/784.long It is a shape-correlation metric that is rather insensitive to global shape changes, but sensitive to local ones. Maybe that's what you need. It's also much faster to compute than RMSD. I have attached a python code snippet that computes a BC distance matrix for a set of proteins defined by CA coordinates. Kind regards, Dmytro. On 02/07/14 17:15, Patrick. C wrote: > 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 > > > ------------------------------------------------------------------------ > 3D Earth Screensaver Preview <http://www.inbox.com/earth> > *Free 3D Earth Screensaver* > Watch the Earth right on your desktop! Check it out at > www.inbox.com/earth <http://www.inbox.com/earth> > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

11 years, 7 months

Search results for query "look through"