Search results for "look through"

[phenixbb] Clashscore and average B

by Sam Tang

Hello. I am refining a structure with Phenix.refine and encounter an issue which I appreciate your comments. The structure is in P1 and refined to 36A-3A. Rw/Rf = 23.9%/29.1%, RMS bonds 0.002, RMS angles 0.544, Ramachandran favoured 97.5%. The statistics is acceptable to me but two numbers raised my concern. First is the clashscore of 7.7, which is below minimum of other structures shown by Polygon. Second is an average B of 37, with a minimum of 9.2. When I checked again in Coot (Average Temp fact. analysis), none of the residues or water look abnormal. I refined both individual and group B-factors and applied 'Optimize X-ray/adp weight'. So my questions are: (1) if a clashscore too high means a lot of bad contacts, how do you comprehend a clashscore too low? How can I modify my strategy to get around? (2) is there an acceptable low value of B? (I sort of went through a similar thread in phenixbb appeared 9 years ago but seems the discussion did not come to a conclusion). Any advice I should reliax or tighten the adp restraints? PS - it may be worth mentioning the structure contains a OMU nucleotide. The .cif file I used was generated by elbow. The nucleotide looks normal in coot w.r.t. contact or B-value. Thanks a lot! Sam

6 years, 2 months

Re: [phenixbb] hydrogens in riding model create steric clashes after refinement

by Jeff Headd

>No, I didn't previously have hydgrogens. This is the first time I looked > at close contacts with hydrogens present. I submitted my pdb to the the > PDB auto Deposition input tool which defines "close contacts" as less > then 2.2 A > After looking at these I could see that many were between hydroens of one > side chain and usually an amid or sometimes CA of the mainchain. > Sometimes they appeard hydrogen bonded but the hydrogens had to be rotated > away. All I had to do was rotate the hydrogens. I was just suprised that > this would not have been done in automatically in the refinement. Hi Yarrow, Have you run your model through the MolProbity server, or are you basing your clash analysis only on the PDB tools? MolProbity will give you a more thorough analysis of your structure, and will allow you to target areas of your model that are showing steric clashes due to misfit residues rather than just slightly out of place hydrogens. Most of the MolProbity validation tools for proteins are also available in the PHENIX validation GUI if you happen to be working in the GUI environment. If you have any MolProbity specific questions, please let me know. Thanks, Jeff

14 years, 10 months

[phenixbb] Odd behaviour of real-space refinement

by Tristan Croll

Hi all, I'm just finalising the re-refinement of a 3.6 Angstrom structure. The stats in general are excellent (Rwork/Rfree = 0.219/0.260; Ramachandran outliers 0.12%; Clashscore < 2; rotamer outliers 2.1%) and I've gone through the whole structure to check and double-check fit to the density. I'm very confident that it's effectively correct. When I run through a fairly standard refinement protocol (XYZ coords, Individual B-factors, optimizing weights, secondary structure restraints), all seems fine - the Rfree rattles around within 0.2% or so. But when I include the real-space refinement option, very strange things start to happen. Each rsrl step causes a 3-4% jump in both Rwork and Rfree, and jumps the Clashscore up to 40 or so. Rotamer outliers briefly go to zero but then increase substantially (to 6+%) in subsequent steps, and the number of Ramachandran outliers increases. I thought I'd missed some dreadful error in my structure until I looked more closely at the results. Some very nonsensical changes have been made - for example, an arginine in the middle of a beta-sheet (admittedly with no observable density associated with its sidechain, but register is well determined by surrounding residues and backbone density is clear) was flipped from its original orientation to point directly into the hydrophobic core of the domain. Somewhat surprising, to say the least. Is this a bug in the algorithm, or is it simply that 3.6A is too low resolution for it to work reliably? My version of Phenix is a nightly build from about 2 weeks ago. Happy to share coordinates and log files if necessary. Thanks, Tristan

10 years, 4 months

[phenixbb] Phenix.refine on coordinate-optimised structures

by Joey Farrell

Hello, I am trying to design a set of input parameters that I will be passing through the phenix.refine function. The structures that I am working with have already had their X,Y, and Z orthogonal Å coordinates optimised via separate protocol. I am looking for advice on which strategies and parameter values to use with phenix.refine to improve the crystallographic R-factors of such structures while preserving their earlier optimisation in real space. I have been having some success using “strategy = tls+individual_adp+occupancies” (where tls = “chain A”, tls = “chain B”, etc.) as well as adjusting the wxu_scale value until R-work and R-free are minimised. Are there other strategies or phenix.refine functionalities that may also prove helpful with this end in mind? I believe there may be ways to further improve R-work and R-free with this software that I am not yet aware of. Thank you for your help! Best, Joey

4 years, 10 months

Re: [phenixbb] phenix automr

by Randy J. Read

Hi, Tom has already said most of what I would have said. Most importantly, a negative LLG tells you that the model is not fitting the data as well as Phaser expects it to, given what you have told it about the model completeness and assumed RMS error. It may be that the model is too poor to solve the structure, but sometimes there is a clear solution, even though the final LLG is negative. You can only really tell if the solution is a clear one by looking at the details of the solution statistics. I would look closely at the log file, to see whether the solution has decent signal-to-noise. What you would like to see is that the Z-scores (at least for the second copy) are reasonably high and, in particular, that the packing check did not eliminate potential solutions with much higher Z-scores. It would probably be worthwhile looking at the section in our web page on how to work with difficult cases: http://www-structmed.cimr.cam.ac.uk/phaser/documentation/phaser-2.0.html#MR…. Best wishes, Randy Read On Mar 30 2009, sbiswas2(a)ncsu.edu wrote: >Hi all, > >I tried to use phenix automr by using the gui and also I am using the >latest version of phenix (courtesy of the phenix development team). I >asked it to search for two molecules in the asymmetric unit but it finds >just one also I am getting negative (-29) LLG value for the final >solution. The map also does not look good. I also asked it to search for >all possible space group, although I processed the data with P43212 phenix >automr finds a different one P41212.Will fixing the space group fix the >problem? Does anyone know what is going on? I tried running phaser >separately through ccp4 and phaser did find two molecules although the map >did not look good in this either. >Shya >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb >

16 years, 3 months

[phenixbb] Student/postdoc fellowships for Understanding Biology through Structure, March 16-20, 2020

by Tom Terwilliger

Hi Structural biologists, particularly students and postdocs! Student/postdoc fellowships still available for Understanding Biology through Structure 2020 (https://cvent.me/4kq9P, March 16-20, 2020 in Santa Fe,NM). The fellowships cover registration and hotel (you still have to get there) and are being awarded after registration on a competitive rolling basis based on a publication you upload. Speakers at the symposium will be encouraged to present sufficient background and experimental detail so that students can understand the significance, promise, and limitations of their work. Each talk will have a full 10 minutes of discussion (15 minutes for Keynote talks). Moderators for each session will help include students and postdocs in the discussion. Students and postdocs will have many opportunities to talk with more senior researchers at conference breaks, meals, receptions and poster sessions. The last conference was a huge success (see https://bit.ly/2Gfkm4t and https://bit.ly/2Gg39rm) and this one is looking great (see https://cvent.me/4kq9P) We have a super group of speakers (keynote speakers are Ilme Schlichting, David Stuart, Erica Ollmann Saphire, Robert Stroud, Suzanne Scarlata, David Eisenberg, Wayne Hendrickson, Yvonne Jones, Eva Nogales, and Tom Blundell) After the main conference there will be an optional Phenix workshop with lectures and hands-on sessions on using Phenix for crystallography and cryo-EM. You can register now at https://cvent.me/4kq9P ! Best regards, Tom T Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

5 years, 10 months

Re: [phenixbb] How to use phenix for SAD data

by Erik Mckee

here is my suggestion: mosflm data needs to be scaled (use scala in ccp4) (make sure anomalous is turned on) (this should give you a mtz file with anomalous data) then in the phenix gui under wizards, choose AutoSol the first screen will ask you to choose your mtz and experiment type (sad) the next screen will ask the file name again, but will be already filled in, leave it the next screen will ask what columns to output, you can remove all but the anomalous I's (either the +/- or the DANO/SIGDANO format) (will be written as a sca file after this step) the next screen will look like the first, and should just have a single sca file on it (output from the previous screen) the next few screens allow you to set the experiment parameters if all goes well, auto sol should start running after 3 or 4 more screens On Tue, 11 Jul 2006 pramod(a)cdfd.org.in wrote: > Hi all > i am using the Phenix-GUI first time ,for solving the sad data. I processed > my raw data with the mosflm.Further output of the mosflm were used for > getting other information or working through this data.so, i started with > the strteiges of solve through mad. after setinmg up all the anamolous > parameters ,this is always displaying red in the very first in the setup > anamolous data gui with the information that format error.i used the format > ccp4 unmerged i.e the direct output of the mosflm after integration.i also > used the conversion of mtz file into hkl through ccp4 scaling and merging > intensities-in which one option i used is the get output as unmerged intensities > but, that also didnot worked. > suggestions will be appreciated > and also i want the deatiled information about how to use the phenix gui > properly. > with regards > > Pramod Kumar > Junior Research Fellow > c/o-Dr.Shekher C Mande > Center for DNA Fingerprinting and Diognostics > ECIL road > Nacharam > Hyderabad-76 > > > > > > - > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

18 years, 11 months

Re: [cctbxbb] dependency on phenix

by Pavel Afonine

Hi Roger, thanks for pointing this out. This must be an overlook. I will see what can be done to eliminate this. Pavel On 12/10/14 5:17 AM, Roger Martin wrote: > Hi, > > looking through > http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/minimi… > shows at line 61 > from phenix.refinement import weight_xray_chem > and > http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/occupa… > line 134 > > Is weight_xray_chem.py code that could move to cctbx? > (cctbx_project/mmtbx/refinement/weight_xray_chem.py) > > Are there other cross dependencies? > > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb

10 years, 6 months

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

by Ed Pozharski

On Mon, 2011-07-11 at 13:56 -0400, zhangh1(a)umbc.edu wrote: > but I only have model Fc available You don't need a model to expand to P1. All you need is the symmetry operators. If you want to comb through cctbx code or other (e.g. I gleaned a lot of this stuff from clipper libs), the expansion is routinely done upon map calculation. I do have some code that may help you, albeit it may need to be modified a bit depending on your specifics (warning: it's all python). I've done some of this looking to calculate the electron density curvature, and the first step is to expand to P1 before you can do fourier transforms and such. Cheers, Ed -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

13 years, 11 months

Re: [phenixbb] protein-ligand complex structure

by Kendall Nettles

Hi Wei, In our experience this can be caused by having an incorrect cif file for the ligand, especially if you see it fits well in Coot but looks wrong after refinement. It's a pain to go through the cif file by hand, but you can read through it and see if all the restraints are correct, or take a close look at the geometry of the refined ligand. You might be to try generating the cif file with ProDRG and the PHENIX tool, and compare refinement done with each. Of course, the easiest solution is to take up Pavel on his offer to take a look at it! He and others on the PHENIX team have helped us quickly resolve similar problems with the ligands a number of times, and we ended up on a paper together on one particularly nasty case that he spent more time on. all the best, Kendall On Oct 24, 2013, at 10:19 PM, Wei Shi <wei.shi118(a)gmail.com> wrote: > Hi all, > I am working on a structure of protein-ligand complex. Four ligands are placed for the dimer protein and the density for the two ligands of the first monomer is better than the density for the other two ligands of the second monomer. Ligand is moved to fit density better in Coot (and for two ligands of the first monomer, they fits the density almost perfectly), but after a refinement in phenix (default settings + NCS restraints + Secondary structural restraints + Optimize X-ray/stereochemistry weight +Optimize X-ray/ADP weight), some part of the ligand which fits density good before moved out of the density again...Besides, it always shows green density in Coot for the ligand region even in places where the ligand is in density... > Any suggestions or ideas about how to fit the ligand better and why the density for ligands of the second monomer is worse than that for the first monomer and why the ligands would move out of density after refinement? > Is it because the protein model is not good enough to get the ligand density good? There is a conformational change upon ligand binding, and I rebuilt some part of the protein manually, and the density for a region of about 30 residues is not very good, and I tried to mutate those to alanies and refine, but it didn't help me see the density better... > Any suggestions or ideas on how to improve this protein-complex structural model? Thank you so much! > The statistics for the current best model is as follows, and the resolution of the dataset is 2.8Å. > > start final > ------------------------------ > ---------------- > R-work: 0.3359 0.2993 > R-free: 0.3619 0.3558 > RMS(angles): 1.03 1.55 > RMS(bonds): 0.006 0.007 > > MolProbity validation > Ramachandran outliers: 4.7% (Goal: < 0.2%) > Ramachandran favored: 85.3% (Goal: > 98%) > Rotamer outliers: 4.5% (Goal: 1%) > C-beta outliers: 0 (Goal: 0) > Clashscore: 7.43 > Overall score: 2.56 > > Thank you so much! > > Best, > Wei > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

11 years, 8 months

Search results for query "look through"