Search results for "look through"

[phenixbb] Judging AutoSol Output

by agb838＠mail.usask.ca

I have some basic questions about the output from Phenix. Basically I have a data set that gave a solution, but I am not exactly sure how to tell about the quality of the solution from the outputs. The overall score is 110. I am not sure exactly what that refers to or how good/bad it is. I have attached the AutoSol.output file. Any basic suggestions at what I should be looking at, or if this is even the right file, would be helpful. The resolve.mtz and resolve.pdb look alright. They are a good start, but much improvement is needed. If anyone has some suggestions as to how to improve the output, that would also be helpful. I have also run the data through solve/resolve through the command prompt and it repeatedly locates four heavy atom sites (the data set is SAD). Yet, when Phenix is used, 16 sites are found. Why the difference and how do I tell what is working better and why. Thank you, Angela Hoffort

19 years, 9 months

[phenixbb] few questions about resolving new structure through MR

by Zhihong Yu

Hi, all I'm a rookie in resolving a brand new structure. I have some questions for my current case and look forward to some suggestions. Now I’m working on a protein like this: N-ter(55aa)—domainA(110aa)—linker(30aa)—domainB(150aa)—C-ter(20aa), I got a diffraction data just to 3.5Å, and there is no complete homology structure in pdb bank, but only a homology structure (named as structureX later) for domainB with ~30% sequence identity, so I have some questions as following: 1. Is it possible to find a resolution through MR approach using structureX as a search model? Especially considering that the resolution is only 3.5Å. Currently I just tried once using phaser and refine the structure for 3 cycyles, I can get a R/Rfree of 0.45/0.55, and it looks like most of backbone in the structureX, especially those within helix or sheet, can be well described by 2Fo-Fc density. Is this primary result promising or not? 2. If it’s possible, what’s the general optimal procedure I should follow? Really thanks for any advice and suggestions! Zhihong

12 years, 3 months

[phenixbb] Submitting SLURM jobs through PHENIX GUI

by Thomas Cleveland

Hi all, Has anyone gotten SLURM job submission to work through the PHENIX GUI? Under Preferences/Processes, I set Queueing system to SLURM with queue submit comand "sbatch." The job does indeed submit to the queue, and I can see it in the listing using the "squeue" command. However, there is quickly an error, "OSError : [Errno 2] No such file or directory: '/home/clevelandt/data/MX/181016_P1_merge/phenix/.phenix/tmp/10.libtbx_info.LOCK'". I've attached the full error log. Basically the program is looking for a lock file that isn't there. I'm not sure why it's not there. All compute nodes should have access to this directory, and there is no caching of any kind, so any files placed there should immediately be accessible. I can manually submit e.g. phenix.refine jobs to the queue using the command line and everything works fine. It would be really nice to have it through the GUI though. Thanks for any help, Tom

7 years, 3 months

Re: [phenixbb] phenix refinement question

by Pavel Afonine

Hello, >> I have only started using PHENIX and have made an interesting observation. >> If I run my model through PHENIX refine (individual sites, individual ADPs, >> occupancies, optimized X-ray/stereochemistry weight, optimized X-ray/ADP >> weight options selected) I obtain R/Rfree 0.15/0.18 and very nice geometry >> values (data is to 1.7A). However, if I now take this refined model and run >> it through Refmac (without any refinement) I obtain R/Rfree of 0.19/0.21. sounds good to me, I would be worried otherwise. >> Can anyone explain why is there such a big difference? Will this be an issue >> during PDB submission? Have a look at this: J. Appl. Cryst. (2010). 43, 669-676 phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart and P. D. Adams > Take a look at what phenix.refine reports for the number of > reflections used for refinement in the logfile - I believe it will > discard reflections that are flagged as suspicious (can't remember the > reference, I think it's one of Randy Read's papers), It is typically from zero to a few dozens of reflections and unless they are ~1.e+9 removing them rarely visible in terms of R-factor (if you just re-compute it). Pavel.

15 years, 2 months

[phenixbb] Where is phenix.refine finding starting r values?

by Bart, Aaron G

Greetings, I am fairly new to crystallography, and have just started to use Phenix for structural refinement. I am currently working on a 2.8A structure that was run through multiple rounds of rigid body refinement via Refmac and manual revision using Coot. I eventually got stuck where large portions of my molecule had very poor density and the rwork and rfree stayed around 0.3. I then performed a TLS refinement which resulted in better density, and tried running it through phenix.refine with default ADP settings, as well as simulated annealing. It worked beautifully, however when I looked at the log file for the refinement, phenix was reporting a starting rwork and rfree that represented my first stage of refinement in refmac, 0.38/0.44. My question is, is phenix somehow neglecting the refinement that was done in refmac? Regards -Aaron

16 years

Re: [phenixbb] few questions about resolving new structure through MR

by Nathaniel Echols

On Thu, Nov 7, 2013 at 8:34 AM, Zhihong Yu <nkyuzhih(a)gmail.com> wrote: > 1. Is it possible to find a resolution through MR approach using > structureX as a search model? Especially considering that the resolution is > only 3.5Å. Currently I just tried once using phaser and refine the > structure for 3 cycyles, I can get a R/Rfree of 0.45/0.55, and it looks > like most of backbone in the structureX, especially those within helix or > sheet, can be well described by 2Fo-Fc density. Is this primary result > promising or not? > No, that's a classic example of model bias. Positive (and continuous) mFo-DFc density outside of the placed atoms is what you should be looking for, but I suspect there will be very little. It's basically impossible to tell from this result whether the placement of structureX is even correct, although the Phaser statistics may be informative. One unrelated suggestion: given the low sequence identity, I think it will be very important to properly prepare the input model (use Sculptor for this). 2. If it’s possible, what’s the general optimal procedure I should follow? > I confess I haven't had to solve a structure like this myself - just seen a bunch of datasets where similar attempts didn't work - but it's hard to see how it can be solved without experimental phasing information (SeMet, etc.). The good news is that if you can get a correct MR solution for domainB, you can use MR-SAD to find heavy atom sites and solve the structure, which should be easier than starting from no phases at all. -Nat

12 years, 3 months

[phenixbb] phenix automr

by sbiswas2＠ncsu.edu

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

16 years, 10 months

[cctbxbb] dependency on phenix

by Roger Martin

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?

11 years, 2 months

Re: [cctbxbb] Not wishing to raise this again but...

by Luc Bourhis

> That's right. In practice I bisect the date instead; that way I can issue the same command in all my svn source directories from sf.net and lbl.gov. For example: > > svn update -r "{2014-03-08 18:00}” You can do that with git as well but it looks more geeky: git checkout `git rev-list -n 1 --before="2014-03-08 18:00” master` although you could easily put that in a tiny script called checkout-date and then issue “git checkout-date”. In any case, git bisect is easy to run in the simple case where you know HEAD is broken but 3c303a24 is good: % git bisect start HEAD 3c303a24 — This will checkout some version half-way through. You test and you find it’s broken: % git bisect bad If on the contrary, you find it works fine: % git bisect good Either of those commands will again checkout some version half-way through. Then you continue until git tells you the bisection is done.

9 years, 7 months

Re: [phenixbb] Phenix-RSR model fit issue in CS-Map

by Pavel Afonine

Hi Pramod, I need to see the map and models before and after refinement to diagnose the issue. Can you share the files? I will have a look once I have the files. Pavel On 10/22/19 10:34, pramod kumar wrote: > Dear Experts, > > I have a map generated through cryosparc (ab initio-reconstr and > homo-refine at 3.7A* FSC and sharpened in Scipion and separately in > EMAN2). I have build the initial pdb through BALBES which has perfect > validation parameters and nice fitting in the map (with the mtz > output) but the co-ordinates are shifted from the true origin of > CS-map. I used phenix-RSR to fit and refine, but validation results > remained too far to accept the model as good solution and also a small > region entered in wrong nearyby densities. > > So far following independent and downstream approaches I have taken:- > > In phenix; dock in map, map to model, rigid body refine followed by > real space refine (with both .map and converted .mtz), using only > chain A-map boxing and model generation through NCS. > > I have tried chimera fit for entire assembly and also only one chain > in boxed map and full map but still the validation remained far from > acceptable values and a small region in wrong neighboring density. > > Please help. > > > -- > Best regards, > Promod

6 years, 3 months

Search results for query "look through"