- phenixbb - phenix-online.org

Restraints file for a new amino acid residue
by Joseph Noel 14 Aug '10

14 Aug '10

Hi All, How does one create a new CIF file using Elbow for a non-natural amino acid not found yet in the PDB? I know how to carry it out for the isolated residue readily (but of course thinks it is isolated and doesn't include the necessary peptide bonding) but how does one ensure the correct backbone restraints for it are included since it is not isolated but part of the chain? Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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too many outliers
by intekhab alam 13 Aug '10

13 Aug '10

Hi there I have recently solved a structure at 2.71A resolution using CCP4 (Refmac5) with R and R free of 22 and 29 respectively. The model is nicely fitted in the map and everything looks except in some loop region where the map is not fitted well. I just finished modelling and checked ramachandran plot which is showing unreasonably high number of outliers (12%) with only 65% in the favoured region. I am thinking to use phenix_refine with simulated annaeling and using the option fix bad chain rotamers. What else i can do aprt from this. i will be highly thankful for the suggestions. Apart from this can anyone let me know how -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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wxu for anisotropic ADP refinement
by Joseph Noel 13 Aug '10

13 Aug '10

Dear Phenix User Community, If one would like to try different weights for anisotropic ADP refinement (ie fixing wxu) should one be focusing on numbers like - wxu = 199.878301 - instead of the usual low numbers such as - wxu = 0.25 - found during isotropic ADP refinement? While optimize X-ray/ADP weight is useful in phenix, I am still getting anistropic ADP values that are a bit outside what one might expect at 1.5 A compared to the PDB. For the latter, I check things using Parvati (http://skuld.bmsc.washington.edu/parvati/). Thanks! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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difference in estimated error between phenix and refmac
by Ling Qin 13 Aug '10

13 Aug '10

Dear Colleagues, I am refining a 2.15 A structure that was previously refined with refmac by someone else. Without changing anything in the refmac-refined model and using all the default phenix.refine settings, I am getting pretty much the same R and Rfree (from 19.3%/21.7% to 18.9%/21.8%), with an ML estimated error of 0.22 A. In the refmac-refined pdb file, the estimated error is much lower: 0.16 (based on R), 0.144 (based on Rfree), and 0.096 (based on ML). I am using phenix.refine version 1.6_289, but also tried 1.5_2 with the same result. Is there an underlying reason for this difference? Thank you very much for your insightful opinions in advance. Cheers, Ling

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autosol
by Abd Ghani Abd Aziz 12 Aug '10

12 Aug '10

Dear All, Just been trying to run autosol for SAD data with the new phenix (1.6.4-486) on ubuntu, but I get an error message: *********************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked ********************************************************************** xtriage appears to run OK, and I get the same error with unmerged or merged scalepack data. The same files in 1.6-289 (admittedly on OSX) work fine. I wonder if there is a known problem with this version of phenix? Thanks for any suggestions, Ghani

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Disappearing density?
by Kyle Dolan 12 Aug '10

12 Aug '10

Hi all, I attempted to improve the density around a helix and short linker region using an average kick map but it didn't make things look much better. I then tried creating a composite iterative-build omit map from phenix.autobuild, but in this case the electron density around the helix/linker in question largely disappeared! Is there another approach I can use that might improve my maps, or should I start questioning my data? The dataset has >95% completeness to 2.7 A so I am very curious as to why I am missing the backbone now, where before I was only missing the side chain densities. One thing I am wondering is if the problem could have something to do with symmetry; the part of the map I am looking at may be close to a two-fold crystallographic symmetry axis and I have been told that these regions tend to be very noisy and hard to model--comments? Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago ktd(a)uchicago.edu

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Statistics for pdb deposition
by Elwood A. Mullins 12 Aug '10

12 Aug '10

I apologize if this has already been addressed. I'm trying to deposit a model to the pdb database, but there are a few required values in the Refinement Statistics section that I'm not sure where to find. 1,2) Cut-off sigma (F), Number unique reflections (observed) Looking at the log file, it appears that the cut-off is 0, which results in 330 reflections being rejected. The pdb header, however, lists the number of reflections at a value corresponding to 352 reflections being rejected. Why are these numbers different and which should I report? 3) R-factor (all) R-factor (all) includes both the working and test sets in addition to reflections rejected by the sigma cut-off. Does PHENIX calculate this value? I know R-factor (observed), which includes the working and test sets but not rejected reflections, is calculated. Thanks, Elwood

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elbow: more detailed website : 404
by Lepore, Bryan 12 Aug '10

12 Aug '10

this link : http://www.phenix-online.org/elbow/docs/index_image.html is 404 the link is found on this page : http://www.phenix-online.org/documentation/elbow.htm ... IS there a "more detailed website"? i saw the reel site. -bryan

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Random seeds?
by Joseph Noel 11 Aug '10

11 Aug '10

Hi All, Okay, a fairly mundane question concerning random seeds in Phenix. Obviously they are random but any restrictions on how many digits phenix will accept? Any other restrictions? Are they (it) only used for coordinate refinement or do the random seeds get used for other things as well? I know about hydrogen building but wandering about other refinement protocols and the use of "new" random seeds. I realize some use different random seeds to create slightly different models after refinement. Is it useful to change the number from time to time when going through iterative rounds of re-building and coordinate refinement? What about ADP refinement? Sorry for the mundane questions! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Restraint creation for ligand
by Hermella Woldemdihin 10 Aug '10

10 Aug '10

Hi! I was trying to fit my ligands into my model and density. And I have successfully fitted 2 ligands (same molecule) but my 3rd ligand is different molecule. After fitting my 3rd ligand (with COOT) and merged it with my protein, II created a restraint file with: phenix.elbow my_model_coot-0..pdb --do-all --output=all_ligands It created all_ligand.cif, which I used for in my next refinement with Phenix (GUI). I supplied my density, model and the restraint file and run phenix.refine. Unfortunatate I'm getting this error message when it starts to run phenix.refine and opening COOT window: Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 1 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands. I have use the same procedure for fitting my first 2 ligands. and it worked. But this time it failed! What do you think I should do? Thanks Hermi

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