- phenixbb - phenix-online.org

Re: [phenixbb] Restraints file for a new amino acid residue
by Joseph Noel 16 Aug '10

16 Aug '10

Pavel, I sent you the associated pdb file as an attachment. The site in question is 169 in both monomer A and monomer B. I think one way around the problem for me is to create alternative conformations for the residues on either end of the modified cysteine. In that way I can refine each as a section of alternative conformations and then I think things should link up both in Phenix and COOT. COOT is particularly problematic. It only recognizes conformer A and not any additional conformers for a particular position if the name of the amino acid changes. I guess my case is not that common - ie a mixture of oxidation states of a regular amino acid. 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 ___________________________________________________________

1 0

Re: [phenixbb] Restraints file for a new amino acid residue
by Joseph Noel 13 Aug '10

13 Aug '10

Thanks all for the advice. Basically that is what I have been doing. It is actually an oxidized cysteine to sulfenic acid. I am refining the site as alternative conformers with the normal Cys, the single oxidation state to sulfenic acid (CSO) and the double to sulfinic acid (CSD). I know that CSO is in the phenix library but it adds hydrogens to the amino group every time I run elbow or ready set. I then I have to edit the PDB file to delete the hydrogen or Phenix will not refine. I also have problems in COOT. It will not let me move the residues torsional angles. I have checked other structures in the PDB and the density fits perfectly with the structures of many such oxidized systems but for some reason Phenix is giving me some problems. I was going to create a "new" residue and explicitly define the oxygen as charged rather then protonated since the pKa of sulfenic acid is quite low. Maybe the problems all stem from refining this particular position with three alternative "conformers", each conformer of which is chemically distinct. For now, I have CSO labeled as convention BCSO for conformer B. Cys is ACYS. 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 ___________________________________________________________

2 1

Autobuild error message
by bschmidt＠berkeley.edu 13 Aug '10

13 Aug '10

Hello all, I am trying to use phenix.autobuild from the command line to generate either composite omit maps or prime and switch maps. In either case, when I try, the program starts to run for a while before failing and giving me the following error message: "Failed to carry out AutoBuild_build_cycle: Sorry...the file AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz is missing..." I'm not sure why that would be the case, or where that mtz is supposed to come from. Can anyone explain what might be the problem? Thanks, Bryan

2 2

Phaser SAD module - resolution question
by Peter Grey 13 Aug '10

13 Aug '10

Dear Phenix community, I am using Phaser SAD module with a poor MR model to locate the initial heavy-atom sub-structure. I have a 3A dataset but the anomalous signal is weak at the higher resolution shells. I would like to ask for your advice regarding the resolution I should use in Phaser. I thought that for the sake of just locating the sites I should use relatively low resolution (let's say 3.5 or even 4A) and then run Phaser a second time. In this second run I would use the highest-resolution and let Phaser only refine the sites (located in the first run) during one cycle and calculate the combined phases. Thank you in advance for your suggestions and advice, Peter

2 1

Where to find optimized wxc_scale/wxu_scale weighting factors after optimization
by amadrona＠uci.edu 13 Aug '10

13 Aug '10

Hello, I ran a refinement optimizing geometry and B factor weighting factors using optimize_wxc=true optimize_wxu=true. I was given these statistics in the pdb header: Rwork Rfree Bonds Angles start .1588 .1838 .007 1.235 end .1454 .1780 .016 1.601 (1.37 A resolution) 1. I would like to find the optimized weighting factors in the log file but cannot. Instead I find the following (pasted below). However, the scale here doesn't make sense to me because many our greater than 0.5. How do I find the optimized values so that I can use them in further rounds of refinement? I'm sorry if this has been covered in previous posts but I could not find an answer. 2. Can anyone explain the concept of optimizing the B-factor? I don't understand how changing it brings you closer or further from an ideal model as oppose to xray. (which is how I make sense of refining the geometry) Thank you -Yarow ================================ xyz refinement =============================== Start r_work= 0.1462 r_free= 0.1784 bonds= 0.015 angles= 1.53 r_work= 0.1492 r_free= 0.1792 bonds= 0.005 angles= 1.08 scale= 1.00 r_work= 0.1484 r_free= 0.1788 bonds= 0.006 angles= 1.14 scale= 1.40 r_work= 0.1480 r_free= 0.1787 bonds= 0.007 angles= 1.19 scale= 1.80 r_work= 0.1476 r_free= 0.1785 bonds= 0.008 angles= 1.23 scale= 2.20 r_work= 0.1473 r_free= 0.1785 bonds= 0.008 angles= 1.26 scale= 2.60 r_work= 0.1471 r_free= 0.1784 bonds= 0.009 angles= 1.29 scale= 3.00 r_work= 0.1469 r_free= 0.1784 bonds= 0.010 angles= 1.32 scale= 3.40 r_work= 0.1467 r_free= 0.1783 bonds= 0.010 angles= 1.34 scale= 3.80 r_work= 0.1465 r_free= 0.1782 bonds= 0.011 angles= 1.36 scale= 4.20 r_work= 0.1464 r_free= 0.1782 bonds= 0.011 angles= 1.39 scale= 4.60 r_work= 0.1463 r_free= 0.1782 bonds= 0.011 angles= 1.40 scale= 5.00 r_work= 0.1461 r_free= 0.1781 bonds= 0.012 angles= 1.45 scale= 6.00 r_work= 0.1458 r_free= 0.1781 bonds= 0.013 angles= 1.49 scale= 7.00 r_work= 0.1456 r_free= 0.1781 bonds= 0.014 angles= 1.53 scale= 8.00 r_work= 0.1454 r_free= 0.1781 bonds= 0.015 angles= 1.57 scale= 9.00 r_work= 0.1453 r_free= 0.1780 bonds= 0.016 angles= 1.60 scale= 10.00 r_work= 0.1495 r_free= 0.1794 bonds= 0.005 angles= 1.05 scale= 0.85 r_work= 0.1501 r_free= 0.1797 bonds= 0.005 angles= 1.02 scale= 0.70 r_work= 0.1507 r_free= 0.1800 bonds= 0.004 angles= 0.98 scale= 0.55 Final r_work= 0.1453 r_free= 0.1780 bonds= 0.016 angles= 1.60

4 6

Restraints file for a new amino acid residue
by Joseph Noel 13 Aug '10

13 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 ___________________________________________________________

3 2

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

2 1

wxu for anisotropic ADP refinement
by Joseph Noel 12 Aug '10

12 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 ___________________________________________________________

2 1

difference in estimated error between phenix and refmac
by Ling Qin 12 Aug '10

12 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

3 2

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

3 4

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

4 6

Statistics for pdb deposition
by Elwood A. Mullins 11 Aug '10

11 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

2 1

elbow: more detailed website : 404
by Lepore, Bryan 11 Aug '10

11 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

2 1

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 ___________________________________________________________

3 2

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

3 2

monomer-dimer
by intekhab alam 10 Aug '10

10 Aug '10

Hi everyone Sorry for some non specific query!!!!! i am working with a protein that shows a dimer in the crystal structure but when i tried to figure out that with standard molecular markers in gel filteration (superdex-200, 24ml column) it turned out to be a monnomer. Native gel analysis after incubating the protein at 20 degree, 37 degree showed more dimer at 20 degree celcius as compared to 37. I tried similar strategy in gel filteration by incubating my protein at various temperature,where a lot of precipitation was observed at 37 degree celcius and after removing the precipitates i run the gel filteration that has 0.5 ml higher elution volume as compared to samples incubated at 20 degree celcius and 4 degree celcius.( Is this significant) Furthermore i have done some experiments in cold room (4 degree) where the elution volume is stuck at a point irrespective of the conditions (as Flow rate, concentration of protein etc) and that is higher than that of the room temperature by 1 ml. Standard moleculr weight markers also show higher elution volume in cold room in comparison to the room temperature by 1 ml. I will be highly obliged if someone suggest some literature or any otherway to do gel filtrtaion so that i can clearly resolve this issue. Also let me know if there is some literature available on effect of temperature on the elution volume of proteins. Thanks in advance -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

2 2

Phenix reflection statistics
by Lepore, Bryan 07 Aug '10

07 Aug '10

in this table : Overall correlation: 0.901 unused: - 16.7088 [ 0/9 ] bin 1: 16.7088 - 2.0456 [5236/5928] 0.858 bin 2: 2.0456 - 1.6241 [5610/5946] 0.744 bin 3: 1.6241 - 1.4189 [5539/5925] 0.641 bin 4: 1.4189 - 1.2892 [5357/5873] 0.516 bin 5: 1.2892 - 1.1969 [5405/5972] 0.497 bin 6: 1.1969 - 1.1263 [5241/5939] 0.464 bin 7: 1.1263 - 1.0699 [5067/5903] 0.408 bin 8: 1.0699 - 1.0234 [4960/5934] 0.416 bin 9: 1.0234 - 0.9840 [4808/5941] 0.376 bin 10: 0.9840 - 0.9500 [4700/5931] 0.348 unused: 0.9500 - [3339/6874] 0.330 the average CC is 0.508 +/- 0.17 if y is the correlation, and x is bin number, and 0.330 is excluded, that line fits with a CC=-0.941 (therefore R^2=0.885) is the median resolution per bin used for the overall CC? how is "unused" treated? -bryan

2 1

syntax for Averaged Kicked maps and maps.param
by amadrona＠uci.edu 07 Aug '10

07 Aug '10

Hello, Disclaimer: I am a newbie to both crystallagraphy and Phenix. I am running phenix.refine (v1.6-289) in the command line 1. I want to make averaged "kicked-maps" but I keep getting a syntax error. I tried renaming "maps.param" but this file was not recognized. 2. When I enter Phenix.maps into the command line I get a message that syas "not implemented" I am trying to get the latest versiou of phenix installed. The following is the syntax I put in my custom_params file Thanks -Yarrow refinement.main.number_of_macro_cycles = 2 #refinement.main.fix_rotamers = True refinement.refine.strategy = individual_sites+individual_adp refinement.output.prefix = CIN4_refine_omit refinement.output.serial = 12 refinement.output.write_def_file = True refinement.target_weights_wxc.scale = 0.2 refinement.main.max_number_of_interations=15 refinement.electron_density_maps { map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "FOFCWT_kicked" mtz_label_phases = "PHFOFCWT_kicked" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = false }

3 3

high average b-factor vs. Wilson B
by Geoffrey Feld 07 Aug '10

07 Aug '10

Dear PhenixBBers, I'm working on a 1.45 A structure I solved using MR (phaser) and I'm pretty close to finishing, just plopping in waters and fixing rotamers. Rw = 19.8 Rfree= 22.8. I am a little concerned because my Wilson B is 27.00 while my average B for macromolecule is more like 43, and for solvent is 48. I have enough data to use anisotropic ADP refinement, which was a big help in bringing down the Rfree, but the average B hasn't really moved much. Should I be concerned about this? Should I try adjusting the wxu, or some other parameter? Thanks! -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

7 13

Phenix reflection statistics
by James Fraser 06 Aug '10

06 Aug '10

What does the correlation coefficient that is reported at the end of phenix.reflection_statistics represent? (I would assume the CC of F1 vs F2 for all reflections with an observation in datasets 1 and 2). The documentation "...the output will also show the correlations between the datasets and, if applicable, between the anomalous differences, both as overall values and in bins." is a bit ambiguous. Also in the below comparison, how would the overall correlation be 0.901 when all the bins have correlations between 0.330-0.858? CC Obs 2 3 0.901 h,k,l Correlation of: 2: 1.mtz:F-obs,SIGF-obs 3: 2.mtz:F-obs,SIGF-obs Overall correlation: 0.901 unused: - 16.7088 [ 0/9 ] bin 1: 16.7088 - 2.0456 [5236/5928] 0.858 bin 2: 2.0456 - 1.6241 [5610/5946] 0.744 bin 3: 1.6241 - 1.4189 [5539/5925] 0.641 bin 4: 1.4189 - 1.2892 [5357/5873] 0.516 bin 5: 1.2892 - 1.1969 [5405/5972] 0.497 bin 6: 1.1969 - 1.1263 [5241/5939] 0.464 bin 7: 1.1263 - 1.0699 [5067/5903] 0.408 bin 8: 1.0699 - 1.0234 [4960/5934] 0.416 bin 9: 1.0234 - 0.9840 [4808/5941] 0.376 bin 10: 0.9840 - 0.9500 [4700/5931] 0.348 unused: 0.9500 - [3339/6874] 0.330 Thanks, James -- James Fraser jaimefraser(a)gmail.com Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

3 2

indicating proper SUBJECT
by Alexandre Urzhumtsev 06 Aug '10

06 Aug '10

Hello, Sorry to interfere, in no case I want to play a police. However, I would like to ask all phenixbb-participants to respect other and when sending their mails : - to USE the "subject" in all sending mesages (no mails with empty "subject") and - to use it PROPERLY (just recently we had several examples of irrelevant subject; I do not want to point them out explicitly) Indicating a proper subject is a matter of saving time of others, making proper archives and facilitating searches in them later. This problem is also relevant to the CCP4bb even when a similar request of putting proper "subject" was posted there many times. (Personally, I think this should be done in ANY correspondence, even to your friends, not only to phenixbb or ccp4bb.) In addition, I think that a presence of your name at the end of your mail is also a rule of a politeness (that is also not respected in a number of letters to our bb-s). With best regards, Sacha

2 1

unknown parameters file format?
by Kyle Dolan 06 Aug '10

06 Aug '10

Hi all, I tried to create my own set of refinement parameters by copying sections of a .def file to a new file I called myrefine1.params. When I tried to use this for phenix.refine from the command line I received this error message: Sorry: Unknown file format: myrefine1.params What should I do? Thanks, Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago ktd(a)uchicago.edu

3 2

Re: [phenixbb] follow up on message 2: phenix.maps --Message: not implemented
by amadrona＠uci.edu 06 Aug '10

06 Aug '10

Hello Pavel, The averaged kicked map looks great! I am able to see loop density that I could not see before. However, I still have one question: The kicked map were created when I put the map parameters in my custom_par file however, I was unable to run Phenix.maps in the command line. When I do this I get a message "Not implemented". I would like to create a ccp4 map for viewing in pymol without running refinement again. Do you know what could be causing this message? If I create "maps.params" by inserting the commands from the .def file Phenix does not recognize this file format. Any help would be appreciated. Thank you. -Yarrow > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://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. syntax for Averaged Kicked maps and maps.param (amadrona(a)uci.edu) > 2. Re: syntax for Averaged Kicked maps and maps.param (Pavel Afonine) > 3. Re: Phenix Autobuild (Thomas C. Terwilliger) > 4. New version complaint (Simon Kolstoe) > 5. Re: New version complaint (Nathaniel Echols) > 6. Re: New version complaint (Douglas Jacobsen) > 7. Re: New version complaint (Nathaniel Echols) > 8. Adequate size for Free R test set? (Joseph Noel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 Aug 2010 17:38:05 -0700 > From: amadrona(a)uci.edu > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] syntax for Averaged Kicked maps and maps.param > Message-ID: > <c56fb1561f816b0462d50ccdeb996317.squirrel(a)webmail.uci.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Hello, > > Disclaimer: I am a newbie to both crystallagraphy and Phenix. > > I am running phenix.refine (v1.6-289) in the command line > > 1. I want to make averaged "kicked-maps" but I keep getting a syntax > error. I tried renaming "maps.param" but this file was not recognized. > > 2. When I enter Phenix.maps into the command line I get a message that > syas "not implemented" > I am trying to get the latest versiou of phenix installed. > > The following is the syntax I put in my custom_params file > Thanks > > -Yarrow > > refinement.main.number_of_macro_cycles = 2 > #refinement.main.fix_rotamers = True > refinement.refine.strategy = individual_sites+individual_adp > refinement.output.prefix = CIN4_refine_omit > refinement.output.serial = 12 > refinement.output.write_def_file = True > refinement.target_weights_wxc.scale = 0.2 > refinement.main.max_number_of_interations=15 > > > refinement.electron_density_maps { > map { > mtz_label_amplitudes = "2FOFCWT_kick" > mtz_label_phases = "PH2FOFCWT_kick" > likelihood_weighted = True > obs_factor = 2 > calc_factor = 1 > kicked = True > fill_missing_f_obs_with_weighted_f_model = True > } > map { > mtz_label_amplitudes = "FOFCWT_kicked" > mtz_label_phases = "PHFOFCWT_kicked" > likelihood_weighted = True > obs_factor = 1 > calc_factor = 1 > kicked = True > fill_missing_f_obs_with_weighted_f_model = false > } > > > > ------------------------------ > > Message: 2 > Date: Mon, 02 Aug 2010 17:48:45 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] syntax for Averaged Kicked maps and maps.param > Message-ID: <4C57676D.9000901(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Yarrow, > > you can use GUI or the command line for doing this. > > 0) It would be best if you update to the latest version, although I > believe it might work with the one you have too: > > http://www.phenix-online.org/download/ > > 1) GUI: launch PHENIX GUI and go to Maps -> Create Maps. then just add > as many maps you want (or use pre-defined ones) and check a box for kick > map. > > 2) From the command line type: > > phenix.maps > > and hit Enter (Return). That will create a file called something > maps.params. Edit that file to add/remove the maps you need/ don't need > and set > > kicked = True > > for the one you want to be "kicked", and then run > > phenix.maps maps.params > > Let me know if you have any questions or problems. > > Good luck! > Pavel. > > > On 8/2/10 5:38 PM, amadrona(a)uci.edu wrote: >> Hello, >> >> Disclaimer: I am a newbie to both crystallagraphy and Phenix. >> >> I am running phenix.refine (v1.6-289) in the command line >> >> 1. I want to make averaged "kicked-maps" but I keep getting a syntax >> error. I tried renaming "maps.param" but this file was not recognized. >> >> 2. When I enter Phenix.maps into the command line I get a message that >> syas "not implemented" >> I am trying to get the latest versiou of phenix installed. >> >> The following is the syntax I put in my custom_params file >> Thanks >> >> -Yarrow >> >> refinement.main.number_of_macro_cycles = 2 >> #refinement.main.fix_rotamers = True >> refinement.refine.strategy = individual_sites+individual_adp >> refinement.output.prefix = CIN4_refine_omit >> refinement.output.serial = 12 >> refinement.output.write_def_file = True >> refinement.target_weights_wxc.scale = 0.2 >> refinement.main.max_number_of_interations=15 >> >> >> refinement.electron_density_maps { >> map { >> mtz_label_amplitudes = "2FOFCWT_kick" >> mtz_label_phases = "PH2FOFCWT_kick" >> likelihood_weighted = True >> obs_factor = 2 >> calc_factor = 1 >> kicked = True >> fill_missing_f_obs_with_weighted_f_model = True >> } >> map { >> mtz_label_amplitudes = "FOFCWT_kicked" >> mtz_label_phases = "PHFOFCWT_kicked" >> likelihood_weighted = True >> obs_factor = 1 >> calc_factor = 1 >> kicked = True >> fill_missing_f_obs_with_weighted_f_model = false >> } >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > > > > ------------------------------ > > Message: 3 > Date: Tue, 3 Aug 2010 07:26:46 -0600 (MDT) > From: "Thomas C. Terwilliger" <terwilliger(a)lanl.gov> > To: "Md. Munan Shaik" <munanbt2004(a)YAHOO.COM> > Cc: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Phenix Autobuild > Message-ID: <24375.128.165.0.81.1280842006.squirrel(a)webmail.lanl.gov> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Munan Shaik, > > Phenix autobuild can read several types of sequence files, but the basic > format is very simple: enter one copy of the sequence of each chain, > separated by a blank line or a line starting with ">" between chains. > You can optionally add any lines starting with ">" which will be ignored. > So here is an example: > >>>> alpha subunit (type 1) > MTMPYYASAEQIMRDRSELARKGIARGRSVVVLTFRDGVLFVAENPSTALHKVSELYDRL > GFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTEQPKPYEV > EICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLDLEAA > VGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIAGTALEQLVPAEPAAAS > ESAPEPKPDTETKPADTQD >>>> beta subunit (type 1) > MTADRPALRTGDRDTRLSFGSNLSSFTDYLRGHAPELLPENRIGHRSHSTRGGDGMESGD > LAPHGTTIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIEL > VRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGNLGAAMQGLAVVPLLVGYDLDADDES > RAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEETALRAAIESLYDAA > DDDSATGGPDLTRGIYPTAVTITQAGAVHVSEETTSELARRIVAERTEQGGSAR > > Please let me know if that doesn't do it! > > All the best, > Tom T > > > > > > >>> Hi everybody, >>> I have a problem with Phenix autobuild. I want to input sequence file >>> together >>> with the pdb and mtz that I got from molecular replacement. But I have >>> no >>> idea >>> which types of sequence files its required. if anybody please help me >>> out. >>> >>> >>> thanks >>> =================================================== >>> Md. Munan Shaik >>> Department of Chemical Biology >>> University of Padova >>> via G. Colombo 03 >>> Padova 35131, Italy >>> >>> >>> > > > > ------------------------------ > > Message: 4 > Date: Tue, 3 Aug 2010 15:31:46 +0100 > From: Simon Kolstoe <s.kolstoe(a)ucl.ac.uk> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] New version complaint > Message-ID: <8976EDFE-4E7E-42FD-96FE-319B56DE5413(a)ucl.ac.uk> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi there, > > I've been using version 1.6.2-432 on a Macbook and was particularly > enjoying the "Show Histograms" button on the POLYGON results page. > However today I updated to version 1.6.4-486 using the dmg installer, > and that useful option has disappeared! Is there a good reason for the > absence of this function, and if not can we get it back? > > Thanks, > > Simon > > --------------------------------------------------------------- > Dr Simon Kolstoe > Laboratory for Protein Crystallography > Centre for Amyloidosis & Acute Phase Proteins > UCL Medical School > Rowland Hill Street, London NW3 2PF > > Tel: 020 7433 2765 > http://www.ucl.ac.uk/~rmhasek > -------------------------------------------------------------- > > > > ------------------------------ > > Message: 5 > Date: Tue, 3 Aug 2010 07:39:11 -0700 > From: Nathaniel Echols <nechols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] New version complaint > Message-ID: > <AANLkTikU_SS2Z2VU0aZuqRNgrYUiiXLCTfztYy7NZjOF(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Tue, Aug 3, 2010 at 7:31 AM, Simon Kolstoe <s.kolstoe(a)ucl.ac.uk> wrote: > >> I've been using version 1.6.2-432 on a Macbook and was particularly >> enjoying the "Show Histograms" button on the POLYGON results page. >> However >> today I updated to version 1.6.4-486 using the dmg installer, and that >> useful option has disappeared! Is there a good reason for the absence of >> this function, and if not can we get it back? >> > > There is a reason, but not a good one. I'll fix it later today. FYI, the > "PDB Statistics" tool offers another way to view histograms, although it > requires that you manually specify the resolution range. > > -Nat >

6 14

B-factors
by Hermella Woldemdihin 06 Aug '10

06 Aug '10

Hi All! Where can I set B-factor for water in phenix.refine on the GUI version of phenix? Thanks!

3 2

r-work and r-free for specific resolution range(s)
by Kay Diederichs 04 Aug '10

04 Aug '10

Hi, is there a way to get the R-factor statistics from phenix.refine, for a specific resolution range, e.g. 2.5-2.6A ? The reason I ask is that I would like to specify the same resolution range as the data reduction program does. I tried with phenix.reflection_statistics x_map_coeffs.mtz x_data.mtz --low-resolution=2.6 --resolution=2.5 but with the default settings, phenix.refine writes 2FOFCWT and FOFCWT, but not FC . So it looks like I have to re-run phenix.refine and make it write out FC? Or is it easier to run phenix.xmanip for that purpose? thanks, Kay

3 2