- phenixbb - phenix-online.org

phenix.cif_as_mtz
by Bryan W. Lepore 12 Nov '09

12 Nov '09

[ v. 1.5 release tag 2 intex-linux-2.6 redhat-e4.8 ] `phenix.cif_as_mtz file.cif --symmetry=FILE.pdb --show-log --show-details-if-error` .. reports "No data extracted from input cif file.", nothing else. command works w/ other .cif/.pdb's, CRYST1 lines, etc. look comparable between them,... not sure where to look next. thanks for any suggestsions. -bryan

2 1

Nino Campobasso is out of the office.
by Nino.2.Campobasso＠gsk.com 11 Nov '09

11 Nov '09

I will be out of the office starting 11-Nov-2009 and will not return until 12-Nov-2009.

1 0

Failed to make map after phenix.refine
by Zhou, Tongqing (NIH/VRC) [E] 11 Nov '09

11 Nov '09

Hi, All I am having problem with the new 1.5.2. After few rounds of refinement, the program failed to write out maps. It ended with: "Sorry: Duplicate mtz_label_amplitudes:FOFCWT" Here is the portion in my param file which worked fine before: electron_density_maps { map_format = *xplor map_coefficients_format = mtz *phs suppress = None map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 } } Thanks in advance for your help. Tongqing

2 1

C-ter amidation of peptide
by Nate Nicely 10 Nov '09

10 Nov '09

Dear all, How best to handle a C-terminally amidated peptide in phenix? I defined the atom as 'N' and the resname as 'NH2' following a structure I found that also bears a C-terminally amidated peptide. However phenix.refine seems not to be making the linkage between the amide and the preceding residue. Putting the structure into phenix.elbow returns, "No unknown residues." Thanks, Nate N.

3 2

Glycan refinement
by Zhou, Tongqing (NIH/VRC) [E] 10 Nov '09

10 Nov '09

Dear All, I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don't know how to do the "apply_cif_link' for the extensions such NAG-NAG, NAG-MAN, MAN-MAN...., any suggestions are appreciated. Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

5 9

Problem reading ".edits" parameter file
by John Pascal 06 Nov '09

06 Nov '09

Hello, On a previous version of PHENIX, 1.4-153, I was able to read in a parameter file with geometry constraints. Upon loading the file, the program asked when to execute the commands, I said at run time, and everything worked fine. Using the same parameter file in PHENIX 1.5-2, I am no longer asked about when to execute the file, and when I proceed to run the refinement, the program quits stating an unexpected character. I can't find anything obviously wrong with the parameter file. Any suggestions? The previous version of PHENIX (the one that worked) is no longer located on my server, so I can't easily return to that version. Thanks. Best Regards, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

2 1

Phaser question : RMS deviation and FOM
by Peter Grey 06 Nov '09

06 Nov '09

Dear Phenix developers, The expected RMS deviation input to Phaser affects the FOM estimation of phases quality. This in-turn affects the sigmaa weighted maps and most importantly the density modification steps that follow phaser. I would like to ask if, based on the phaser solution and the LLG parameter, one could optimize the RMS estimation or know the real RMS deviation that would result in more true FOM. Thanks, Peter With condolences to the family of Warren DeLano who will be sorely missed

2 1

Analyzing MIR datasets
by Rajagopalan, Senapathy 06 Nov '09

06 Nov '09

Hi All, I am a new user to Phenix and am trying to process MIR datasets from a parameter file typing 'phenix.autosol mir.eff' and keep running into the error message saying: _______________ Possible choices: /Users/sena/data/crystallography/raw1025/Processing/iafinal_d212121.mtz:I,SIGI,merged /Users/sena/data/crystallography/raw1025/Processing/iafinal_d212121.mtz:IPR,SIGIPR,merged Please use scaling.input.xray_data.obs_labels to specify an unambiguous substring of the target label. Unable to get range of aniso B from xtriage output Multiple equally suitable arrays of observed xray data found. ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mir: Sorry, there is something wrong with the file /Users/sena/data/crystallography/raw1025/Processing/iafinal_d212121.mtz ... xtriage cannot analyze it? ******************************************************************************** ___________________ The 'mir.eff' file contains: ------------------ # autosol { seq_file = sequence.dat #scaling.input.xray_data.obs_labels='I SIGI' # xray_data_labels = FP, SIGFP # autosol.input.xray_data.labels=FP labels='I SIGI' crystal_info { space_group = p212121 unit_cell = 49.020 73.140 187.350 90.000 90.000 90.00 } native { data = iafinal_d212121.mtz } deriv { data = s10final_d212121.mtz atom_type = I sites = 2 inano = noinano *inano anoonly } deriv { data = s13final_d212121.mtz atom_type = I sites = 1 inano = noinano *inano anoonly } deriv { data = s23final_d212121.mtz atom_type = I sites = 1 inano = noinano *inano anoonly } } ----------------- I guess the error comes because the program is not able to make a choice as to which columns to take from the mtz file. But no matter what 'label' syntax I use or where I use it, it doesn't seem to help. Obviously, I am missing something here. So could someone please help me with this. Also, I tried the same thing using the phenix wizard and it still gives me the same error. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Ranked No. 8 on FORTUNE magazine's list of the "100 Best Companies to Work For" in 2009 Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

molecular replacement - restricting rotation around a specified orientation
by Christine Gee 06 Nov '09

06 Nov '09

Dear Phenix developers, We have a protein with two sub domains (N-lobe and C-lobe) we are trying to solve by MR. The C-terminal sub domain solves fine (TFZ 11.1), but the N-terminal lobe is not being placed correctly. I read in the online documentation that you can specify a limited rotation range around the orientation you would expect for the N-lobe based on the C-lobe orientation. My question is, how do specify what orientation to start with? I know I need some Euler numbers, but are they just the same ones that the C-lobe writes out with and I use an N- lobe that is basically the other half of the C-lobe pdb (ie the X,Y,Z co-ordinates are consistent with each other at the beginning of the search)? Or do I need to position the N-lobe with the solution C-lobe and write it out for use in the search model, and then how do I specify the Euler? Also we were going to try and use normal mode perturbation to generate an ensemble and I was wondering if there is more documentation somewhere on how to do that? Regards Christine

2 1

about Turbo Frodo
by Zhongli Cui 06 Nov '09

06 Nov '09

Dear all, I have ever used Turbo Frodo as the modelling software in protein crystallography. It is a very convinient software to learn. But it seems that the lience email of turbo is out of work. Does anyone know if Turbo is still maintained by AFMB and the new email for lience? Thanks Zhongli ---------------- Cui Zhongli Professor, Ph.D Dept. of Microbiology College of Life Sciences Nanjing Agricultural University 1 Weigang, Nanjing, 210095 Jiangsu Province P.R. China. Mail: czl(a)njau.edu.cn Tel: 86-25-84396753 Mob: (0)13951080529

1 0

Running Phenix 1.5.2 with Martin Horvath
by Raghav Kalia 04 Nov '09

04 Nov '09

I recently downloaded and installed phenix 1.5-2. I can launch the GUI by double clicking on the phenix icon. However, I cannot get to run phenix.refine on the command line. How does one set paths so that phenix.refine will be recognized in a terminal window? Raghav Kalia

2 1

Re: [phenixbb] phenixbb Digest, Vol 48, Issue 4
by Leo Sazanov 04 Nov '09

04 Nov '09

Thanks, restore results works fine for what I need now. phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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. Re: re-run jobs in GUI (Nathaniel Echols) > 2. Elbow ligand building (Joe Krahn) > 3. Re: Elbow ligand building (Nigel W Moriarty) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 4 Nov 2009 08:34:24 -0800 > From: Nathaniel Echols <NEchols(a)lbl.gov> > Subject: Re: [phenixbb] re-run jobs in GUI > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <529970F2-E319-4152-B4F1-E46184755554(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes > > On Nov 4, 2009, at 8:08 AM, Leo Sazanov wrote: > >> Hi, in a new GUI how can one re-run previous jobs (to make some >> modifications to them)? >> > > Open the main GUI (the command 'phenix', or click the home button on > the toolbar of any other program), click the "job history" toolbar > button, select a job from the list, and click "restore results". This > should restore both the results tab or window, and the configuration. > There is also a "restore last job [for the current project]" button on > the toolbar. Any inconsistencies here are definitely a bug, but it > was working for most programs in 1.5-2. (The main exception is the > reflection file editor, but that will also save/restore results in the > next available nightly build.) > > >> If I just try to open parameter (.eff) file from the main file menu in >> Autobuild, the file does not show up, even though it exists. >> Just adding it to the list of input files works, but the information >> is >> not passed on into GUI? >> > > > It's a little complicated right now. If you want to apply the > contents of a parameter file, this is best done at startup - e.g. drag > and drop the file onto the launch icon, or use it as a command line > argument ('phenix.autobuild params.eff'). For phenix.refine, you can > also save default parameters (Preferences->Refinement, or project > settings, or from the utilities menu) and it will start with them pre- > loaded. Once the program window is drawn, however, it's clumsier - > files *should* be passed down to the command-line module (if not, also > a bug), but they won't immediately be applied to the GUI, because of > the way it tracks parameters internally. > > I can't promise that every pre-existing configuration file will be > processed cleanly by the GUI - it's difficult to anticipate what users > will try to do. If you encounter cases where the parameters are > misinterpreted, let me know. > > -------------------- > Nathaniel Echols > Lawrence Berkeley Lab > 510-486-5136 > NEchols(a)lbl.gov > > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 04 Nov 2009 12:35:01 -0500 > From: Joe Krahn <krahn(a)niehs.nih.gov> > Subject: [phenixbb] Elbow ligand building > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <4AF1BB45.20707(a)niehs.nih.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I am having some problems building ligand parameters with elbow. > > I have an accurate reference structure, but elbow seems to "regularize" > the coordinates in a way the distorts the structure. Is there a way to > disable this? > > With --opt, QM optimization should hopefully remove distortions, but it > is not doing a very good job for this molecule. So, I decided to > optimize using Gaussian, and a better basis set. > > It seems that the Gaussian interface is still fairly simple, and it > seems that you have to edit the Gaussian.csh template. So, I did that, > but got the "Gaussian does not seem to be installed" message. > Unfortunately, elbow runs the Gaussian script with output to /dev/null, > so there is no way to see any error messages. Maybe that should be done > only when the --quiet flag is given. > > I edited the Python source to let errors go to the tty, and found that > the problem is in the way the script is invoked using "csh -c %s.csh". > That only works if "." is in your $PATH, which is often the case. It > also invokes an extra instance of csh, because it is invoked as a system > command. The correct way to run a shell script is to leave out the '-c'. > Elbow makes the script executable, so an even better approach is to just > leave out "csh", and do "os.system('./%s.csh' % project)". Then, the > script can be in sh/bash/etc. Maybe the was the intent of using '-c'? > > Thanks, > Joe Krahn > > > ------------------------------ > > Message: 3 > Date: Wed, 04 Nov 2009 10:09:47 -0800 > From: Nigel W Moriarty <NWMoriarty(a)lbl.gov> > Subject: Re: [phenixbb] Elbow ligand building > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <4AF1C36B.3010500(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Joe > > On 11/4/09 9:35 AM, Joe Krahn wrote: > >> I have an accurate reference structure, but elbow seems to "regularize" >> the coordinates in a way the distorts the structure. Is there a way to >> disable this? >> >> > eLBOW will always run a simple optimisation unless you specify the final > geometry you like using > > phenix.elbow --final-geometry accurate.pdb > > Naturally, you are smart to use a better input format thus > > phenix.elbow filename.sdf --final-geometry accurate.pdb > >> With --opt, QM optimization should hopefully remove distortions, but it >> is not doing a very good job for this molecule. So, I decided to >> optimize using Gaussian, and a better basis set. >> >> > Good thinking. > >> It seems that the Gaussian interface is still fairly simple, and it >> seems that you have to edit the Gaussian.csh template. So, I did that, >> but got the "Gaussian does not seem to be installed" message. >> Unfortunately, elbow runs the Gaussian script with output to /dev/null, >> so there is no way to see any error messages. Maybe that should be done >> only when the --quiet flag is given. >> >> > Maybe I'll implement this with a --verbose flag. > >> I edited the Python source to let errors go to the tty, and found that >> the problem is in the way the script is invoked using "csh -c %s.csh". >> That only works if "." is in your $PATH, which is often the case. It >> also invokes an extra instance of csh, because it is invoked as a system >> command. The correct way to run a shell script is to leave out the '-c'. >> Elbow makes the script executable, so an even better approach is to just >> leave out "csh", and do "os.system('./%s.csh' % project)". Then, the >> script can be in sh/bash/etc. Maybe the was the intent of using '-c'? >> > This is old code from before PHENIX had a smart module for running > commands. I'll update to code. > > Nigel > > -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

1 0

Elbow ligand building
by Joe Krahn 04 Nov '09

04 Nov '09

I am having some problems building ligand parameters with elbow. I have an accurate reference structure, but elbow seems to "regularize" the coordinates in a way the distorts the structure. Is there a way to disable this? With --opt, QM optimization should hopefully remove distortions, but it is not doing a very good job for this molecule. So, I decided to optimize using Gaussian, and a better basis set. It seems that the Gaussian interface is still fairly simple, and it seems that you have to edit the Gaussian.csh template. So, I did that, but got the "Gaussian does not seem to be installed" message. Unfortunately, elbow runs the Gaussian script with output to /dev/null, so there is no way to see any error messages. Maybe that should be done only when the --quiet flag is given. I edited the Python source to let errors go to the tty, and found that the problem is in the way the script is invoked using "csh -c %s.csh". That only works if "." is in your $PATH, which is often the case. It also invokes an extra instance of csh, because it is invoked as a system command. The correct way to run a shell script is to leave out the '-c'. Elbow makes the script executable, so an even better approach is to just leave out "csh", and do "os.system('./%s.csh' % project)". Then, the script can be in sh/bash/etc. Maybe the was the intent of using '-c'? Thanks, Joe Krahn

2 1

re-run jobs in GUI
by Leo Sazanov 04 Nov '09

04 Nov '09

Hi, in a new GUI how can one re-run previous jobs (to make some modifications to them)? If I just try to open parameter (.eff) file from the main file menu in Autobuild, the file does not show up, even though it exists. Just adding it to the list of input files works, but the information is not passed on into GUI? -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

2 1

low resolution, high B, low R
by gerwald jogl 03 Nov '09

03 Nov '09

Hi All, I am working on a 4.2 A structure and feel somewhat uneasy about my refinement results. First, my R/Rfree at the moment is 0.18/0.25. The refinement is not complete and weights are not optimized, so the gap may get smaller. It's just that at 4.2 A, I don't quite expect such low R factors... There is nothing funny with the data, no messing around, no conversions - straightforward data set and a basic rigid body, individual_sites+group_adps, simulated annealing, no tls yet, no ncs. I am aware that one possible answer is that phenix is just really good... The other issue is about B factors. Phenix will happily refine B factors to values of 300 if there is no density in the region and that brings up the question about how to deal with disordered regions in general. Are there any current opinions out there about what would constitute 'reasonable' B factors? Conversely, when would a B factor indicate that it is better to remove the residue from the model instead of leaving it and calling it disordered. Also, this is after group_adp at 4.2 A - should I maybe take this as an indication that this is asking too much from the data and go back to a single adp per chain and tls? All comments are appreciated. Thanks! Gerwald

2 1

Re: [phenixbb] phenixbb Digest, Vol 48, Issue 2
by Xuewu Zhang 03 Nov '09

03 Nov '09

You are right. It started in the 2nd macro cycle. I should have been a little more patient. Sorry about it. Thanks, Xuewu On Tue, Nov 3, 2009 at 2:00 PM, <phenixbb-request(a)phenix-online.org> wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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. Re: optimization of wxc and wxu (Xuewu Zhang) > 2. Re: optimization of wxc and wxu (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Nov 2009 08:28:58 -0600 > From: Xuewu Zhang <xuewu.zhang(a)gmail.com> > Subject: Re: [phenixbb] optimization of wxc and wxu > To: phenixbb(a)phenix-online.org > Message-ID: > <926abad50911030628h31d09c53m59c2c84f1d024596(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi phenix developers/gurus, > > I am using the latest night build of phenix on OS X snow leopard. I found > that phenix ignores these lines in my custom refinement file: > > refinement.target_weights.optimize_wxc="True" > refinement.target_weights.optimize_wxu="True" > > Manually setting up the scale factors however works. I am not sure whether > this is a bug or a platform related issue. > > Thanks, > Xuewu Zhang >

2 1

Re: [phenixbb] optimization of wxc and wxu
by Xuewu Zhang 03 Nov '09

03 Nov '09

Hi phenix developers/gurus, I am using the latest night build of phenix on OS X snow leopard. I found that phenix ignores these lines in my custom refinement file: refinement.target_weights.optimize_wxc="True" refinement.target_weights.optimize_wxu="True" Manually setting up the scale factors however works. I am not sure whether this is a bug or a platform related issue. Thanks, Xuewu Zhang

2 1

GUI and X servers
by Leo Sazanov 02 Nov '09

02 Nov '09

Hi, I am accessing our linux server (where phenix sits) via Exceed X server from Windows machine, and everything used to work fine until recent (I think from v.1-5-2) versions of phenix. Now if I launch new GUI, mouse position is not recognised anymore not only by phenix, but then also by other programs - so if I click on something, something else completely gets activated. I did not change any Exceed settings, so the problem seems to be due to phenix. Also, same thing happens with Xming server. If I access from Mac machine, everything seems to be OK. Has anybody seen it and what could be the reason for that? Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

3 3

Error message when starting phenix gui
by Folmer Fredslund 30 Oct '09

30 Oct '09

Dear all Should I be concerned about this error message when starting phenix 1.5-2?: Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory Best regards, Folmer Fredslund

3 4

Converting .mtz to xplor or having phenix output to xplor file
by Sam Stampfer 28 Oct '09

28 Oct '09

Hi, This isn't exactly phenix-related but someone might know an easy solution. I'm trying to open an electron density map in pymol. It won't open .mtz files and the .xplor files I generated from ccp4i don't seem to work either. I need to have my density as a .xplor file in order for pymol to open it (I think). How would I generate a .xplor file from .mtz? Or, alternately, how can I set phenix to output a .xplor file? I've had it output to a cns file instead of .mtz but that didn't help me get it in .xplor format. Thanks! -Sam

5 6

external program interference : libwx_gtk2ud-2.8.so.0 not found on ubuntu 64 bit
by hari jayaram 27 Oct '09

27 Oct '09

I just downloaded and installed phenix 1.5.2 . I want to run phenix with the GUI on my 64 ubuntu 8.04 box When I run phenix I get the following error: hari@charlie:~$ phenix Traceback (most recent call last): File "/usr/local/phenix-1.5-2/phenix/wxGUI2/command_line/main.py", line 13, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.5-2/phenix/wxGUI2/command_line/main.py", line 7, in run from wxGUI2 import App File "/usr/local/phenix-1.5-2/phenix/wxGUI2/__init__.py", line 109, in <module> import wx File "/rawdata12/wx-widgets-read-only/wxPython/wx/__init__.py", line 45, in <module> from wx._core import * File "/rawdata12/wx-widgets-read-only/wxPython/wx/_core.py", line 4, in <module> import _core_ ImportError: libwx_gtk2ud-2.8.so.0: cannot open shared object file: No such file or directory I know that I should not be getting this error because I have wxwidgets and wxpython installed and I have wx working on this machine for other apps. Consequently I do have a libwx_gtk2ud-2.8.so.0 on my LD_LIBRARY_PATH. I tried with and without a libwx_gtk2ud-2.8.so.0 in my LD_LIBRARY_PATH and I still got the same error. Any ideas why phenix GUI does not start? Thanks Hari hari@charlie:~$ which phenix /usr/local/phenix-1.5-2/build/intel-linux-2.6-x86_64/bin/phenix hari@charlie:~$ echo $LD_LIBRARY_PATH /home/hari/ccp4-6.0.99e/lib::/home/hari/ccp4-6.0.99e/extralib

2 3

Command to call/read external file when running phenix.refine from
by Ashley Pike 23 Oct '09

23 Oct '09

Hi, I am running phenix.refine(v.1.5.2) from the command line using a batch file containing all my customised options ie. phenix.refine my_parameters. From this batch file (my_parameters) I also want to include additional geometric and NCS restraints. Rather than have them clutter things up, I want to call/invoke them from an external file instead. I had been told that this is possible using the command 'include file <filename>' but it seems that this is not doing what I had hoped. When run in this way phenix.refine doesn't complain but is not using the restraints. Needless to say everything is fine when I actually include the information directly in the batch file. Any hints what I am doing wrong? Cheers, Ashley

5 6

1.5.2 and validation
by Mark Collins 23 Oct '09

23 Oct '09

Hi I just installed 1.5.2 and tried it out for a few hours this afternoon. Is it possible to run the phenix programs from the command line without being forced to launch the shiney new gui? I have 3 structures I had considered finished by R/Rfree and Molprobity. I was playing around with polygons (great way to quickly assess the structure) and found that 2 of the 3 strucutres are "bad" with very low RMSDs for bonds, angles, chirality, dihedrals and planarity. All were refined with phenix 1.3, but they are all fairly small ~80-90 residues. So do I need to go back and revisit these, advice much appreciated? Also I found that I can edit the validate_0.eff (from phenix/project_data/ ) and run the file from the command line. But is there a way to actually change keys_to_show and fiters for polygon in the gui? Also it seems that the *twinned crashed the validation when run this way (bug reported). Thanks Mark

2 1

The new GUI is really nice!
by Laurie Betts 23 Oct '09

23 Oct '09

I think I initially sent this to the wrong address, sorry. Just wanted to say: I just downloaded the new version of PHENIX (1.5-2) on my Mac; I had a lot of trouble with previous versions using the GUI (but really like the command line driven flexibility), but now playing around with the new one, I think I will become hooked. Thank you all VERY much from all of us phenix-o-philes. Laurie Betts

1 0

new GUI is really nice
by Laurie Betts 23 Oct '09

23 Oct '09

I just downloaded the new version of PHENIX (1.5-2) on my Mac; I had a lot of trouble previously using the GUI (but really like the command line driven flexibility), but now playing around with the new one, I think I will become hooked. Thank you all VERY much from all of us phenix-o-philes. Laurie

1 0

Re: [phenixbb] AutoMR and capsids
by SIPPEL,KATHERINE H 22 Oct '09

22 Oct '09

Dear Randy, > If you're sure that there are 3 full copies (and that you > couldn't, say, have six half-copies sitting on crystallographic > 2-folds), the best would be to search for full capsids. Now, for > each copy there are 60 different ways that the capsid could be > oriented, but the version of Phaser distributed with the latest > Phenix release should recognize the internal symmetry -- let us > know if it doesn't! I'm pretty sure its not actually full copies. The unit cell is 262.9, 262.9, 609.1 with an R32 space group. I'm downloading the latest release at the moment. > If it turns out that a capsid is sitting on a symmetry axis, > Phaser will probably reject it because of an outrageous number of > clashes. In that case, you should turn off the clash test, just > look for one copy, and then examine the overlapped solution to > see which part of the capsid is crystallographically unique. Thanks for the tips on the ASU, I wouldn't have thought of that. > Hi Katherine, > Back when I did this with HBV I had one capsid per > crystallographic AsU and I >used Amore (pre-phaser or phenix). I > searched with the icosohedral ASU >looking for 60 copies, and was > surprised how easily the solution fell out. If >you use this > strategy, you really just need one icos ASU per capsid and you > >can then expand the rest using standard icos symmetry. > I think the answer will be do what's easiest, and if it's 99% ID > it should >fall out pretty easily anyway. Bear in mind that > depending on what you've >done to these capsids the icos ASU's > may have slightly re-oriented (in my case >I had added a drug > that kept the icos ASU identical but had tilted the whole >thing > relative to the plane of the capsid). This may also guide your > strategy. > Good luck, > Christina Our standard protocol is Amore with CNS. When Amore failed I thought I might try something different. I have really enjoyed Phenix for my small proteins and thought that I might take advantage of that lovely NCS feature in phenix.refine. I just wasn't sure how to proceed within the AutoMR program. Obviously in the end I will go with what works. > PS- Isn't Mavis around in Florida somewhere, or are you even in > her lab? She >and Rob are a great resource.... I do work for Rob and Mavis and they are a fabulous resource. Best bosses ever (and no they won't see this, its just the truth). Thanks for the help, Katherine > On Oct 22 2009, SIPPEL,KATHERINE H wrote: > >> Dear all, >> >> I am currently trying to use AutoMR to do molecular replacement >> on an icosahedral virus capsid. It is a T=1 capsid so there are >> 60 copies of the monomer per capsid and based on the Matthews >> coefficient there are ~3 capsids in the unit cell. The search >> model is 99% identical (thank God) but I am unsure how to >> approach this. >> >> Do I used the 60-mer as the model and search for three copies? >> Do I use a monomer for the model and search for 180 copies? >> Should I break the model down to smaller pieces (i.e. a 30-mer >> and copies=6, or 12-mer and copies=15)? >> >> I would appreciate any help I can get on this one. >> >> Thanks, >> >> Katherine >> >> -- >> SIPPEL,KATHERINE H >> Ph. D. candidate >> Department of Biochemistry and Molecular Biology >> College of Medicine >> University of Florida >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > -- SIPPEL,KATHERINE H Ph. D. candidate McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine University of Florida

1 0

Another questions: water for adp and partial occupancy
by Young-Jin Cho 22 Oct '09

22 Oct '09

Hi, I thought we should put water molecules as isotropic and full occupancies. However, I saw different cases. So I am wondering the reasons for putting waters as anisotropic and with partial occupancies in an active sites. Does any one have this kind of experience or can you explain the advantage or disadvante of this types of strategy? Thanks in advance, Young-Jin Cho

2 1

AutoMR and capsids
by SIPPEL,KATHERINE H 22 Oct '09

22 Oct '09

Dear all, I am currently trying to use AutoMR to do molecular replacement on an icosahedral virus capsid. It is a T=1 capsid so there are 60 copies of the monomer per capsid and based on the Matthews coefficient there are ~3 capsids in the unit cell. The search model is 99% identical (thank God) but I am unsure how to approach this. Do I used the 60-mer as the model and search for three copies? Do I use a monomer for the model and search for 180 copies? Should I break the model down to smaller pieces (i.e. a 30-mer and copies=6, or 12-mer and copies=15)? I would appreciate any help I can get on this one. Thanks, Katherine -- SIPPEL,KATHERINE H Ph. D. candidate Department of Biochemistry and Molecular Biology College of Medicine University of Florida

3 2

Partially occupied SO4 and waters
by Chris Waddling 21 Oct '09

21 Oct '09

I have a partially occupied sulfate ion that is refining to 55% along with one of two arginine side chains. Associated with the second conformation of the arginine, there is positive density for three partially occupied waters. In Shelxl, I can use the PART identifier to specify that the sulfate ion and the waters are not present simultaneously and are associated with their respective Arg side chain conformation. Is there a way to do this in Phenix? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco

3 2

Re: [phenixbb] Molprobity percentile statistic
by hari jayaram 20 Oct '09

20 Oct '09

Thanks Nat and Pavel for your emails, Thanks for the suggestion of using phenix.polygon. The comparative analysis of my structure relative to others at my resolution was what I was after. And thats the reason I liked the molprobity statistics expressed as percentile since it helped me realize how far I have to go relative to other structures at the PDB. If its not too difficult can I cast my vote to report it inside the phenix GUI. Its just that running the full analysis inside of phenix is significantly faster than running it on the duke webservers. In molprobity If I remember correctly the overall score is some weighted average, and the molprobity paper also cautions against taking it too literally. Also If I remember the molprobity percentiles are absolute and not only composed of structures at similar resolutions . Regardless thanks for the hint about phenix.polygon . I just looked at my phenix.polygon report and I am afraid its a little asymmetric. Hari On Mon, Oct 19, 2009 at 9:58 PM, hari jayaram <harijay(a)gmail.com> wrote: > Thanks Nat and Pavel for your emails, > Thanks for the suggestion of using phenix.polygon. The comparative > analysis of my structure relative to others at my resolution was what > I was after. > > And thats the reason I liked the molprobity statistics expressed as > percentile since it helped me realize how far I have to go relative to > other structures at the PDB. If its not too difficult can I cast my > vote to report it inside the phenix GUI. Its just that running the > full analysis inside of phenix is significantly faster than running it > on the duke webservers. > > In molprobity If I remember correctly the overall score is some > weighted average, and the molprobity paper also cautions against > taking it too literally. Also If I remember the molprobity percentiles > are absolute and not only composed of structures at similar > resolutions . > > Regardless thanks for the hint about phenix.polygon . > I am attaching a snapshot of my polygon ..I an afraid its a little > asymmetric. > > Hari > > On Mon, Oct 19, 2009 at 7:48 PM, Pavel Afonine <PAfonine(a)lbl.gov> wrote: >> Hi Hari, >> >> if you run phenix.model_vs_data you will get those numbers (namely: >> Ramachandran outliers, clashscores, CB-deviations; although you will not >> get "Molprobity score" simply because I don't know what it is and so I >> didn't add it): >> >> phenix.model_vs_data model.pdb data.mtz >> >> Nat: every time time you run model_vs_data for whatever purpose (getting >> fmodel, etc...) you get an object that contains all these numbers. >> >> Pavel. >> >> >> On 10/19/09 3:32 PM, hari jayaram wrote: >>> Hi i just started using the phenix GUI front-end to Molprobity . Its >>> really nice the way it plugs into coot and displays all the statistics >>> etc. >>> Is there any place that it also reports the percentile clashscore and >>> percentile Molprobity score for overall model quality a la the >>> webserver at molprobity.biochem.duke.edu >>> >>> Thanks >>> Hari >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >

2 1

Molprobity percentile statistic
by hari jayaram 19 Oct '09

19 Oct '09

Hi i just started using the phenix GUI front-end to Molprobity . Its really nice the way it plugs into coot and displays all the statistics etc. Is there any place that it also reports the percentile clashscore and percentile Molprobity score for overall model quality a la the webserver at molprobity.biochem.duke.edu Thanks Hari

3 2

Re: [phenixbb] pseudo-merohedral twinning or pseudo-symmetry?
by Gino Cingolani 17 Oct '09

17 Oct '09

Laurie, I had a similar problem. Scaling statistics in P212121 were OK, and - of course - no twinning was detected ... but nothing made sense during refinement. Looking at the data more carefully I found that if one rescales in P21, the b-angle was stably refined to 90.20 with ~30% better Rsym than in orthorhombic. When running xtriage on the P21 data, I found the data were indeed "pseudomerohedrally-twinned" with twinning fraction ~0.38. Good luck! Gino

3 2

pseudo-merohedral twinning or pseudo-symmetry?
by Laurie Betts 16 Oct '09

16 Oct '09

Hi - We have a data set that seems to process well in primitive orthorhombic. a=80, b=87, c=114. The data has overall Rsymm around 10% to 2.6 Angstrom, where I/sigI > 2, and Chi-squared is around 1.4. Phenix.xtriage shows some pathology in intensity statistics such that the L-test indicates <|L|> = 0.414 and <L^2> = 0.241, with the L-test Z score = 7.334. The Wilson ratio for acentric refls is 1.774. According the xtriage, There were no "pseudomerohedral" twin laws found, and the comments at the end say "As there are no twin laws possible given the crystal symmetry, there could be a number of reasons......" Is it more likely that this is a case of pseudo-symmetry, or would one not expect the intensity statistics to have the values they do in that case. Also, is the absence of twin laws defined by the fact that proper merohedral twinning is not possible for P222 space groups? Still confused, Laurie Betts

2 1

autobuild
by Colin Levy 16 Oct '09

16 Oct '09

Hi, can autobuild be setup to use kicked maps when starting from a molecular replacement model? Thanks Colin

2 1

Re: [phenixbb] grouped occupancy definitions
by Dr. Mark Mayer 15 Oct '09

15 Oct '09

Hi Pavel, I'm digging in docs and list serv but could not find out, and figured you probably know faster. I need to make an occ.params file for some groups of non adjacent side chains which interact with each other, and associated waters. 1) How do I select ACs 2) How do I constrain water occupancies so that their Q + that of coupled protein atomes does not exceed 1. If I match the AC flags for the waters and side chains will this take care of it. e.g. if residues 2 and 21 have coupled ACs and waters 101 and 102 move in when residue 21 is in one of its ACs how would I define below? refinement { refine { occupancies { constrained_group { selection = chain A and resseq 2 selection = chain A and resseq 21 selection = chain W and resseq 101 selection = chain W and resseq 102 } } Thanks !!! -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Mark Mayer Ph.D.

2 2

low resolution refinement question
by Peter Grey 15 Oct '09

15 Oct '09

Dear Phenix users, I refine a large complex with three monomers in ASU at very low resolution - 4.5A - and would like to ask two questions. - Could you give some tips about refinement at this resolution other than rigid body refinement - Can TLS and grouped B-factors work at this poor resolution ? - I would really prefer that rigid body refinement will strictly obey the NCS that was found in the molecular replacement solution. I understand constrained NCS does not exist yet in phenix but is there something approximate that can be used in rigid body refinement ? I tried the conventional restrained NCS and the result was just like without restrains. Thank you for your time , Peter.

3 2

Why is CIF monomer data split into individual files?
by Joe Krahn 14 Oct '09

14 Oct '09

Is there a good reason not to merger all monomer data into a single file, similar to PDB's components.cif? My first thought is that it is a performance issue. However, I wrote a simple CIF parser in Tcl, and found that carefully designed regexp processing can index data segments very fast. The entire components.cif takes just a few seconds. (The key is to use a regexp that matches an entire data block, and not tokenize the whole file.) So, I am thinking that a single merged file might be better. With separate files, there is already a need for a list of residues (mon_lib_list.cif) which could just as well be file offsets. So, even if parsing is not so fast, it is not an issue because we already have an index file. One problem with separate files is that it relies on the 3-letter residue name to be unique. With a merged file, a different database key can be used without concern for filename restrictions. The PDB format was originally designed so that HET 3-letter codes only need a file scope, where HETNAM defines the full name of each HET residue in a file. Everyone has been using HET codes the same as standard residues, which has cause the 3-letter codes to become meaningless database keys rather than useful abbreviations. Eventually, we will run out of 3-letter codes, and will have to change. Why not start sooner rather than later? Even now, there are potential conflicts. For example, CCP4 has DNA residues using a lower-case d, which may not provide a unique filename for non-POSIX case-insensitive operating systems. If anyone actually wants a Tcl CIF parser, I can share it. I only wrote it as a simple and efficient way to read CIF files from a CCP4i script. Joe Krahn

1 0

Re: [phenixbb] Autobuild for very elongated models
by Gino Cingolani 14 Oct '09

14 Oct '09

Thanks Tom! Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ---- Original message ---- >Date: Wed, 14 Oct 2009 08:28:09 -0600 >From: Tom Terwilliger <terwilliger(a)lanl.gov> >Subject: Re: [phenixbb] Autobuild for very elongated models >To: Gino.Cingolani(a)jefferson.edu,PHENIX user mailing list <phenixbb(a)phenix-online.org> > >Hi Gino, > >Here is how to specify a mask in phenix.autobuild (see https://www.phenix-online.org/documentation/faqs.htm >#anch68): > >----------------- >How can I specify a mask for density modification in AutoSol/AutoBuild? >If you want to specify a mask, add this command: > >resolve_command_list=" 'model ../../coords.pdb' 'use_model_mask' " >where there are " and ' quotes and coords.pdb is the model to use for >a mask. Note the "../../" because coords.pdb is in your working >directory but when resolve runs the run directory is 2 directories >lower, so relative to that directory your coords.pdb is at "../../ >coords.pdb". You will know it is working if your resolve_xx.log says: >"Using model mask calculated from coordinates" >----------------- >I am not so sure this is the problem, however. I would suggest that >you do a quick composite omit map before refinement on your mr model: >phenix.autobuild data=data.mtz model=MR.1.pdb >composite_omit_type=simple_omit >It is important that this start with you MR unrefined model so that >you have no worries about model bias. This procedure will omit a >region, refine, calculate a 2Fo-Fc map for the omitted region, then >repeat for all other parts of your model and paste them all together >and put it in >AutoBuild_run_1_/OMIT/resolve_composite_map.mtz >which you can use to calculate a map with LABIN="FP=FP PHIB=PHIM >FOM=FOMM" (you need to include the FOM). >If this map shows density for your whole model...you are in great >shape and the problem may indeed be the mask. If it does not...then >the model may not be very close and it may be difficult to proceed. >All the best, >Tom T > >On Oct 14, 2009, at 7:57 AM, Gino Cingolani wrote: > >> Hi Everyone, >> >> I am trying to solve a very elongated structure (~180A-long) formed >> by two long a-helices. I have a good MR solution (Log-Likelihood >> Gain ~168.537 to 3.0A resolution), which refines OK immediately >> after MR (Rfactor/Rfree 46/50%). The electron density has clear side >> chain features and high res data is available to ~2.1A resolution. >> >> Logically, I should be able to plug everything into Autobuild and >> get a good final model (or at least something better than my input >> MR solution). I have tried a million time using different parameters >> and datasets, but Autobuild always breaks up my long helical model >> into short helical bundles, that refine to random Rfree. In other >> words, if my starting MR model is a continuous >> 80aa-long helix, Autobuild fragments it into three helices of ~30aa >> each packed laterally (I see back my initial model if I visualize >> symmetry-related atoms in Coot). >> >> In parallel, I have made the following observation. >> If I use DM to improve my phases, prior to Autobuild, I noticed that >> something similar happens. DM gives great density for less than half >> of my long helix while the rest is flattened. >> If I look at the solvent mask generated by DM, it basically flattens >> half of my elongated model. It seems that at least DM fails to >> generate a solvent mask that makes sense with such an elongated >> structure (by the way, the unit cell is a=25, b=37, c=220 in >> P212121). This problem can be circumvented in DM where >> an outside solvent mask can be inputted, but what about in phenix? >> >> Is it possible that Autobuild is failing because Resolve also makes >> a poor solvent mask? Is there a way to see and/or edit the solvent >> mask generated by Resolve? Or even better, can I input a new solvent >> mask in Autobuild? >> >> Thanks in advance for the feedback! >> >> Gino >> >> >> ****************************************************************************** >> Gino Cingolani, Ph.D. >> Associate Professor >> Thomas Jefferson University >> Dept. of Biochemistry & Molecular Biology >> 233 South 10th Street - Room 826 >> Philadelphia PA 19107 >> Office (215) 503 4573 >> Lab (215) 503 4595 >> Fax (215) 923 2117 >> E-mail: gino.cingolani(a)jefferson.edu >> ****************************************************************************** >> "Nati non foste per viver come bruti, ma per seguir virtute e >> conoscenza" >> ("You were not born to live like brutes, but to follow virtue and >> knowledge") >> Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > >Thomas C. Terwilliger >Mail Stop M888 >Los Alamos National Laboratory >Los Alamos, NM 87545 > >Tel: 505-667-0072 email: terwilliger(a)LANL.gov >Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov >PHENIX web site: http:www.phenix-online.org >ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu >TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB >CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss > > > > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb

2 1

Autobuild for very elongated models
by Gino Cingolani 14 Oct '09

14 Oct '09

Hi Everyone, I am trying to solve a very elongated structure (~180A-long) formed by two long a-helices. I have a good MR solution (Log-Likelihood Gain ~168.537 to 3.0A resolution), which refines OK immediately after MR (Rfactor/Rfree 46/50%). The electron density has clear side chain features and high res data is available to ~2.1A resolution. Logically, I should be able to plug everything into Autobuild and get a good final model (or at least something better than my input MR solution). I have tried a million time using different parameters and datasets, but Autobuild always breaks up my long helical model into short helical bundles, that refine to random Rfree. In other words, if my starting MR model is a continuous 80aa-long helix, Autobuild fragments it into three helices of ~30aa each packed laterally (I see back my initial model if I visualize symmetry-related atoms in Coot). In parallel, I have made the following observation. If I use DM to improve my phases, prior to Autobuild, I noticed that something similar happens. DM gives great density for less than half of my long helix while the rest is flattened. If I look at the solvent mask generated by DM, it basically flattens half of my elongated model. It seems that at least DM fails to generate a solvent mask that makes sense with such an elongated structure (by the way, the unit cell is a=25, b=37, c=220 in P212121). This problem can be circumvented in DM where an outside solvent mask can be inputted, but what about in phenix? Is it possible that Autobuild is failing because Resolve also makes a poor solvent mask? Is there a way to see and/or edit the solvent mask generated by Resolve? Or even better, can I input a new solvent mask in Autobuild? Thanks in advance for the feedback! Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

2 1

use get_cc_mtz_pdb to calculate the cc between model and map
by 丁玮 14 Oct '09

14 Oct '09

Hi, everyone: When I use get_cc_mtz_pdb to calculate the cc between model and map, two values is output: （1）Overall map correlation: （2）Map correlation in region of model: What is the different between them? Whether the "Map correlation in region of model" is the correlation between model and the density map superimposing on it and the "Overall map correlation" is the correlation between model and the overall density map? Thanks a lot! dream dingding830106(a)sina.com 2009-10-14

2 1

autosol import failed
by Jan Abendroth 14 Oct '09

14 Oct '09

Hi all, I am trying to run Phenix AutoSol on a SAD data set. Sadly enough, it fails on me during reading in the mtz file with the error message below. The same happens with both intensities or amplitudes. phenix version 1.5-2 run through the gui where I read in the mtz file and specified I+, I-, ... Any ideas? Thanks Jan ~~~~~~~~~~~~~ error message: ImportRawData_output_files ImportRawData Run 3 Tue Oct 13 18:14:37 2009 NOTE: Input labels currently restricted to: I(+),SIGI(+),I(-),SIGI(-) Note also: a group of labels needs to be enclosed with quotes Skipping labels I(+) SIGI(+) I(-) SIGI(-) which do not match requested labels **************************************** AutoSol Input failed -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

2 1

New GUI, MTZ, multiple data sets
by Graeme Winter 12 Oct '09

12 Oct '09

Hi Folks, I just tried reading an MTZ file full of MAD data (from xia2) with the new GUI, and it seems like you can't read more than one data set from a given file - is this the case? It did correctly find all of the columns that were in there. Reading in scalepack format files, one per wavelength, seemed to work fine. Browse then selecting the same file again didn't seem to work, couldn't find the "add another dataset" button... it of course works just fine from the command-line with the .eff file. Thanks, Graeme

3 2

Re: [phenixbb] Does PHENIX exclude Rfree reflections in maps?
by Thomas C. Terwilliger 12 Oct '09

12 Oct '09

Hi Pavel and Joe, I carried out a test to see if (1) excluding a super-free set completely from automated structure solution affects the results and (2) if the super-free R that results is different from the standard free R obtained with all data and excluding the free set only from refinement. Here are the results: A = structure B, C and D are for the run with a super-free set excluded from all calculations. B and C are work and free R for the reflections included in the calculation. D is the R for the super-free set. E and F are work and free R for the same datasets, run in the same way, but without any super-free set. A B C D E F ---super-free-run---- --standard run-- structure work free super-free work free 1029B 0.31 0.38 0.41 0.29 0.36 1038B 0.22 0.26 0.26 0.24 0.28 1071B 0.28 0.33 0.35 0.26 0.30 rab3a-sad 0.31 0.35 0.38 0.29 0.34 rnase-p 0.28 0.32 0.31 0.28 0.29 calmodulin 0.26 0.27 0.27 0.27 0.29 cobd-sad 0.24 0.26 0.26 0.24 0.28 insulin 0.27 0.30 0.29 0.25 0.26 nsf-n 0.23 0.26 0.26 0.21 0.24 ut-synthase 0.24 0.29 0.28 0.24 0.28 mean 0.26 0.30 0.31 0.26 0.29 Conclusions: (1) super-free is very nearly the same as free in the matched set. (2) leaving out super-free data does not make a lot of difference in these actual cases. (Perhaps it might in worse data sets) (3) so it would be ok to take out super-free set, but it is not necessary. All the best, Tom T >> Hi Pavel and Joe, >> >> I'm glad you put that option in, Pavel. However for model-building it is >> not so straightforward. Normally we are building into density-modified >> maps. Density modification works poorly when a significant set of >> reflections is excluded, so this becomes impractical. We could exclude >> those reflections in the map only, but they will have been used in density >> modification so they are no longer truly free. I don't have a good >> solution for that. >> >> I am guessing that for model-building, the free R is hardly affected, >> compared to refinement against the map, though I haven't tested this. >> >> All the best, >> Tom T >> >>>> Hi Joe, hi Tom, >>>> >>>> until recently, all reflections (work and test) were used in map >>>> calculation. When I added a real-space refinement option to >>>> phenix.refine I spent a day thinking hard about why Rfree was almost >>>> always equal to Rwork after real-space refinement, until I realized >>>> that >>>> I have to exclude test reflections from map calculation, and that fixed >>>> the problem. >>>> >>>> I think it depends on the task: >>>> >>>> - for things like real-space refinement (where the map is heavily used) >>>> or automated model building, the test reflections have to be excluded >>>> from map calculation; >>>> >>>> - for catching a tiny detail (looking at weak ligand density = slight >>>> map use) or fixing a few side chains, all reflections should be used, >>>> since 10% of data put aside may sometime significantly affect map >>>> quality. >>>> >>>> Pavel. >>>> >>>> >>>> On 9/30/09 11:51 AM, Tom Terwilliger wrote: >>>>> Hi Joe, >>>>> In PHENIX R-free reflections are included in your maps. >>>>> All the best, >>>>> Tom T >>>>> >>>>> On Sep 30, 2009, at 12:47 PM, Joe Krahn wrote: >>>>> >>>>>> Does PHENIX exclude R-free reflections when computing maps? IMHO, it >>>>>> is >>>>>> bad to use test reflections in maps, or anywhere else other than >>>>>> computing R-free, but opinions vary. If some people still want test >>>>>> reflections in maps, maybe it could be an option. >>>>>> >>>>>> Thanks, >>>>>> Joe Krahn >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>> >> >>

1 0

Re: [phenixbb] FreeR set reduced by half in twin crystal refinement?
by lauren 08 Oct '09

08 Oct '09

Hi all Thanks for all your reply, really helpful Joe wrote, >My first guess is that the R-free set generated in CCP4 is not set to follow twin laws, so you have work and free reflections associated by twinning. However, I would expect PHENIX >to check this. >As for the reduced size, that probably comes from the way the twinned test set is calculated. Maybe it is a bug. Are you using anomalous data? No anomalous >What is the PHENIX version? Peter wrote, >- you have at least n% of free flags, but not more then 2000+epsilon >(typically) >- it follows any possible twin law (not user specified, it follows symmetry of the lattice) After I change the setting "xray_data.r_free_flags.max_free ", and set it up to 5000. xray_data.r_free_flags.fraction=0.05, the results look normal. Final: r_work = 0.1782 r_free = 0.2285 bonds = 0.007 angles = 1.186 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1807 REMARK 3 R VALUE (WORKING SET) : 0.1782 REMARK 3 FREE R VALUE : 0.2285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.07 REMARK 3 FREE R VALUE TEST SET COUNT : 2776 Best Regards Lauren

1 0

parallel phaser?
by Francis E Reyes 08 Oct '09

08 Oct '09

Did phaser get OpenMP/parallelized or was I just having a dream? If so, how's it work? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

4 6

FreeR set reduced by half in twin crystal refinement?
by lauren 07 Oct '09

07 Oct '09

Hi everyone, I have a P31 twin crystal, resolution 2.0, and with twin fraction 0.451. I use phenix.refine to refine the structure and with freeR set to 8%. % phenix.refine data.sca model.pdb twin_law="h,-h-k,-l" xray_data.r_free_flags.generate=True xray_data.r_free_flags.fraction=0.08 Result: Final: r_work = 0.1793 r_free = 0.2258 bonds = 0.011 angles = 1.557 REMARK 3 FREE R VALUE : 0.2258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.67 REMARK 3 FREE R VALUE TEST SET COUNT : 2013 After the refinement, it seems like my freeR set size reduced by half (3.67%). Is it due to the twin effect, or something is wrong with my refinement? And if I use ccp4 program "scalpeak2mtz " to convert the .sca to .mtz and with freeR fraction set to 8%. Then refine it with phenix. % phenix.refine data.mtz model.pdb twin_law="h,-h-k,-l" Final: r_work = 0.1669 r_free = 0.1970 bonds = 0.010 angles = 1.406 REMARK 3 FREE R VALUE : 0.2022 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.80 REMARK 3 FREE R VALUE TEST SET COUNT : 4326 It turns out, my test set is still 8%, and R/Rfree looks even better than the first one. So I am wondering which one is the correct one and why? Thanks! Lauren

3 2

difference map peaks
by RAVINDRA D MAKDE 07 Oct '09

07 Oct '09

Hi everyone, I would like to have commnets from experts on the following issues. I am refining DNA-protein complex at 3 A resolution and my current Rfree is 21.5 % (phenix.refine). 1. I am getting difference map peaks (in Coot) of magnitude less than -5 sigmas (0.24 e/A3) (~10 or more peaks) and equal number of positive peaks of same magnitudes.The positive peaks hardly have 2fo-fc of more than 1.0 sigma level. I presumed this well could be due to bulk solvent or improper mask. Therefore I optimized the mask parameters (by giving option under "General refinement parameters" in phenix.refine GUI). I could get my R free lower as expected but I still got these peaks back. Although I am not absolutely sure, but positive peaks are more in polar pocket of protein and negative peaks are more in non-polar and aromatic pockets. I have PEG, Na acetate in my crystal soup. What these negative peaks represent for? 2. During addition of atoms like Na+, Cl- in map, do one need to careful about of the its coordination valency in surrounding pocket. ? I will be highly thankful to you for the same. Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

4 6

prime_and_switch, error in input mtz label assignment
by Tatyana Sysoeva 07 Oct '09

07 Oct '09

Dear all, I have a question to your kindest attention. We were trying to run today phenix on distant cluster (phenix-1.3) with next command line *phenix.autobuild data=data.mtz solvent_fraction=0.6 ps_in_rebuild=True \ input_pdb_file=model.pdb maps_only=True* Autobuild failed with these last lines in the Autobuild_run_1_1.log Failed to carry out AutoBuild_multiple_models: *Sorry, subprocess failed...message is: ******************************************************************************** phenix.autobuild \ write_run_directory_to_file=/home/btn1/tn_phenix/refine/final_loops/with_ncs_H/no_wateradd_noH/prime_switch/AutoBuild_run_1_/TEMP0/INFO_FILE_1 Reading effective parameters from /home/btn1/tn_phenix/refine/final_loops/with_ncs_H/no_wateradd_noH/prime_switch/AutoBuild_run_1_/TEMP0/PARAMS_1.eff Sending output to AutoBuild_run_1_/AutoBuild_run_1_1.log ******************************************************************************** Failed to carry out AutoBuild_build_cycle: failure ******************************************************************************** * in Autobuild_run_1_/TEMP0/Autobuild_run_1_/Autobuold_run_1_1.log the failure message is next: *Columns of data in AutoBuild_run_1_/TEMP0/TEMP.mtz: H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT child process stderr output: command: 'AutoBuild_run_1_/TEMP0/temporary.com' resolve_giant: Error in label assignments Failed to run resolve ---------------------------------- TRIED resolve_giant ...but not OK ******************************************************************************** Failed to carry out AutoBuild_build_cycle: failure ******************************************************************************** * There are temporary.com and temporary.com.bak in the folder and there is only difference, except that in temporary.com there is "labin FP=FP FC=FMODEL PHIC=PH2FOFCWT FWT=2FOFCWT" in temporary.com.bak there is "labin FP=FP FC=FMODEL PHIC=PHI2FOFCWT FWT=2FOFCWT" Prime_and_switch.log file ends with *Reading SG information from TEMP.mtz Space group name: P21212 Point group: 222 Space group number : 18 Symmetry operators: 4 Number of columns: 9 H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT *** Warning From LRASSN : User input label PHI2FOFCWT does not match any file label  resolve_giant: Error in label assignments </pre>   </html> * I checked created TEMP.mtz, it looks like: * Column Labels : H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT So the question is next: Why is prime_and_switch process looking for the "right" labels (PH2FOFCWT), which are present in previously created TEMP.mtz file, but sees them wrong (PHI2FOFCWT)? Is this possible that we have somewhat wrong inputs or is there problem with the set of commands? Sincerely, Tanya * *

2 1

log file
by Young-Jin Cho 06 Oct '09

06 Oct '09

Hi, While I refining I found the following is included in the .log file. I am using different pdb files. When I looked up residue number 175, it looked ok to me. Do you guys have any idea how to deal with this? Conformer: "C" Number of residues, atoms: 175, 1321 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 14, 'TRANS': 159, 'PCIS': 1} Chain breaks: 24 Unresolved chain link angles: 14 Unresolved chain link dihedrals: 28 Unresolved chain link planarities: 14 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1313 Thanks in advance, Young-Jin

2 1

PHENIX 1.5 and exploding residues
by Antony Oliver 06 Oct '09

06 Oct '09

Dear all, I am currently refining a structure using PHENIX 1.5-3 and have encountered some problems with "exploding residues". I have attached a image (small PNG file) highlighting the problem. Has anyone had a similar experience? Or know the solution to the problem? Change weighting in favour of geometry ? Many thanks, Tony Oliver . The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

4 4