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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

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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.

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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

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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.

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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. ******************************************************************

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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.

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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

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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.

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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

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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

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