- phenixbb - phenix-online.org

best strategy using two datasets?
by Manoj saxena 05 Oct '10

05 Oct '10

Hi , I have data 2.4 A for a protein ( Se-Met derivative) unit cell dimensions. 53.098,60.207,142.382. I have used this data to solve the partial structure with phenix.autosol and phenix.autobuild. The model from this data was then used as MR model in phaser with another data set from a crystal at 2.2 A (group P212121 ) .unit cell dimensions are 53.86,61.47,142.49. Currently my R free is 23%. My question is 1) Is there a a better way to use the two datasets. can I merge the reflection files from two datasets and does using a merged reflection file have an advantage over the strategy I used. 2) Although not directly related to phenix I was wondering can we use the merged reflection file for PDB depositions? Thanks . I will greatly appreciate any suggestions and guidance in this regard Manoj

2 1

Re: [phenixbb] Help on multi-start-simulated-annealing sigmaA-weighted 2fofc map - WORKING EXAMPLE
by Pavel Afonine 03 Oct '10

03 Oct '10

Hi Fengyun, no problems, here is the updated script and inputs files to illustrate how it works: http://cci.lbl.gov/~afonine/mssa2/ All it needs is a bunch of PDB files and corresponding map coefficients. Let me know if you have any questions. Pavel. On 9/9/10 7:48 PM, fn1(a)rice.edu wrote: > Hi Pavel, > > The script works fine. I hope you could slightly revise the script for > me. > > Since right now, I could run the multi-sa on different nodes at the > same time. So I could get the refined models in the name of sa-#.pdb > within a short time. > > So I could begin with the different models and combine them to > "all.pdb" and calculate the average map after that. But I don't know > how to revise the run.py to do that. > > Wait for your help. > Thanks! > Fengyun > > 引用 Pavel Afonine <pafonine(a)lbl.gov>： > >> Hi Fengyun, >> >> my previous email actually doens't answer your question - I realized >> this after I pushed Sent button -:) >> >> To really answer your question I just wrote a Python script that does >> the following: >> - run multi-start Simulated Annealing, >> - combine all refined models into one multi-model PDB file (models >> separated by MODEL-ENDMDL records), and >> - compute averaged 2mFo-DFc map. >> >> The complete working example is here: >> >> http://cci.lbl.gov/~afonine/mssa/ >> >> You have two options at this point: >> >> - take this example, slightly change inputs by editing the run.py >> file (change input data and model file names, number of SA runs, etc) >> and run it as following: >> >> phenix.python run.py >> >> (since I spent 15 minutes on writing this script it's obviously not >> thoroughly tested or parameter-optimized, although I believe it >> should do the job right) >> >> or >> >> - wait a few days for one of the next PHENIX nightly builds where the >> above script will be available as a user-friendly either >> phenix.multi_start_sa command or an option of phenix.maps (I haven't >> decided yet what is better). >> >> Let me know if you have any questions. >> >> Pavel. >> >>> I read on the paper that they use CNS (model_map.inp) to calculate >>> the avarage sigmaA-weighted 2fofc map. Right now I have set up the >>> simulated annealing with different random seeds. I wonder whether >>> phenix could calculate the average map with the multiple coordinates >>> from different starts? >> >> >> > > >

2 3

Job Opening Announcement
by Lance Westerhoff 01 Oct '10

01 Oct '10

Hello All- We have a number of computational chemist and computational crystallographer post doc positions available. One has a significant focus on x-ray refinement method development, and the other one will explore computational chemistry method research and development. We are excited to fill these openings with talented individuals, so if you think you would be a good fit, we invite you to take a look at our careers website below and submit your CV (along with cover letter) to careers(a)quantumbioinc.com http://www.quantumbioinc.com/careers/ Thank you for your time! -Lance ____________________ Lance M. Westerhoff, Ph.D. General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

1 0

using custom_param file from the gui
by Sebastiano Pasqualato 01 Oct '10

01 Oct '10

Hi all, I have a custom parameter file that I used to use running phenix.refine from the command line. Is there a way to use it from the gui? ciao, s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

1 1

question on the weight for adp
by fn1＠rice.edu 30 Sep '10

30 Sep '10

Hi everyone, I have some questions the weight for adp. My case is that some part of the model will be refined to large B values (about 100) if the default value of wxu_scale (1.0) is used. The other part of the model will have average B value of about 40, which the wilson B is about 35. The corresponding 2FOFC map has very poor density for the region with large B values. If the value of wxu_scale set to be 0.1, that part with large B will be refined to about 80 for B. The corresponding 2FOFC map has some better (but not good enough) density for this region. My question is that can I keep the wxu_scale at the small value for the refinement? Or finally do I need to loose this value? Thanks! Fengyun

4 5

Seeking Postdoctoral Researcher
by Francois Berenger 29 Sep '10

29 Sep '10

Laboratory: Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, Japan. (Unit Leader: Dr. Kam Zhang) Job title and Job description: Postdoctoral Researchers Job description: We are seeking a highly motivated and experienced computational structural biologist to join the Zhang Initiative Research Unit at RIKEN. The successful candidate will use computational tools to tackle problems in the area of protein folding, structure prediction, and structure-based drug design. Our ability to predict the structure of proteins from their primary sequences will greatly facilitate our understanding of the important biological functions that proteins play in their host systems. The 3D structure information will also facilitate the rationale design of drugs for the treatment of various diseases with unmet medical needs. Qualifications: This position requires a PhD in areas related to biophysics, biochemistry, computational chemistry, bioinformatics, or structural biology with experience in employing computational tools to solve biological or chemical problems. Experiences in protein folding, protein structure prediction, protein structure analysis, protein crystallography, or structure-based drugs are highly desired. Proficiency in object-oriented programming such as C++, Java, scripting languages such as Python, Perl are also desired. Experiences in high performance computing, network computing, or grid computing would be a plus. The ideal candidate should possess a track record of accomplishments demonstrating technical proficiency, independent thinking, and scientific creativity. The research environment will be international and hence communication in English is encouraged. The complete job ad, as well as how to apply can be viewed here: http://www.riken.jp/engn/r-world/info/recruit/k100817_s_asi.html Best regards, Francois.

1 0

Ligand restraints editing with REEL -summary
by Joseph Brock 28 Sep '10

28 Sep '10

Hi all, I just wanted to post a quick summary of how my problem was resolved. I later realised that the 'native glutahione' molecule I was transferring ligand restraints from was actually produced by eLBOW released under the Phenix package v1.4, and was therefore defined differently to those restraints created by v1.6.4-486. I was advised by Nigel (author of eLBOW and REEL) to download the latest nightly build (dev-541) and create a clean subdirectory. Copying my model.pdb and data.mtz file into this, running phenix.ready_set on these files and running phenix.refine with the resulting .pdb and .cif files, resulted in a ligand that was correctly restrained to refine into the density extremely well. Hope this is of help to anyone with a similar problem. Cheers, Joe. > From: phenixbb-request(a)phenix-online.org > Subject: phenixbb Digest, Vol 58, Issue 18 > To: phenixbb(a)phenix-online.org > Date: Sat, 18 Sep 2010 12:00:01 -0700 > > 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. Ligand restraints editing with REEL (Joseph Brock) > 2. Re: Ligand restraints editing with REEL (Ralf W. Grosse-Kunstleve) > 3. Resolve NCS masks (Florian Schmitzberger) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 18 Sep 2010 08:09:23 +0000 > From: Joseph Brock <joeylives2ride(a)hotmail.com> > To: <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Ligand restraints editing with REEL > Message-ID: <SNT120-W580E16EA4DC524ED59A3209B7C0(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi all, > > I'm working on a 1.5A structure that contains a novel ligand within the active site, which is an Arsenic derivative of Glutathione, using the Phenix GUI, version 1.6.4-486. > > I have been using the 'Molinspiration' webpage (http://www.molinspiration.com/docu/webme/) to generate a smiles string, which I then feed into ELBOW. Although the structure/chemical restraints of Glutathione should be unchanged by the covalent linkage to arsenic through the cysteinyl sulfur, the resulting restraints file consistently restricts one of the dihedrals to a value that is incompatible with the (quite clear) electron density. This occurs regardless of wether i use AM1 optimization, and is unresponsive to using native Glutathione (which refines into the corresponding density extremely well) as an input geometry file with any of the available 'Use geometry for' options (final geometry, initial geometry, etc). > > I then tried opening the output file in REEL and manually changing the corresponding dihedrals to those of glutathione, however after running simple optimization, the resulting restraints file has the same problem, and upon choosing the 'transer geometry and restraints' option (or any option) midway through running the 'eLBOW optimization' or 'AM1 optimization' options, Phenix consistently crashes. > > Any advice on how to transfer the origional geometry of native Glutathione to my new ligand effectively would be greatly appreciated. I'm a little confused as to the abilities of REEL, and how to affect them. > > Thanks so much in advance. > > Cheers, > > -Joe. > > >

1 0

mlhl refinement
by Florian Schmitzberger 28 Sep '10

28 Sep '10

Dear All, I am running Phenix version 1.6.4.-486 on imac. I just wanted to refine (phenix.refine) a model with MLHL target and experimental phase information. Strange thing is when I load the mtz file, as written out from Phenix Autosol (overall_best_denmod_map_coeffs.mtz) into the GUI, the Phenix refine GUI does not seem to any phase information. Only picks up FP and SIGFP labels; but not the Hendrickson-Lattman coefficients, which are present. The following message comes up when I try to chose mlhl refinement: " You have selected 'mlhl' as the refinement target, but no experimental phases were supplied. If you wish to use phase restraints in refinement, please add or select experimental phases, or choose another target function". I guess it is not such a major problem as I can save the .eff file and manually edit it to include the HL coefficients and then run Phenix (as long as Phenix then recognizes them from the mtz file). I would also like to refine f' and f'', as the data are from a selenomethionine derivatized protein. From what I can see the default in Phenix.Autosol seems to be not to keep the F+/- and Dano labels for the output mtz file? So I suppose I do need to provide the initial mtz file or is there a way to change the output options for the coefficients in Phenix Autosol? Cheers, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

4 4

Does Phenix have the library or program to maintain bond angle and bond length to create an extended chain?
by Rojan Shrestha 27 Sep '10

27 Sep '10

Hello: I am wondering whether Phenix has the library or program to maintain the ideal bond length and bond angle. The torsion angles of residue and xyz of each atoms are already known. I want to juxtapose residue or residues to create an extended chain. Thanks Regards, Rojan

4 3

CCP4 Study Weekend 2011: "Model Building and Refinement and Validation"
by ronan.keegan＠stfc.ac.uk 24 Sep '10

24 Sep '10

Dear All, We're pleased to announce that registration for this coming January's CCP4 Study Weekend meeting is now open. The meeting will take place from January 5th to 7th, 2011 at University of Warwick in the UK. The topic of the meeting will be "Model building and Refinement and Validation". This year's organisers, Roberto Steiner and Bernhard Rupp, have arranged the usual mix of interesting and stimulating lectures from some of the foremost speakers in the field along with the opportunity to see demonstrations of the latest software developments from CCP4 during the lunch-time bytes sessions. For more information on the program and registration details please go to the Study Weekend website: http://www.cse.scitech.ac.uk/events/CCP4_2011/ We look forward to seeing you in Warwick. Best wishes, The CCP4 team -- Scanned by iCritical.

1 0

separate amino acid chains
by Florian Schmitzberger 23 Sep '10

23 Sep '10

Dear All, Quick question regarding the handling of different amino acid chains in the Phenix Autobuild GUI. From the manual I understand that different amino acid chains are separated by > ? I pasted the my amino acid chains in the GUI separated with > ; I don't think in my case Phenix recognizes the different chains as such, but as one contiguous protein. Am I missing anything obvious? Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

2 1

autobuild : use of ncs
by Lepore, Bryan 22 Sep '10

22 Sep '10

i read and see that autobuild finds ncs automatically and uses it. i have one .pdb with one copy of the model for segid's A and B, and chainid's A and B. however, i notice sometimes in density modification that ncs has "NO" flags as to its use, and the output .pdb's have a single chain in them. refinement has sensible .eff's and such for ncs, there's find_ncs_* output, but some .log's suggest it is not specified or used. so just generally, how is ncs used - e.g. is it strict, which would explain a single chain the output .pdb? -bryan

2 3

PDB Tools and CNS formatted structure factors
by Joseph Noel 22 Sep '10

22 Sep '10

Is there anyway with the PDB Tools to renumber protein chains? I have a model that doesn't correspond to the actual sequence, off by a couple of residues and just looking for a quick way to change that. Also, which module in Phenix is used to read in and convert CNS formatted ascii structure factors to the mtz read by phenix other then using ccp4. ___________________________________________________________ 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 ___________________________________________________________

4 3

FYI : autobuild : "refine_pdb_in.mtz is missing" etc.
by Lepore, Bryan 22 Sep '10

22 Sep '10

here's a google-able post of a *solved problem* for the archive : phenix 1.6.4-486 (latest official release as of 21sep2010) building ends (FINISHED) with error messages (see below). some associated job setup details : phenix.autobuild with CL flag refine_eff_file_list=my_refinement_params.eff cartesian or torsion annealing, or start_temperature work OK in building/refinement. two segid's in .pdb, one chain id etc. SOLUTION : use the latest build. i used phenix-dev-533 GNU/Linux 32-bit. and thanks especially to Tom Terwilliger for the solution. [key error messages]: Failed to carry out AutoBuild_multiple_models: Sorry a subprocess has failed... Failed to carry out AutoBuild_build_cycle: Sorry...the file AutoBuild_run_1_/TEMP0/refine_pdb_in.mtz is missing...

1 0

autobuild : annealing
by Lepore, Bryan 21 Sep '10

21 Sep '10

[ phenix 1.6.4-486 ] looks like autobuild annealing is Cartesian. are there any (simple) tricks to get torsion, b/c seems there are no flags for it. -bryan

2 1

deleting jobs in phenix
by Sebastiano Pasqualato 20 Sep '10

20 Sep '10

Hi all, sorry for the maybe silly question, but I don't seem to find a way to delete jobs from a project in phenix (I'm using ver. 1.6.2-473 on a MacBook Pro). The 'job history' tab on the main window does not allow that, so I was wondering if there's an easy way to do it. Thanks a lot for the great software suite, keep it up guys, ciao s. -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990

2 4

Phenix renewal support
by Paul Adams 20 Sep '10

20 Sep '10

Dear Phenix Users, I hope that Phenix has been helpful in your work. We are in the process of submitting a renewal for funding of the Phenix project and I would be most appreciative of your support for our renewal. If you would be willing to write me a short note, before September 18th, in the form of a signed letter (PDF) that indicates how much Phenix has helped your research, that would be incredibly helpful for our renewal. You can send your letter to me at PDAdams(a)lbl.gov Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ KLMoody(a)lbl.gov ] [ 1-510-495-2506 ] --

2 1

R factor
by zhangh1＠umbc.edu 19 Sep '10

19 Sep '10

Hi, I want to calculate Fc based on the PDB file and reproduce the R factor in it. I first tried phenix.model_vs_data. It optimized ksol bsol and b_cart, and the output R factor (0.2143) is close enough to that in PDB (0.215). However, it didn't generate mtz files containing the calculated Fc. Then, I take the optimized ksol bsol and b_cart as the input and tried phenix.fmodel. I wrote my own code to calcuate the R factor. However, I got a lower R factor (0.2078). I think the reason might be my R calculation formula (sigma(fo-fc)/sigma(fo)) is wrong; or model_vs_data did more than just did flat solvent correction and anisotropic scaling. So, I am wondering whether phenix can: (1) Do the similar thing as model_vs_data (hope can be somehow faster:), but generate Fc-containing mtz file; (2) Do a simple R factor calculate to see whether my code is wrong (maybe answered already:) Thanks! Best Regards, Hailiang

2 7

generate Rfree flag for twinned crystals with 3 twin fractions
by Zheng Zhou 19 Sep '10

19 Sep '10

Dear all After reading the informative posts in mailing list, I started to deal with my first twinning dataset. The space group is P3. Xtriage found 3 twin laws. R vs R statistics indicated perfect twinning for two twin laws and one is twin with RPS. I realize that twin-related reflections should be in the same work or free group. Could phenix handle the Rfree flag correctly for me when there are more than one twin fraction identified? By applying one twin law, the Rfree dropped from 37% to 28% using phenix. When I use Refmac, the twin fractions are refined and the Rfree is down to 26%. I copied the Rfree flag from phenix to the ccp4 in this case. When I let ccp4 generate Rfree flag automatically, the Rfree is refined to 26% too. Should I label the Rfree at a higher space group? Thanks for your advice Best, Zheng (Joe) Zhou

2 1

Resolve NCS masks
by Florian Schmitzberger 18 Sep '10

18 Sep '10

Dear All, I would have a question regarding the use of masks in Resolve in Phenix for density modification: Is it possible to output the NCS and/or solvent masks Resolve is using during the Autosol run (similar as the options from the stand alone Resolve version) such as: mask_as_mtz ncs_mask_file mask.mtz protein_mask_file What are the best criteria (other than the final maps of course) within the output from Phenix.resolve to judge if the NCS (and/or solvent) mask was chosen adequately? (NCS_overlap?) I am mostly concerned if the masks chosen do include some of the more peripheral parts of my protein molecule and do not flatten these regions. Secondly, it is possible within Phenix Autosol wizard to supply a pdb file (with dummy atoms) for the mask for Resolve to construct the NCS mask? i.e. similar to set mask_pdb file= dummyatom.pdb Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

2 1

Ligand restraints editing with REEL
by Joseph Brock 18 Sep '10

18 Sep '10

Hi all, I'm working on a 1.5A structure that contains a novel ligand within the active site, which is an Arsenic derivative of Glutathione, using the Phenix GUI, version 1.6.4-486. I have been using the 'Molinspiration' webpage (http://www.molinspiration.com/docu/webme/) to generate a smiles string, which I then feed into ELBOW. Although the structure/chemical restraints of Glutathione should be unchanged by the covalent linkage to arsenic through the cysteinyl sulfur, the resulting restraints file consistently restricts one of the dihedrals to a value that is incompatible with the (quite clear) electron density. This occurs regardless of wether i use AM1 optimization, and is unresponsive to using native Glutathione (which refines into the corresponding density extremely well) as an input geometry file with any of the available 'Use geometry for' options (final geometry, initial geometry, etc). I then tried opening the output file in REEL and manually changing the corresponding dihedrals to those of glutathione, however after running simple optimization, the resulting restraints file has the same problem, and upon choosing the 'transer geometry and restraints' option (or any option) midway through running the 'eLBOW optimization' or 'AM1 optimization' options, Phenix consistently crashes. Any advice on how to transfer the origional geometry of native Glutathione to my new ligand effectively would be greatly appreciated. I'm a little confused as to the abilities of REEL, and how to affect them. Thanks so much in advance. Cheers, -Joe.

2 1

autobuild : MSE's keep coming back
by Lepore, Bryan 17 Sep '10

17 Sep '10

i used "semet=False" the .pdb has MET the .seq has M the output models, however, keep getting MSE's in them, complete with selenium. am i missing something? -bryan

5 6

Re: [phenixbb] Something that came up on the CCP4 list...
by Simon Kolstoe 16 Sep '10

16 Sep '10

Just for the record I've had it make a big difference a number of times as well with both refmac & shelx. I was under the impression that phenix.refine was "cleverly" allowing me to use that trick by just starring the add riding hydrogens in the def file however it seems not - something worth knowing! Simon On 16 Sep 2010, at 20:01, Phil Jeffrey wrote: > I've had it make a big difference in certain circumstances. And in > other circumstances not so much. Definitely worth a try. I do not > use the technique routinely. > > Phil Jeffrey > Princeton > > > > On 9/16/10 11:49 AM, Simon Kolstoe wrote: >> So just to clarify further - if i am having problems with the final >> geometry of a model (eg clashscore as reported by molprobity), is >> it an >> appropriate trick to add hydrogens and then refine in phenix.refine >> using the riding hydrogens option, or does this not really change >> anything? >> >> Simon >> >> On 16 Sep 2010, at 14:26, Pavel Afonine wrote: >> >>> Hi Simon, >>> >>>> Could I just seek some clarification? I was under the impression >>>> that >>>> phenix.refine calculated riding hydrogens by default and took these >>>> into account as a restraint on the geometry? >>> >>> if you want hydrogen atoms to be used in refinement (as "riding >>> model" >>> or explicit) your need to make sure the PDB file that you give to >>> phenix.refine contains H atoms. That is you need to add them using >>> programs like phenix.reduce or phenix.ready_set or using >>> corresponding >>> functionality in the GUI. >>> >>> phenix.refine will not add them internally as part of refinement IF >>> hydrogen atoms are NOT present in input PDB file. >>> >>> Adding hydrogen atoms as 'riding model' does not add any refinable >>> parameters, but the scattering contribution from them is included >>> most >>> of the time. This is why we do not use H atoms silently but require >>> them to be in input PDB file - simply to make sure the reported >>> statistics (such as R-factors) is easily reproducible. >>> >>> All the best! >>> Pavel. >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >

2 1

LABIN labels for Autosol/resolve NCS scores
by Florian Schmitzberger 16 Sep '10

16 Sep '10

Dear All, I would have a number of Phenix related questions: Firstly, I used the anisotropy server ( to anisotropically truncate my mtz file with anomalous signal (SAD data). My question is if the labels (for F+/F- and SIGF+/SIGF- are correctly recognized by Phenix (Autosol). The columns labels are: F_ref for FP; QSIGF_ref for SIGFP; GF(+)pk for F(+); LSIGF(+)pk for SIGF(+), GF(-)pk for F(-); LSIGF(-)pk for SIGF(-). It seems QSIGF and GF(+)pk/LSIGF(+)pk etc. are , but I am uncertain if it recognizes F_ref, because for the LABIN INPUT LABELS it says "NONE" for"F". Phenix does not seem to detect the anistropy ("Not using aniso- corrected data files as the range of aniso b is only 19.52 and 'correct_aniso' is not set); so I suppose I should use the correct_aniso=True keyword. Secondly, what are good values for the evaluation of the NCS mask and NCS averaging Resolve is using in Phenix; NCS overlap values (e.g. in my case 1.1) and NCS_CORR (in my case 0.52) in the "resolve.scores" file. Does an NCS overlap value of greater than 1 make sense? I am working with a (anisotropic) dataset with 4.1/4.5 A resolution, 78 % solvent content, 2-fold NCS; Perhaps a naive question: It is not possible to use B-factor sharpened maps for autobuilding with Phenix Autobuild is it? Thank you for any comments! Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

2 3

f', f'' of Bromide?
by Tri Ngo 16 Sep '10

16 Sep '10

Dear Phenix-BB members, I am trying to solve the MAD data of one bacteria protein. The crystal was soaked with 1M Sodium Bromide. The data were collected at three different wavelength. I intend to use Autosol to solve this structure, but I am not sure which parameter I should put in the field: f' and f''? I think there is a table in the synchrotron but maybe I didn't notice about that. So now what should I do? Thank you very much for your input! Best wishes, -- * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150

4 3

Intl Conf on Structural Genomics, Toronto, Canada, May 10-14, 2011
by Thomas C. Terwilliger 16 Sep '10

16 Sep '10

Dear Colleagues, We are pleased to let you know about the upcoming International Conference on Structural Genomics 2011, to be held in Toronto, Canada on May 10-14, 2011. This meeting is the 6th in this series of biennial meetings of the International Structural Genomics Organization. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics and structural/chemical biology, and their impact on research in biology, medicine and disease. A limited number of student travel fellowships will be available for travel to this meeting. A substantial number of short talks will be selected from poster abstracts. Please see http://www.icsg2011.org for further details. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

1 0

64-bit Snow Leopard support
by Nathaniel Echols 16 Sep '10

16 Sep '10

Mac users-- The latest nightly version of Phenix (dev-532) is now capable of compiling 64-bit objects on Snow Leopard, which should help those of you working on very large and/or high-resolution structures. You will need to use the source installer for this; it will automatically recognize the machine type as "mac-intel-osx-x86_64" and use the correct sources. There are several things to be aware of before trying this: 1. I had to switch to the development version of wxPython to get the GUI working, and it's both inherently less stable and based on fundamentally different OS libraries, which may cause problems. I've fixed some of the most obvious issues and everything appears to run now, but I expect to find more glitches. (This shouldn't affect command-line users.) 2. We haven't extensively tested 64-bit Phenix on Mac; there may be undiagnosed low-level bugs, even for command-line-only use. This should change soon. 3. For the above reasons, and because source installation is generally difficult to support, we recommend that you continue to use the 32-bit binary installer if you are not experiencing memory problems. (It will figure out what you are trying to do and correct the machine type accordingly.) 4. One side effect of this change is that an installation made on Leopard will not work on Snow Leopard, and vice-versa. I may be able to fix this. Hopefully there will be a binary installer in the near future, if I can ever figure out how to fix NFS on my workstation. -Nat

3 3

Something that came up on the CCP4 list...
by Simon Kolstoe 16 Sep '10

16 Sep '10

In the fascinating current discussion on the ccp4 list Pavel said: >Dear Ed, > >no, if you start with model that has no hydrogens, they will not be generated internally. > >Pavel. > On 9/15/10 2:58 PM, Ed Pozharski wrote: > Sure. But if I start with model that has no hydrogens, they will be > generated but not passed to the output, right. just like refmac. > > On Wed, 2010-09-15 at 14:52 -0700, Pavel Afonine wrote: >> Dear Ed, >> >> On 9/15/10 2:47 PM, Ed Pozharski wrote: >>> On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote: >>>> So the riding hydrogen model is imperfect. At least with >>>> phenix.refine >>>> you can measure it, unlike the default behavior of REFMAC. (But >>>> you >>>> can >>>> tell it to write hydrogens out, I believe). >>>> >>> My impression is that default behavior of phenix.refine is the >>> same - I >>> had to change parameters to include hydrogens in the output. >> No, if your input file contains H atoms, the output file will contain >> them too (in phenix.refine). You don't have to change any >> parameters for >> this. >> >> Pavel. Could I just seek some clarification? I was under the impression that phenix.refine calculated riding hydrogens by default and took these into account as a restraint on the geometry? Simon

2 3

nqh-flip option
by Christian Roth 16 Sep '10

16 Sep '10

Dear all, I put manually in the parameterfile from the gui the option nqh_flips=True. After the run starts, a popup comes up claiming about an invalid unsupported option and the refinement stops without producing any file, even not a log-file. Does the nqh option not longer exists or what happend here? I use at the moment phenix 1.6-289. Thanks for your help. Christian

5 10

Re: [phenixbb] autobuild : MSE's keep coming back
by Thomas C. Terwilliger 15 Sep '10

15 Sep '10

Hi Bryan, Hmmm...I can't seem to make it happen with my standard inputs. Can you possibly send me directly (terwilliger(a)lanl.gov) your AutoBuild_run_1_/autobuild.eff file or better yet that plus your input files and I'll try that out here? Thanks a lot, All the best, Tom T >>> are you using a recent version? >> >> v1.6.4 release tag 486 >> >>> is this rebuild_in_place or not? >> >> well, i did not specify rebuild_in_place, however, i poked around and can >> see that autobuild has switched on rebuild_in_place so i call that a >> "yes". >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

1 0

Re: [phenixbb] autobuild : MSE's keep coming back
by Lepore, Bryan 15 Sep '10

15 Sep '10

> are you using a recent version? v1.6.4 release tag 486 > is this rebuild_in_place or not? well, i did not specify rebuild_in_place, however, i poked around and can see that autobuild has switched on rebuild_in_place so i call that a "yes". -bryan

1 0

Re: [phenixbb] [ccp4bb] Deposition of riding H
by Dr. Mark Mayer 15 Sep '10

15 Sep '10

>However this thread appears to have reached the point where not much new >ground is being broken. As the person who started this thread I'll second Phil Jeffrey's comment. I chose to continue my depositions with riding H, and the rcsb agreed to accept the coordinates. Its been great hearing the experts weigh in on this. I've learned a lot, and clearly there is no consensus. As one of the vast majority of crystallographers dependent on all the hard work that program developers undertake to support structural biology, I'm happy to follow advice given by the developers of the various programs I use, and for Phenix the current advice is to deposit with riding H. -- Mark

1 0

Re: [phenixbb] [ccp4bb] Deposition of riding H
by Felix Frolow 15 Sep '10

15 Sep '10

Pavel, Shelxl is working in correct coordinates - fractional... Many things are easier in fractional coordinates. Are you sure that Phenix does not go orthogonal -> fractional -> orthogonal in internal calculations? When fixing of parameter is made in fractional coordinates it does not produce confusion. Shelxl also make fractional -> orthogonal (AKA PDB) which is also correct. Constrain is not transferred there. BTW Shelxl knows symmetry very well and will constrain atoms that occupying symmetry elements. Shortly Shelxl knows crystallography best. When you will see number of lines in Shelxl Fortran code ( do not kill Fortran to early) you will be surprised. There are not so many of them. No graphical user interface yet, but COOT is of great help. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfrolow(a)post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 15, 2010, at 19:11 , Pavel Afonine wrote: > Hi Tim, > >> The pdbe.org, for example allows to upload auxiliary files and in my opinion the >> uploading of the final .ins-file (not the .res-file!) should be made mandatory >> in the case of shelxl refinement. >> >> Since coot has now become utterly convenient even for shelxl refinement, there >> is no reason one should not deposit the .ins-file ([flame] and the PDB-file >> probably for legacy reasons [/flame]). > > I was always wondering but never had a good occasion to ask (my Shelxl knowledge is limited and may be outdated so I apology in advance if my questions are too dummy; also I realize that I'm asking a non-CCP4 question on CCP4bb for which I apology again): > > - how .ins file encodes the information about NCS groups used in refinement (atom selection for NCS groups, restraint weights for different groups, etc? > > - how .ins file encodes the information about TLS (again, atom selections for TLS groups, TLS matrices, etc)? Related, does it have a concept of having TLS and other components to the total atomic displacement parameter (ADP)? > > - If I recall it correctly, to fix (=not refine) a certain parameter (say occupancy or B-factor) in Shelxl you need to add a number 10 to it. Is it true? IMHO, this might lead to confusion if such a file gets deposited to PDB. > > All the best! > Pavel.

2 1

How does phenix.fmodel treat isotropic and anisotropic B?
by zhangh1＠umbc.edu 15 Sep '10

15 Sep '10

Hi, I am doing a phenix.fmodel calculation for a PDB structure containing anisotroipc B. If I understand it correctly, the B factor is composed of both the isotropic B for ATOM line (Biso) and the anisotropic B from ANISOU line (Uani): Fc=sigma ( fi * exp (-Biso*s*s) * exp (-st*Uani*s) * exp (i*r*s) ) Please correct me if the above equation is wrong. I also noticed that in PDB, the Uani (after scaling by 10^-4) is generally much smaller than Biso. So I assume that Biso has a much bigger contribution than Uani, the latter only implying the vibrational anisotropicity. However, I did a test calculation by setting all Bio to 0 whereas keeping Uani unchanged. Due to the above assumption, I expected the results should be very different from the native structure; however, coot told me they were just so close... Maybe I am wrong somewhere... Best Regards, Hailiang

2 5

Sep 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 Sep '10

14 Sep '10

Dear Users, The deadline for Nov/Dec 2010 Collaborative Crystallography proposals will be *Sep 15, 2010. * ---------------------------------------------------------------------------------------- Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for Nov/Dec 2010 allocation period, proposals must be submitted by *Sep 15, 2010.* The deadline for CC proposals for the time period Jan/Feb 2010 will be Nov 15, 2010. Regards, Banumathi Sankaran

1 0

Reproducibility of R-factors
by miket＠chem.ucla.edu 14 Sep '10

14 Sep '10

Hi All, I recently used phenix.model_vs_data to evaluate a structure that was refined using Refmac. The R_work and R_free calculated by refmac are 0.18 and 0.20, while model_vs_data calculates them as 0.20 and 0.22. Should I be concerned about this discrepancy? Is it typical for different programs to calculate different values for R-factors using the same data, and if so what is the source of this difference? Seems to me like there shouldn't be much of a difference (at least not 2%). Maybe I'm wrong. Any insight/advice would be appreciated. Thanks, Mike Thompson -- Michael C. Thompson Graduate Student Yeates Lab Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

3 2

Deposition of riding H
by Dr. Mark Mayer 14 Sep '10

14 Sep '10

Here's one for the community, which I'll post to both Phenix and CCP4 BBs. Where does the crystallographic community stand on deposition of coordinates with riding hydrogens? Explicit H are required for calculating all atom clash scores with Molprobity, and their use frequently gives better geometry (especially at low resolution). Phenix uses explicit riding H for refinement, and outputs these in the refined PDB. Refmac also uses riding H but does not output H coordinates. While depositing a series of structures refined at 1.4 - 2.75 A with Phenix got the following email from the RCSB, who asked I resupply coordinates without H for two of the structures. Since we can't see H even at 1.4 Å I don't understand why an arbitrary cut off of 1.5 Å was chosen, and also why explicit H atoms used in refinement and geometry validation should be stripped from the file. FROM RCSB We encourage depositors not to use hydrogens in the final PDB file for the low resolution structures (> 1.5 A). Please provide an updated PDB file. We request you to use processed PDB file as a starting point for making any corrections to the coordinates and/or re-refinement. -- Mark

2 1

Re: [phenixbb] Deposition of riding H
by Jeff Headd 14 Sep '10

14 Sep '10

Hi Mark, If hydrogens are used to arrive at a final refined model (whether riding or not) it is essential for the reproducibility of results that the H atom records be included in the deposited model. How B-factors are specified and some final atomic positions (such as rotatable methyl groups) are difficult or impossible to predict once removed, so without their deposition this information would be lost and any published statistics would not be reproducible as published. This point is illustrated in one of our recent papers: Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Cryst. 2010, 43, 669-67. Further, there is no universal standard currently in use that specifies H bond-lengths (some use electron cloud distances, others neutron distances, some a mixture of both), meaning that without inclusion of H atom records (or at least a reference to which library was used) it is very difficult to know where the H atoms were placed. Thanks, Jeff On Tue, Sep 14, 2010 at 10:32 AM, Dr. Mark Mayer <mayerm(a)mail.nih.gov> wrote: > Here's one for the community, which I'll post to both Phenix and CCP4 BBs. > > Where does the crystallographic community stand on deposition of coordinates > with riding hydrogens? > Explicit H are required for calculating all atom clash scores with > Molprobity, and their use frequently gives better geometry (especially at > low resolution). Phenix uses explicit riding H for refinement, and outputs > these in the refined PDB. Refmac also uses riding H but does not output H > coordinates. > > While depositing a series of structures refined at 1.4 - 2.75 A with Phenix > got the following email from the RCSB, who asked I resupply coordinates > without H for two of the structures. Since we can't see H even at 1.4 Å I > don't understand why an arbitrary cut off of 1.5 Å was chosen, and also why > explicit H atoms used in refinement and geometry validation should be > stripped from the file. > > FROM RCSB > > We encourage depositors not to use hydrogens in the final PDB file for > the low resolution structures (> 1.5 A). Please provide an updated PDB > file. We request you to use processed PDB file as a starting point for > making any corrections to the coordinates and/or re-refinement. > -- > > Mark > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

1 0

Re: [phenixbb] autobuild : change reflection file mid-job?
by Thomas C. Terwilliger 14 Sep '10

14 Sep '10

Hi Bryan, Yes, I think to change the reflections file you will have to rerun the job as the reflections are read once in autobuild and propagated from there out. All the best, Tom T >> [it was inevitable..] >> >> if i swap the reflection file mid-job - THAT sounds like catastrophe : >> >> so does autobuild determine the format *only* from the .sca, .mtz affix? >> >> and it looks like reflections are read once at startup, and propagated >> from there out? >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

1 0

autobuild : change reflection file mid-job?
by Lepore, Bryan 14 Sep '10

14 Sep '10

[it was inevitable..] if i swap the reflection file mid-job - THAT sounds like catastrophe : so does autobuild determine the format *only* from the .sca, .mtz affix? and it looks like reflections are read once at startup, and propagated from there out? -bryan

1 0

Palestrant, Deborah is out of the office.
by deborah.palestrant＠novartis.com 13 Sep '10

13 Sep '10

I will be out of the office starting 09/13/2010 and will not return until 09/15/2010. I have limited access to email and will respond to your message when I return.

1 0

Re: [phenixbb] autobuild : change .seq mid-job?
by Thomas C. Terwilliger 13 Sep '10

13 Sep '10

Hi Bryan, I think that you can do this, though I have not tried it. You need to replace two files: 1. your original sequence file wherever it is "/wherever/.../myseq.dat 2 a file with the same name "myseq.dat" or whatever, in the directory AutoBuild_run_1_/TEMP0 I would expect all model-building after that to have the new sequence. (Note that runs that are already going as sub-processes will keep their sequences). Now if this is rebuild_in_place, this would not be a good idea. I am assuming it is rebuild_in_place=False, and so it should work... Let me know how it turns out, -Tom T >> i have a long autobuild job going. i'd like to change the .seq files as >> its going - if i keep residue 1 numbered, could this still be a >> catastrophe? >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

1 0

autobuild : change .seq mid-job?
by Lepore, Bryan 13 Sep '10

13 Sep '10

i have a long autobuild job going. i'd like to change the .seq files as its going - if i keep residue 1 numbered, could this still be a catastrophe? -bryan

1 0

debugger pdb
by Krista Joosten 10 Sep '10

10 Sep '10

Hi all, I'm working with Tom Burnley on the development of time_averaging.py. I would like to use the debugger pdb, but am not sure how to do this and whether it's possible. After some googling, I tried to hack into phenix.time_averaging adding -m pdb when the variable DEBUG==1, but I got the error message 'no module called pdb'. Bye Krista

2 1

Beamtime at the ALS-BCSB beamlines
by Peter Zwart 09 Sep '10

09 Sep '10

Dear All, July 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal cycle. All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal screening and data collection. Remote data collection is available on all BCSB beamlines, providing the user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. The main difference between local operation and remote operation, is the length of the network cable! This enhanced remote operation capability is coupled with 22hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Remote users can furthermore be kept up-to-date on changes in ring status via an SMS service ( http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Ph…) or via twitter (@AlsRingStatus). Specific features are summarized below. Beamlines 5.0.1, 5.0.2, 5.0.3: -------------------------------------- Beamline 5.0.2 is equipped with a novel variable collimator allowing users to adjust the beamsize continuously and on the fly between 25 and 100 micron, both horizontally and vertically. With a collimator setting of 30x30 micron, typical exposures are around 1 to 2 second. The Berkeley Automounter sample handling system has a routine capacity of 96 samples (6 pucks). In a typical high-throughput screening mode, the mount-to-mount time is around 2.5 minutes per sample, allowing users to screen a full puck within 45 minutes. The sector 5 beamline user stations are equipped with fully high-adjustable, ergonomically friendly work stations. Beamlines 8.2.1 and 8.2.2: ----------------------------------- To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioningstage. Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer (Actor), allowing remote operations to now be a routine mode of access for these beamlines. Data analyses in the BCSB is facilitated by software maintained by sbgrid ( http://www.sbgrid.org). A 16 core linux machine is available for our users to process their data and solve/refine their structure. An additional mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please contact BCSBBeamtime(a)lbl.govfor more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/ Scroll down to "Structural Biology beamines (includes protein SAXS)." Click on "New Proposal." If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

1 2

Help on multi-start-simulated-annealing sigmaA-weighted 2fofc map
by fn1＠rice.edu 09 Sep '10

09 Sep '10

Hi everyone, I read on the paper that they use CNS (model_map.inp) to calculate the avarage sigmaA-weighted 2fofc map. Right now I have set up the simulated annealing with different random seeds. I wonder whether phenix could calculate the average map with the multiple coordinates from different starts? Thanks! Fengyun

2 4

Can phenix calculate R factor based on the only given mtz file containing Fo and Fc?
by zhangh1＠umbc.edu 07 Sep '10

07 Sep '10

Hi, I am wondering whether phenix can calculate R factor based on the only given mtz file containing Fo and Fc? Thanks! Hailiang

2 1

will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb?
by zhangh1＠umbc.edu 07 Sep '10

07 Sep '10

Hi, For the pdb file generated by refmac which contains only the residual-B, will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Thanks a lot! Best Regards, Hailiang

2 5

constrained occupancy groups in phenix.refine
by Lionel Costenaro 03 Sep '10

03 Sep '10

Hello, A portion of my structure have two conformations at an interface between two (NCS) protein chains -in addition to other alternates conformations elsewhere. In both chains, I defined alt_A as one conformation and alt_B as the second conformation, and also for the waters in this region. I would like to constrained the occupancy of these conformations. I though that the following selections would do the job: occupancies { constrained_group { selection = "(chain A or chain B) and (resseq 105 or resseq 110:112 or resseq 140:143) and altid A" After refinement, all alt_A selected residues do have the same occupancy, but not the same occupancies for alt_B and the sum for one residue (occu alt_A +occu alt_B) is not 1. Adding a second group with the same selection but "altid B", constrains also the alt_B occupancies but the sum is still not 1. How should I defined my group(s)? Is it possible to select several non continuous residues from one chain (that's for the waters) without repeating each time "or resseq" ? Best regards, Lionel

4 6

Re: [phenixbb] Can we untoggle molecular weight mean deviation check on ensembles in autoMR?
by James Thompson 03 Sep '10

03 Sep '10

A postdoc in my lab with many more files inside his Phenix build directory just showed me that the Mwt mean deviation check on input ensembles is hard-coded in Phaser. A seemingly arbitrary value of 20% is set within the file emsembles.cc. So, the answer to my previous question is presently NO. We users cannot untoggle or alter this mean deviation value without some recompile of Phaser. I will play with my Sculpt'ed output from the Mustang server to reduce the Mwt deviations within the ensemble of coordinates that I want to feed to Phaser-MP to get by. James R. Thompson <thompson.james at mayo.edu> > Can folks untoggle the molecular weight mean deviation check in > phenix.autoMR on the ensembles input? > > I want to use an ensemble of coordinates generated by the Mustangs > server from a SSM alignment. Therefore, by design the 10 PDBs input to > phenix.autoMR vary greatly in molecular weight from their mean value, > but the whole is likely an excellent probe for molecular replacement. > However, I am stymied by phenix.autoMR: > > ------------------------------------------------------------------------------------- > FATAL RUNTIME ERROR: Molecular weight of > /home/jrt04/Desktop/GB1STAS/MUSTANGServer_10_1.6_0_sculpt-coot-0.pdb > (6610.56) deviates more than 20% from the mean (3977.08). This pdb file > may contain domains or water not present in the other files. > ------------------------------------------------------------------------------------- > > I understand why this check might be of utility to the unobservant. How > can I disable this test? > > Many thanks, > Jim > > -- > James R. Thompson <thompson.james at mayo.edu>

3 2