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General Questions about Joint x-ray/neutron refinement
by Louis Lazar 17 Jun '11

17 Jun '11

Developers/all: I have been running some Joint X/N jobs, and I have some questions that perhaps you can help me with. First, doing joint refinement gave a total of 53 waters (thanks to ordered_solvent=true), yet the electron density seems to show that there are several more waters that are actually present (however it should be noted that there is no nuclear density associated with those waters, and in some cases no nuclear density associated with the 53 that were chosen by ordered_solvent=true). Should I add in manually to the electron density what I believe are these extra waters, or simply ignore them? Second, when I try to real space refine any of the residues, I get an error message telling me about exploding atoms. What is the cause of this message, and is it possible to real space refine any of these residues and specifically the hydrogen atoms associated with them. Third, during the joint refinement run, I chose to refine occupancies of all atoms. This breaks down into several questions: A) Should I be refining occupancies at 2.0 A resolution (of the neutron structure; 1.05A for the X-ray)? B) How does Phenix go about refining occupancies of hydrogen/deuterium sites? C) If the resulting occupancies result in values of, for example, 60% deuterium and 40% hydrogen, am I to presume that deuterium presence is significant if the nuclear density looks "good". At what point of deuterium occupation (while examining the nuclear density), would I say that there is likely no deuterium present (or that it is insignificant)? Hopefully all of these questions make sense, and if I need to clarify anything, please let me know. Thanks so much in advance for the help, I appreciate it as always. Regards, Louis

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tls group and anisotropic
by ChenTiantian 16 Jun '11

16 Jun '11

Dear Phenixers, I refined my structure with TLS, I did not mean to refine it with anisotropic strategy, but I got ANISOU record. As the manual metioned, when doing TLS refinement, It always happens like this. What does this ANISOU record mean ? Does that mean TLS is a grouped anisotropic refinement? Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

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no density on the anchored proteins
by zhangh1＠umbc.edu 16 Jun '11

16 Jun '11

Hi, I am using phenix.refine to calculate the map of the 50S RNA (1FFK). It is weird that there is no density on the anchored proteins even for the Fc map. Following is the code I am using: phenix.refine ${f}.pdb ${f}.mtz main.number_of_macro_cycles=0 xray_data.high_resolution=${res} xray_data.r_free_flags.generate=True export_final_f_model=mtz Thanks for any advice! Hailiang

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Re: [phenixbb] rosetta fragment files -- adjusting residue numbers to combine them
by Thomas C. Terwilliger 16 Jun '11

16 Jun '11

Hi Leonid and others wanting to use phenix.mr_rosetta with large chains, After looking at the Rosetta code and conferring with Frank DiMaio from the Baker laboratory... You can paste several fragment files together to represent your entire chain, but you need to edit all but the first one to set the position in the sequence file that each set of fragments goes with. Here is a little script that will take a fragments file that you have created that started with residue 651 and edit it in a way that you can just add to the end of your fragments file for residues 1-650. Run it with: phenix.python adjust_robetta_resid.py \ fragments_in fragments_adjusted 651 -------------------------------- # adjust_robetta_resid.py # use: phenix.python adjust_robetta_resid.py fragments_in fragments_adjusted 651 # to adjust the first residue of fragments_in to be 651 import sys args=sys.argv[1:] if len(args) != 3: print "USE: phenix.python adjust_robetta_resid.py fragments_in fragments_adjusted <start_resno>" sys.exit() file_in=args[0] file_out=args[1] start_resno=int(args[2]) print "Copying %s to %s offsetting start residue number to %d" %( file_in,file_out,start_resno) f=open(file_out,'w') new_resno=0 for line in open(file_in).readlines(): if line.find('position:') > -1 and line.find('neighbors:')>-1: spl=line.split() current_resno=int(spl[1]) new_resno=current_resno+start_resno print "Residue %d changed to %d" %(current_resno,new_resno) spl[1]=" %d " %(new_resno) new_line=" ".join(spl) else: new_line=line print >>f, new_line.rstrip() f.close() -------------------------------- I will add this to phenix as "phenix.adjust_robetta_resid" as well. However...there still is a problem if you have multiple chains...as mr_rosetta has only one set of fragments files the same fragments files are being applied to all your chains. I will add a way to specify which fragments files go with which chains. All the best, Tom T >> [phenixbb-bounces(a)phenix-online.org] On Behalf Of Leonid Sazanov [sazanov(a)mrc-mbu.cam.ac.uk] >> Sent: 16 June 2011 13:11 >> To: phenixbb(a)phenix-online.org >> Subject: [phenixbb] rosetta fragment files >> >> Hi, I am trying to use mr_rosetta with phenix-1.7.1-743 and rosetta 3.2.1. All rosetta tests passed OK. >> I have several large protein chains in the starting model (already placed). >> So I had to get several pairs of fragment files from robetta server and list all of them in the script. >> Then mr_rosetta fails at the REBUILD_1 stage with the message: >> could not open file (fragment file), although file is definitely there. Is the reason that one can have only two input fragment files (3/9)? Can several fragment files be combined into two 3/9 ones? >> Thanks >> >> -- >> Dr. Leonid A. Sazanov >> Research group leader >> Medical Research Council >> Mitochondrial Biology Unit >> Wellcome Trust / MRC Building >> Hills Road >> Cambridge >> CB2 0XY >> >> _______________________________________________ >> 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 >>

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rosetta fragment files
by Leonid Sazanov 16 Jun '11

16 Jun '11

Hi, I am trying to use mr_rosetta with phenix-1.7.1-743 and rosetta 3.2.1. All rosetta tests passed OK. I have several large protein chains in the starting model (already placed). So I had to get several pairs of fragment files from robetta server and list all of them in the script. Then mr_rosetta fails at the REBUILD_1 stage with the message: could not open file (fragment file), although file is definitely there. Is the reason that one can have only two input fragment files (3/9)? Can several fragment files be combined into two 3/9 ones? Thanks -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY

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IUCr satellitte
by Gloria Borgstahl 16 Jun '11

16 Jun '11

I am forwarding this information to you on behalf of Marc. Best regards, Gloria The Commission on aperiodic Crystals is organizing a * two days satellite meeting just after the IUCr Congress in Madrid: 'Aperiodic Crystals for Beginners', in Alcala de Henares, 31 August-1st September 2011. ** This school will present in a simple way the methods used for the structural analysis of Aperiodic Crystals*, namely incommensurately modulated phases, incommensurate composites crystals and quasicrystals. It is intended for beginners in the field and will alternate step by step lectures and tutorials. You will find more information in the attached leaflet or on the web site * **http://sig3.ecanews.org/aperbeg2011/aperbeg2011.html*<http://sig3.ecanews.org/aperbeg2011/aperbeg2011.html> Best regards Marc de Boissieu -- -- Marc de Boissieu Sciences de l'Ingéniérie, des Matériaux et des Procédés (SIMaP) Grenoble INP, CNRS, UJF 1130 rue de la piscine BP 75 38402 Saint Martin d'Hères Cedex (France) Tel 33 (0)4 76 82 67 03 Fax 33 (0)4 76 82 66 44 e-Mail: *Marc.de-Boissieu(a)simap.inpg.fr* <Marc.de-Boissieu(a)simap.inpg.fr>

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refinement of twinning dataset
by Ms Chiung-Wen Chang 14 Jun '11

14 Jun '11

hi everyone i have some issues with the refinement of my twinning dataset the dataset has 2.1 A resolution the twin fraction is around 0.43 i did not detwin and ran the refinement directly (with twinning refinement) The attached is the polygon so far the R: 0.1905 Rfree: 0.21 RMSD angles: 0.91 bonds: 0.006 clashscore: 28.176 average B: 45.8 are the clashscore and Average B in the reasonable range ? because the pattern of the polygon is looked wired what can I do more to get them better ? thanks for your help : ) Mary

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[Fwd: Re: elbow.join_cif_files error]
by Maia Cherney 14 Jun '11

14 Jun '11

Hi, I run command line elbow.join_cif_files ligand1.cif ligand2.cif ligand3.cif. As I understand, ligand1.cif and ligand2.cif are cif files present in the directory, the ligand3.cif should be made after joining the first two cifs. I get this error Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/elbow/elbow/command_line/join_cif_files.py", line 245, in <module> run(filenames, target) File "/usr/local/phenix-1.7.1-743/elbow/elbow/command_line/join_cif_files.py", line 145, in run include_commented_restraints=1, #include_commented_restraints, File "/usr/local/phenix-1.7.1-743/elbow/elbow/formats/monomer_library_cif_parser.py", line 185, in parse_cif raise RuntimeError('long tmp') RuntimeError: long tmp Maia

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Using rosetta for domain search with partial model solution
by Daniel Mattle 14 Jun '11

14 Jun '11

Dear Phenix Developers, Is there a possibility within rosetta searching only for a domain (using hhr files) while one has already a partial pdb model lacking a particular domain? I was unable to find this feature? Do you have implemented that? If this is not implemented yet, would it be possible to add this feature? Best, Daniel

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sca file & anomalous difference map: understanding the story from the scratch,
by Haytham Wahba 13 Jun '11

13 Jun '11

i am new user first Q?? with HKL2000 (with scale anomalous option: ON) the output.sca file is like that (for example): 1 -985 38.064 89.066 51.543 90.000 100.446 90.000 p21 0 0 2 3433.6 77.1 0 0 3 735.6 14.0 0 0 11 1564.7 25.4 0 0 12 5643.2 88.3 0 0 13 541.5 9.7 0 0 14 1701.0 27.4 0 1 1 2060.5 47.0 0 1 2 4115.3 75.3 4257.1 97.5 0 1 3 8782.0 280.6 7728.9 173.9 0 1 5 1760.8 28.4 1778.5 33.5 0 1 6 6650.2 122.2 6843.2 126.0 0 1 7 1935.8 36.6 1794.2 29.1 is that one is merged or unmerged????? if i compare with the output.sca with scale anomalous option (off): 0 0 2 3444.4 77.3 0 0 3 734.9 14.0 0 0 4 1705.0 27.5 0 0 5 2693.8 49.4 0 0 6 8383.1 153.9 ------------------------------------------------------- second Q? using output.sca (with scale anomalous option on) for molecular Replacment generate MR.mtz which shows F,SIGF in data labels under phenix.refine the generated (refine_data.mtz) shows: I-obs(+),SIGI-obs(+),I-obs(-),SIGI-obs(-) what is going on in first and second run? ----------------------------------------------------------------- third Q? i want to generate anomalous difference map using phenix.map but when i use output.sca (with scale anomalous option: ON) as reflections file the data label show ((i-obs,sigma)) how to convert this SCA file (if it is merged) to unmerged sca file to creat anomalous difference map for protein contains Br, Sn and Sulpher?? i want to see peaks for these 3 elements to confirm their presence. N.B: the wavelenght was 1.00900 N.B: resolution 1.78 A N.B: i use GUI phenix i am sorry for that long e-mail. thank you in advance haytham wahba biochemi UdeM Canada

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