- phenixbb - phenix-online.org

B-group and TLS
by Engin Ozkan 16 Dec '08

16 Dec '08

Dear phenixbb people, I am performing group ADP refinement and TLS at the same time. At the end, the total B factors in the pdb are not identical within residue groups. ATOM 7 N ILE A 11 23.863 6.894 77.827 1.00151.81 A N ANISOU 7 N ILE A 11 20044 20245 17393 -796 -2448 -568 A N ATOM 8 CA ILE A 11 23.647 6.312 76.502 1.00149.93 A C ANISOU 8 CA ILE A 11 19407 19827 17732 -699 -2577 -541 A C ATOM 9 CB ILE A 11 24.451 7.060 75.423 1.00142.17 A C ANISOU 9 CB ILE A 11 18258 18757 17003 -502 -2834 -817 A C ATOM 10 CG2 ILE A 11 24.819 6.135 74.260 1.00140.21 A C ANISOU 10 CG2 ILE A 11 17760 18301 17213 -445 -3136 -730 A C ATOM 11 CG1 ILE A 11 23.648 8.266 74.929 1.00141.20 A C ANISOU 11 CG1 ILE A 11 17949 18698 17002 -369 -2502 -1103 A C ATOM 12 CD1 ILE A 11 22.184 7.945 74.630 1.00147.23 A C ANISOU 12 CD1 ILE A 11 18421 19495 18025 -392 -2156 -1014 A C ATOM 13 C ILE A 11 24.000 4.831 76.450 1.00152.71 A C ANISOU 13 C ILE A 11 19772 20013 18238 -798 -2860 -201 A C ATOM 14 O ILE A 11 24.895 4.377 77.158 1.00153.29 A O ANISOU 14 O ILE A 11 20114 20074 18055 -857 -3135 -9 A O I would like to know if the refinement was truly grouped B-factor refinement - I am suspecting the residual B-factors might be grouped, but I haven't checked for that. Could anyone, maybe Pavel, confirm that is the case? Is there anyplace in the log files I could see the number of B groups? Thanks, Engin

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Re: [phenixbb] Completeness issue by phenix
by Young-Jin Cho 16 Dec '08

16 Dec '08

Thanks Ralf, You were right. I found that my .log file has Anomalous flag:True. As it was pointed out, my mtz file was came from ccp4 where it uses anomalous data by default. Another small wondering is about differently automatic(?) resolution pick up: my refmac assigned resolution range between 1.48 and 54.23 whereas my phenix.refine set it between 1.363 and 31.041 by default. Also while the refmac provides both entire and high resolution bin completeness, the phenix only gives a whole completeness. Is there any way I can investigate high resolution bin completeness? and why I have different resolution ranges by default without specifically assigning them? Thanks again. YoungJin ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" <rwgk(a)cci.lbl.gov> To: phenixbb(a)phenix-online.org Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Completeness issue by phenix Hi YoungJin, I suspect phenix.refine decided your mtz file contains anomalous data when you actually have non-anomalous data. Could you look in the phenix.refine output for something like this: ================================== X-ray data ================================= F-obs: 1yjp.mtz:FOBS_X,SIGFOBS_X R-free flags: 1yjp.mtz:R-free-flags Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X Observation type: xray.amplitude Type of data: double, size=495 Type of sigmas: double, size=495 Number of Miller indices: 495 Anomalous flag: False ^^^^^ in particular here If you see "Anomalous flag: True" try adding this to the phenix.refine command line: xray_data.force_anomalous_flag_to_be_equal_to=False Let me know if this doesn't help. If it does help, I'd be interested to know how the .mtz file was generated. Ralf _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Re: [phenixbb] Completeness issue by phenix
by Ralf W. Grosse-Kunstleve 15 Dec '08

15 Dec '08

Hi Rupert, Thank you very much for the files! I found a simple, universal trick to "do the right thing", not just in phenix.refine. This will be in future releases. Ralf

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Completeness issue by phenix
by Young-Jin Cho 15 Dec '08

15 Dec '08

Hi, I was happy for using phenix but am struggling with a strange result on completeness calculation. One typical data set I used kept showing low completeness, so I used the same mtz, and pdb file on Refmac: it turned out has more than 98% whereas phenix.refine gave me about 46% completeness. I have slightly lower value of R but higher Rfree from phenix calculation without adding H atoms. I don't know if this is a bug or a problem on my data set (hopefully not). thanks in advance, YoungJin

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phenix GUI takes longer time to comeup
by shivesh kumar 15 Dec '08

15 Dec '08

Dear all The GUI of phenix installed in Fedora 8 takes longer time, sometimes 30mins. Can anyone help in this regard, what is the problem and how it can be sorted out? Thanx in advance Shivesh

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Re: [phenixbb] individual anisotropic adps
by Pavel Afonine 13 Dec '08

13 Dec '08

Currently phenix.refine does not support refinement of individual anisotropic ADP and TLS for the same set of atoms (see my previous email). However, in phenix.refine you can refine TLS and individual anisotropic ADP for non-overlapping set of atoms. Pavel. On 12/11/2008 8:34 AM, gerwald jogl wrote: > Thanks, that's roughly what I thought. How about tls and individual > anisotropic together? same strategy, just observe Rfree?

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individual anisotropic adps
by gerwald jogl 11 Dec '08

11 Dec '08

Hi All, I was wondering if there is information/recommendations out there for the resolution required to refine individual anisotropic adps. I think the recommendation for shelx is at least 1.5 A resolution. In addition, is phenix set up and would it make sense to combine tls with individiual anisotropic adps? All comments welcome, Gerwald

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Keeping the same origin
by Mo Wong 11 Dec '08

11 Dec '08

Hi all, I would like to compare maps from different phasing runs, so it would make my life much easier if I could keep the same origin. I recall this could be done in solve/resolve, but can't seem to find it mentioned in the phenix documentation. Any suggestions? Thanks!

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resolution bins
by Daniele de Sanctis 10 Dec '08

10 Dec '08

Hi, I was wondering how phenix.refine decide the number of resolution bins in which it shows the refinement statistics (R-free, phase error...). In the case I'm working on it prints out only three resolution bins. Thanks d -- Daniele de Sanctis, PhD Macromolecular Crystallography Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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Question regarding phenix.elbow
by Young-Jin Cho 03 Dec '08

03 Dec '08

Hi I would like to know how I can add H atoms to my ligand, ADP in the protein complex. I was trying to add H atoms to one of my ligand, ADP. When I types "phenix.elbow --final-geometry=test10bcoot_h_refine_001.pdb --residue=ADP --output=model_h", it went on but failed with the following error message: Traceback (most recent call last): File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1201, in <module> run() File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1108, in run molecule = post_process(molecule, options) File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 577, in post_process options, File "/home2/yjcho/phenix-1.3-final/elbow/elbow/utilities/optimisation_manager.py", line 331, in optimisation_manager pre_opt)) File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 857, in WritePDB original_order=original_order, File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 965, in WritePDB2String self.AdjustHydrogenNames() File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 940, in AdjustHydrogenNames if test_name[3]==" ": test_name[3]="0" TypeError: 'str' object does not support item assignment FYI. ADP is names as ADP as a residue name in the pdb file but has different chain names. By the way, I should mention that I used phenix.reduce first for adding H atoms but it was not able to add sugar H's in ADP molecule albeit other residues were fine. Thanks in advance for your help. Best, YoungJin

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