- phenixbb - phenix-online.org

AutoSol with 4.2A dataset for a protein/DNA complex
by Wei Shi 16 Feb '12

16 Feb '12

Hi everyone, I have got a 4.2A SeMet MAD dataset for a protein-DNA complex. And, the native dataset for this protein-DNA complex is ~3.2A. The space group for the native and SeMet crystals seem to be different. I am not sure whether it’s possible to solve the structure with the current data I have, and wondering whether any of you have experience with working with this low-resolution data and any suggestion for me. I processed the data with XDS in space group P31, and used *.cns.hkl file from XDSCONV as an input for AutoSol and also include the sequence for protein only. The protein dimer has 418 residues and DNA is 32bp. I run Autosol with the default setting. Below is statistics I got. It seems that I didn’t get anything promising. Any comment or suggestion about what to try next? Thank you so much! Statistics: Top solution: 2 Sites: 11. Space group: P32. FOM: 0.550. BAYES-CC: 8.10. Residues: 465 Side-chains: 0. Chains: 60. Model CC: 0.67 R-work: 0.4100 R-free: 0.4569. Under Heavy-atom search and phasing: Space group # of refined sites FOM Overall score R-factor Map skew Corr. of local RMS density Solution1 P31 11 0.530 8.10+/-11.80 0.4184 -0.12 0.66 Solution2 P32 11 0.550 8.10+/-11.80 0.3881 -0.10 0.66 Best, Wei

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Comprehension of Orotidine 5'-Monophosphate Decarboxylase
by Kevin Jin 16 Feb '12

16 Feb '12

Dear all, I wrote a story for Orotidine 5'-Monophosphate Decarboxylase. http://www.jinkai.org/Enzymology.html Best, Kevin

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Re: [phenixbb] qFit error in fixing alternate conformations
by Subhani Bandara 15 Feb '12

15 Feb '12

Hi, I used qFIT to fix the alternative conformations of my protein with a chelator complex, by submitting a PDB file and a mtz file. But it gave following error. What could be the reason for this. > > ___Run time error messages (if any):___ > xyz.pdb mtz.rfl FP SIGFP > Sorry: No matching array: refinement.input.xray_data.labels=FP,SIGFP > Thanks Subhani

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Re: [phenixbb] Example datasets
by mohamed noor 15 Feb '12

15 Feb '12

Dear Phenix users Is there some examples datasets involving 3-wavelength MAD phasing available? I would like to learn from indexing to structure solution with a combination of CCP4 and Phenix if possible. Thanks.

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cbf file
by Theresa H 15 Feb '12

15 Feb '12

Hi all Is there a utility to convert cbf file from Pilatus detector to mtz in Phenix? Thank you. Theresa

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Re: [phenixbb] alternative conformation of residues
by Subhani Bandara 15 Feb '12

15 Feb '12

Hi all, I have a protein where three consecutive amino acids have alternative conformations. I edited the PDB file to have those altloc and made total occupancy of A and B to 1.00. But after refinement both A and B are overlapping and I could see the positive density for one conformation away from that (may be b'se I didn't change coordinates of B conformation). How can I move the B altloc in to the positive density. Do I have to edit the coordinates on PDB and if so how can Ido that? Thanks in advance for any help Subhani

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problems when adding Free_R_flag
by G Y 14 Feb '12

14 Feb '12

Dear experts I use *Reflection file editor* in phenix GUI to generate Free_R_flag in my mtz file. The original input .mtz file contains arrays of FP SIGFP DANO SIGDANO and ISYM. I just simply click *COPY ALL ARRAYS* and tag on *Generation R free flags if not already present*, then run the software. The problem is that in the output .mtz from phenix I found the value of F and DANO becomes more or less same for each reflection. This is unreasonable for a reflection file. Phenix changed something on the columns of my .mtz file. How? Why? What should I do to keep my .mtz in correct and unchanged form? Thank you very much for your advice. The columns in the original input .mtz file look like H K L FP SIGFP DANO SIGDANO ISYM 0 0 12 319.30 2.64 2.23 5.27 0.00 0 0 16 424.00 3.50 -8.38 7.00 0.00 0 0 20 177.60 1.48 1.77 2.96 0.00 0 0 24 155.10 1.30 3.97 2.61 0.00 0 0 28 195.80 1.64 1.13 3.28 0.00 The output from phenix looks like (FP and DANO become similar in value for each reflection) H K L FP SIGFP DANO SIGDANO ISYM FreeRflag 0 0 12 320.41 3.73 318.19 3.73 0.00 0.00 0 0 16 419.81 4.95 428.19 4.95 0.00 0.00 0 0 20 178.48 2.09 176.72 2.09 0.00 0.00 0 0 24 157.09 1.85 153.11 1.85 0.00 0.00 0 0 28 196.37 2.32 195.23 2.32 0.00 0.00

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Computation Crystallography Newsletter
by Nigel Moriarty 14 Feb '12

14 Feb '12

Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles CCTBX tools for derivative-free optimization Short communications phenix.find_alt_orig_sym_mate Using force field generated models in the refinement of crystallographic structures containing carbohydrates Viewing diffraction images in CCTBX On contribution of hydrogen atoms to X-ray scattering -- Nigel W. Moriarty, Ph.D. Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Statistics from 'Scalepack' log file and 'Xtriage' log file
by Zhang yu 14 Feb '12

14 Feb '12

Dear Phenixer, What is the reason for the inconsistent data statistics from 'Scalpack' and 'Xtriage' ? I scaled my data with 'Scalepack' and got the following statistics (take completeness as an example) Shell I/Sigma in resolution shells: Lower Upper % of of reflections with I / Sigma less than limit limit 0 1 2 3 5 10 20 >20 total 40.00 8.93 0.1 0.2 0.4 0.9 1.5 22.6 97.3 0.0 97.3 8.93 7.10 0.8 1.7 2.7 4.1 7.1 35.8 99.2 0.0 99.2 7.10 6.20 2.0 4.6 7.6 10.9 18.4 56.6 99.5 0.0 99.5 6.20 5.64 2.9 6.5 11.1 16.3 27.5 65.0 99.0 0.0 99.0 5.64 5.24 4.1 8.2 13.7 19.2 33.0 67.3 97.4 0.0 97.4 5.24 4.93 4.3 9.4 14.8 19.9 33.1 67.6 96.1 0.0 96.1 4.93 4.68 5.2 10.1 15.9 21.8 33.9 67.8 95.6 0.0 95.6 4.68 4.48 5.4 11.2 17.6 24.7 37.8 69.0 94.5 0.0 94.5 4.48 4.31 5.8 11.0 18.1 25.1 39.8 71.2 94.0 0.0 94.0 4.31 4.16 6.4 14.3 23.6 32.7 47.2 73.6 93.7 0.0 93.7 4.16 4.03 8.2 16.7 27.2 36.7 53.0 76.5 93.1 0.0 93.1 4.03 3.91 9.3 20.5 32.4 42.6 57.8 79.1 93.5 0.0 93.5 3.91 3.81 9.6 23.1 37.2 47.7 61.4 81.6 93.6 0.0 93.6 3.81 3.72 11.6 26.5 41.3 51.7 66.1 84.5 92.9 0.0 92.9 3.72 3.63 11.6 30.9 47.8 58.4 71.0 86.5 93.7 0.0 93.7 3.63 3.55 14.9 34.4 50.7 62.0 74.3 88.9 94.5 0.0 94.5 3.55 3.48 15.4 37.1 54.7 64.6 76.2 89.5 93.4 0.0 93.4 3.48 3.42 17.2 41.5 60.1 69.4 79.6 90.8 94.0 0.0 94.0 3.42 3.36 18.3 44.6 62.3 70.9 79.7 89.4 92.1 0.0 92.1 3.36 3.30 20.8 46.9 64.2 71.9 79.7 88.3 90.3 0.0 90.3 All hkl 8.6 19.9 30.0 37.4 48.7 72.4 94.9 0.0 94.9 In summary, the overall completeness is 94.9%, while completeness of the lowest shell is close to 100%, and highest shell is 90.3%. But when I input the *.sca file into 'Xtriage', I got the following statistics (also completeness as an example). ---------------------------------------------------------------------------------------- | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | ---------------------------------------------------------------------------------------- | 40.02 - 8.19 | 51.1% | 50.9% | 50.7% | 50.2% | 38.9% | 5.1% | | 8.19 - 6.51 | 50.5% | 49.1% | 47.7% | 45.0% | 27.4% | 3.2% | | 6.51 - 5.69 | 49.0% | 45.7% | 42.9% | 37.1% | 18.0% | 1.4% | | 5.69 - 5.17 | 47.2% | 43.3% | 39.9% | 33.0% | 15.3% | 1.3% | | 5.17 - 4.80 | 45.8% | 41.6% | 38.4% | 31.6% | 14.6% | 1.2% | | 4.80 - 4.52 | 44.4% | 39.7% | 35.9% | 29.1% | 13.5% | 1.1% | | 4.52 - 4.29 | 43.4% | 38.2% | 33.6% | 26.4% | 11.5% | 0.8% | | 4.29 - 4.10 | 41.1% | 34.0% | 29.0% | 21.6% | 9.5% | 0.5% | | 4.10 - 3.95 | 36.1% | 29.2% | 24.6% | 18.5% | 7.6% | 0.3% | | 3.95 - 3.81 | 30.8% | 24.8% | 20.8% | 15.3% | 5.5% | 0.1% | | 3.81 - 3.69 | 27.4% | 21.6% | 17.7% | 12.4% | 3.8% | 0.0% | | 3.69 - 3.59 | 23.8% | 18.7% | 15.2% | 10.2% | 3.0% | 0.1% | | 3.59 - 3.49 | 20.3% | 15.5% | 12.6% | 8.3% | 1.9% | 0.0% | | 3.49 - 3.41 | 17.4% | 12.7% | 10.1% | 6.5% | 1.4% | 0.0% | ---------------------------------------------------------------------------------------- In summary, based on statistics from 'Xtriage', the data is quite incomplete, with only ~50% completeness even at lowest resolution shell. I convert the '*sca' into '*.mtz' file with "Reflection editor", and input the '*.mtz file' into 'Xtriage', I got another totally different statistics (completeness as an example) ---------------------------------------------------------------------------------------- | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | ---------------------------------------------------------------------------------------- | 39.67 - 8.19 | 96.5% | 96.2% | 95.8% | 94.9% | 74.0% | 10.0% | | 8.19 - 6.51 | 96.3% | 94.4% | 92.1% | 87.3% | 54.5% | 7.0% | | 6.51 - 5.69 | 92.6% | 88.1% | 83.3% | 72.7% | 36.2% | 3.5% | | 5.69 - 5.17 | 88.6% | 83.4% | 77.7% | 64.9% | 30.7% | 3.4% | | 5.17 - 4.80 | 85.6% | 80.0% | 74.8% | 62.3% | 29.4% | 3.3% | | 4.80 - 4.52 | 82.6% | 76.4% | 70.1% | 57.4% | 26.9% | 3.0% | | 4.52 - 4.29 | 80.6% | 73.4% | 65.7% | 52.3% | 23.2% | 2.2% | | 4.29 - 4.10 | 74.4% | 65.2% | 56.6% | 42.7% | 19.5% | 1.3% | | 4.10 - 3.95 | 64.2% | 55.7% | 48.2% | 36.7% | 15.5% | 1.0% | | 3.95 - 3.81 | 55.3% | 47.3% | 40.8% | 30.4% | 11.2% | 0.4% | | 3.81 - 3.69 | 48.7% | 40.9% | 34.7% | 24.8% | 8.1% | 0.2% | | 3.69 - 3.59 | 41.8% | 35.8% | 29.7% | 20.2% | 6.1% | 0.1% | | 3.59 - 3.49 | 35.3% | 29.4% | 24.5% | 16.6% | 4.1% | 0.0% | | 3.49 - 3.41 | 30.1% | 24.1% | 19.8% | 13.2% | 2.9% | 0.0% | ---------------------------------------------------------------------------------------- I am confused by the inconsistent statistics, could some explain it? Thanks. Yu

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(no subject)
by intekhab alam 10 Feb '12

10 Feb '12

Hi all I have a 3A dataset for a protein-protein complex. I have successfully build the first protein and refined it to R/Rfree 24/28. I can see some density for my second protein but the density is a bit noisy. I have attached the coot image of the density. I want to model the aminoacid having sequence as given peptide: MGKKGKNKKGRGRPGVFRTRGLTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAIFGDGFGLE 1.Based on map features which segemnt should i start with. 2. Is there anyway that i can build the best fit segment of my second protein. I tried autobuild but it failed to build any peptide for my second protein. Your help is highly appreciated. regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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