- phenixbb - phenix-online.org

Re: [phenixbb] Stalled refinement
by Kay Diederichs 18 Apr '14

18 Apr '14

Hi Yarrow, of course the data quality will suffer but ultimately it depends on the amount of splitting - as long as the integration profile covers both parts then the total intensity is conserved, and recovered. I have seen many datasets with split reflections that were usable for MR and refinement. But I doubt that many of these would be suitable for experimental phasing. best, Kay Am 18.04.14 23:21, schrieb Yarrow Madrona: > Hi Kay, > > Looking at the data I can see that many of the spots are actually split. > I guess this may be causing problems in refinement if split spots are > integrated as a single spot? > > > On Fri, Apr 18, 2014 at 2:17 PM, Kay Diederichs > <kay.diederichs(a)uni-konstanz.de <mailto:[email protected]>> > wrote: > > It is a good idea to try several data processing programs in > difficult cases. > > BTW the latest MOSFLM can also integrate two (or more) lattices. > > Pls report your results. > > Kay > > > Am 18.04.14 22:59, schrieb Yarrow Madrona: > > Thanks Kay, > > XDS kicked out a lot of reflections. There were about 23,000 > rejected > reflections out of ~ 190,000 collected. I can clearly see > another minor > lattice in many frames and I presume that the rejections are > coming from > the minor lattice that was not selected. I was thinking of > processing > with EVAL15 to see if I get better results. Thanks for your > help. Maybe > respond off-line as this is a discussion maybe more suited for > another > mailing list (CCP4?). > > -Yarrow > > > On Fri, Apr 18, 2014 at 7:11 AM, Kay Diederichs > <kay.diederichs(a)uni-konstanz.__de > <mailto:[email protected]> > <mailto:kay.diederichs@uni-__konstanz.de > <mailto:[email protected]>>> > > wrote: > > Hi Yarrow, > > the problem is that during structure solution, many wrong > paths may > have to be followed until finally identifying the correct path. > > So the general answer to this kind of problem is: in some > way, your > parameterization of the experiment is wrong or incomplete. > > From what you write, data quality does not seem to be the > problem. > But: did XDS really integrate _all_ the reflections, or only a > subset (say, every second reflection)? > > Check out > http://strucbio.biologie.uni-____konstanz.de/ccp4wiki/index.____php/Refinem… > <http://strucbio.biologie.uni-__konstanz.de/ccp4wiki/index.__php/Refinement#…> > > > <http://strucbio.biologie.uni-__konstanz.de/ccp4wiki/index.__php/Refinement#… > <http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#what…>> > > If, after thorough attempts, you fail to find the solution, > upload > your current model, sequence and raw data frames to a > Dropbox folder > and post the link here - there may be people who succeed in > processing the data nicely, or otherwise can identify the > problem > based on the data (rather than based on your description only). > > HTH, > > Kay > > Am 18.04.14 01:25, schrieb > phenixbb-request(a)phenix-____online.org > <mailto:phenixbb-request@phenix-__online.org> > <mailto:phenixbb-request@__phenix-online.org > <mailto:[email protected]>>: > > > Date: Thu, 17 Apr 2014 16:25:00 -0700 > From: Yarrow Madrona<amadrona(a)uci.edu > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>>> > To: PHENIX user mailing list<phenixbb(a)phenix-online.____org > <mailto:phenixbb@phenix-__online.org > <mailto:[email protected]>>> > > Subject: [phenixbb] Stalled refinement > Message-ID: > > > <__CAMHjG6bPE4q1xWidpE2VwFMJ9qLS____qjtLRuLMM1ef9vWBHBfZKg(a)mail.____gmail.com > <http://gmail.com> > > <mailto:CAMHjG6bPE4q1xWidpE2Vw__FMJ9qLSqjtLRuLMM1ef9vWBHBfZKg@__mail.gmail.com > <mailto:CAMHjG6bPE4q1xWidpE2VwFMJ9qLSqjtLRuLMM1ef9vWBHBfZKg@mail.gmail.com>>> > > Content-Type: text/plain; charset="utf-8" > > > Hello, > > I using the latest stable build of phenx.refine (1.8.4) > I recently > collected data, processed and obtained an MR solution using > phaser. I am > stuck trying to refine with an Rfree sitting at 40% > > I really want to know if the high Rfree is due to poor data > quality or if > non-crystallographic symmetry involving a near perfect > two fold > rotation > between the two molecules in the ASU could somehow impede > refinement. Stats > and other information is below. Thank you for any help > you can give. > > -Yarrow > > > Visually, the quality of the data is marginal at best > (streaky/ice rings in > many frames) despite good processing stats from XDS. > Processing > with mosflm > or HKL2000 managed to index but failed pretty bad in > integration and > scaling. > > Phaser gave high TFZ scores for 2 molecules in the asu > (see below). > > Density for a cholesterol like ligand shows up even > though not > present in > the search model. > > MolRep Self rotation shows rotational symmetry. > https://www.dropbox.com/s/____2zsajl5o091k50r/CYP142A2-____032814_21_rf%20c… > <https://www.dropbox.com/s/__2zsajl5o091k50r/CYP142A2-__032814_21_rf%20copy.…> > > > <https://www.dropbox.com/s/__2zsajl5o091k50r/CYP142A2-__032814_21_rf%20copy.… > <https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf>> > > The 2 molecules in the ASU are related by almost a 2 > fold rotation: > > Rotation matrix for chain A to chain B: > > new_ncs_group > rota_matrix 1.0000 0.0000 0.0000 > rota_matrix 0.0000 1.0000 0.0000 > rota_matrix 0.0000 0.0000 1.0000 > tran_orth 0.0000 0.0000 0.0000 > > center_orth 15.2016 0.5245 33.7070 > > rota_matrix -0.9860 -0.1636 -0.0309 > rota_matrix -0.1659 0.9511 0.2605 > rota_matrix -0.0132 0.2620 -0.9650 > tran_orth 34.3310 -24.0033 107.0457 > > center_orth 15.7607 7.2426 77.7512 > > RMSD, B onto A = 0.0007 after phaser > RMSD, B onto A = 0.347 after one round of refinement in > phenix > > > Refinement using aniostropically corrected data (ucla > web server: > Services.mbi.ucla.edu/____anisoscale > <http://Services.mbi.ucla.edu/__anisoscale> > <http://Services.mbi.ucla.edu/__anisoscale > <http://Services.mbi.ucla.edu/anisoscale>>) did not improve the > > Rfree in refinement. > > > Statistics are listed below: > > UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21 > > RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS > R-FACTOR > R-FACTOR > COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano > LIMIT OBSERVED UNIQUE POSSIBLE OF DATA > observed > expected > Corr > > 5.99 8280 1927 2087 92.3% > 3.1% > 3.3% > 8246 35.09 3.5% 99.8* 20* 0.909 1296 > 4.30 14606 3401 3487 97.5% > 3.3% > 3.5% > 14580 33.37 3.8% 99.9* 11* 0.843 2273 > 3.53 17961 4244 4445 95.5% > 3.8% > 3.9% > 17944 31.11 4.4% 99.8* -2 0.789 2721 > 3.06 21954 5068 5221 97.1% > 4.9% > 5.1% > 21933 24.81 5.6% 99.7* -2 0.780 3455 > 2.74 25741 5830 5933 98.3% > 7.6% > 7.6% > 25713 18.88 8.6% 99.5* -2 0.782 4165 > 2.51 27859 6311 6483 97.3% > 10.8% > 10.8% > 27824 14.06 12.3% 99.1* -2 0.774 4385 > 2.32 31336 6979 7084 98.5% > 14.9% > 15.3% > 31296 10.49 16.8% 98.5* -4 0.748 5095 > 2.17 32396 7347 7567 97.1% > 22.3% > 22.7% > 32341 7.46 25.4% 97.3* -7 0.728 5055 > 2.05 32254 7339 8047 91.2% > 33.1% > 33.5% > 32075 5.06 37.5% 94.8* -6 0.724 5155 > total 212387 48446 50354 96.2% > 7.8% > 7.9% > 211952 16.57 8.8% 99.7* -3 0.768 33600 > > Processing with mosflm or HKL2000 managed to index but > failed > pretty bad in > integration and scaling. > > > Phaser: > > SOLU SET RFZ=27.5 TFZ=24.2 PAK=0 LLG=1711 RF++ TFZ=64.6 > PAK=0 > LLG=3610 > LLG=4865 >

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Re: [phenixbb] Stalled refinement
by Kay Diederichs 18 Apr '14

18 Apr '14

Hi Yarrow, the problem is that during structure solution, many wrong paths may have to be followed until finally identifying the correct path. So the general answer to this kind of problem is: in some way, your parameterization of the experiment is wrong or incomplete. From what you write, data quality does not seem to be the problem. But: did XDS really integrate _all_ the reflections, or only a subset (say, every second reflection)? Check out http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#what… If, after thorough attempts, you fail to find the solution, upload your current model, sequence and raw data frames to a Dropbox folder and post the link here - there may be people who succeed in processing the data nicely, or otherwise can identify the problem based on the data (rather than based on your description only). HTH, Kay Am 18.04.14 01:25, schrieb phenixbb-request(a)phenix-online.org: > Date: Thu, 17 Apr 2014 16:25:00 -0700 > From: Yarrow Madrona<amadrona(a)uci.edu> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: [phenixbb] Stalled refinement > Message-ID: > <CAMHjG6bPE4q1xWidpE2VwFMJ9qLSqjtLRuLMM1ef9vWBHBfZKg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I using the latest stable build of phenx.refine (1.8.4) I recently > collected data, processed and obtained an MR solution using phaser. I am > stuck trying to refine with an Rfree sitting at 40% > > I really want to know if the high Rfree is due to poor data quality or if > non-crystallographic symmetry involving a near perfect two fold rotation > between the two molecules in the ASU could somehow impede refinement. Stats > and other information is below. Thank you for any help you can give. > > -Yarrow > > > Visually, the quality of the data is marginal at best (streaky/ice rings in > many frames) despite good processing stats from XDS. Processing with mosflm > or HKL2000 managed to index but failed pretty bad in integration and > scaling. > > Phaser gave high TFZ scores for 2 molecules in the asu (see below). > > Density for a cholesterol like ligand shows up even though not present in > the search model. > > MolRep Self rotation shows rotational symmetry. > https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf > > The 2 molecules in the ASU are related by almost a 2 fold rotation: > > Rotation matrix for chain A to chain B: > > new_ncs_group > rota_matrix 1.0000 0.0000 0.0000 > rota_matrix 0.0000 1.0000 0.0000 > rota_matrix 0.0000 0.0000 1.0000 > tran_orth 0.0000 0.0000 0.0000 > > center_orth 15.2016 0.5245 33.7070 > > rota_matrix -0.9860 -0.1636 -0.0309 > rota_matrix -0.1659 0.9511 0.2605 > rota_matrix -0.0132 0.2620 -0.9650 > tran_orth 34.3310 -24.0033 107.0457 > > center_orth 15.7607 7.2426 77.7512 > > RMSD, B onto A = 0.0007 after phaser > RMSD, B onto A = 0.347 after one round of refinement in phenix > > > Refinement using aniostropically corrected data (ucla web server: > Services.mbi.ucla.edu/anisoscale) did not improve the Rfree in refinement. > > > Statistics are listed below: > > UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21 > > RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR > COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano > LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected > Corr > > 5.99 8280 1927 2087 92.3% 3.1% 3.3% > 8246 35.09 3.5% 99.8* 20* 0.909 1296 > 4.30 14606 3401 3487 97.5% 3.3% 3.5% > 14580 33.37 3.8% 99.9* 11* 0.843 2273 > 3.53 17961 4244 4445 95.5% 3.8% 3.9% > 17944 31.11 4.4% 99.8* -2 0.789 2721 > 3.06 21954 5068 5221 97.1% 4.9% 5.1% > 21933 24.81 5.6% 99.7* -2 0.780 3455 > 2.74 25741 5830 5933 98.3% 7.6% 7.6% > 25713 18.88 8.6% 99.5* -2 0.782 4165 > 2.51 27859 6311 6483 97.3% 10.8% 10.8% > 27824 14.06 12.3% 99.1* -2 0.774 4385 > 2.32 31336 6979 7084 98.5% 14.9% 15.3% > 31296 10.49 16.8% 98.5* -4 0.748 5095 > 2.17 32396 7347 7567 97.1% 22.3% 22.7% > 32341 7.46 25.4% 97.3* -7 0.728 5055 > 2.05 32254 7339 8047 91.2% 33.1% 33.5% > 32075 5.06 37.5% 94.8* -6 0.724 5155 > total 212387 48446 50354 96.2% 7.8% 7.9% > 211952 16.57 8.8% 99.7* -3 0.768 33600 > > Processing with mosflm or HKL2000 managed to index but failed pretty bad in > integration and scaling. > > > Phaser: > > SOLU SET RFZ=27.5 TFZ=24.2 PAK=0 LLG=1711 RF++ TFZ=64.6 PAK=0 LLG=3610 > LLG=4865 >

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Re: [phenixbb] Stalled refinement
by Yarrow Madrona 18 Apr '14

18 Apr '14

There is no significant peaks for translational NCS. I also didn't see anything in the patterson map. However, the Multivariate Z score L-test gives 6.218. Also the observed Centric reflections are more intense than they should be but I don't suspect twinning in a monoclinic space group. -Yarrow On Thu, Apr 17, 2014 at 4:37 PM, Paul Adams <pdadams(a)lbl.gov> wrote: > > What does triage say about translation NCS? > > > On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona <amadrona(a)uci.edu> wrote: > >> Hello, >> >> I using the latest stable build of phenx.refine (1.8.4) I recently >> collected data, processed and obtained an MR solution using phaser. I am >> stuck trying to refine with an Rfree sitting at 40% >> >> I really want to know if the high Rfree is due to poor data quality or if >> non-crystallographic symmetry involving a near perfect two fold rotation >> between the two molecules in the ASU could somehow impede refinement. Stats >> and other information is below. Thank you for any help you can give. >> >> -Yarrow >> >> >> Visually, the quality of the data is marginal at best (streaky/ice rings >> in many frames) despite good processing stats from XDS. Processing with >> mosflm or HKL2000 managed to index but failed pretty bad in integration and >> scaling. >> >> Phaser gave high TFZ scores for 2 molecules in the asu (see below). >> >> Density for a cholesterol like ligand shows up even though not present in >> the search model. >> >> MolRep Self rotation shows rotational symmetry. >> https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf >> >> The 2 molecules in the ASU are related by almost a 2 fold rotation: >> >> Rotation matrix for chain A to chain B: >> >> new_ncs_group >> rota_matrix 1.0000 0.0000 0.0000 >> rota_matrix 0.0000 1.0000 0.0000 >> rota_matrix 0.0000 0.0000 1.0000 >> tran_orth 0.0000 0.0000 0.0000 >> >> center_orth 15.2016 0.5245 33.7070 >> >> rota_matrix -0.9860 -0.1636 -0.0309 >> rota_matrix -0.1659 0.9511 0.2605 >> rota_matrix -0.0132 0.2620 -0.9650 >> tran_orth 34.3310 -24.0033 107.0457 >> >> center_orth 15.7607 7.2426 77.7512 >> >> RMSD, B onto A = 0.0007 after phaser >> RMSD, B onto A = 0.347 after one round of refinement in phenix >> >> >> Refinement using aniostropically corrected data (ucla web server: >> Services.mbi.ucla.edu/anisoscale) did not improve the Rfree in >> refinement. >> >> >> Statistics are listed below: >> >> UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21 >> >> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR >> COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano >> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected >> Corr >> >> 5.99 8280 1927 2087 92.3% 3.1% 3.3% >> 8246 35.09 3.5% 99.8* 20* 0.909 1296 >> 4.30 14606 3401 3487 97.5% 3.3% 3.5% >> 14580 33.37 3.8% 99.9* 11* 0.843 2273 >> 3.53 17961 4244 4445 95.5% 3.8% 3.9% >> 17944 31.11 4.4% 99.8* -2 0.789 2721 >> 3.06 21954 5068 5221 97.1% 4.9% 5.1% >> 21933 24.81 5.6% 99.7* -2 0.780 3455 >> 2.74 25741 5830 5933 98.3% 7.6% 7.6% >> 25713 18.88 8.6% 99.5* -2 0.782 4165 >> 2.51 27859 6311 6483 97.3% 10.8% 10.8% >> 27824 14.06 12.3% 99.1* -2 0.774 4385 >> 2.32 31336 6979 7084 98.5% 14.9% 15.3% >> 31296 10.49 16.8% 98.5* -4 0.748 5095 >> 2.17 32396 7347 7567 97.1% 22.3% 22.7% >> 32341 7.46 25.4% 97.3* -7 0.728 5055 >> 2.05 32254 7339 8047 91.2% 33.1% 33.5% >> 32075 5.06 37.5% 94.8* -6 0.724 5155 >> total 212387 48446 50354 96.2% 7.8% 7.9% >> 211952 16.57 8.8% 99.7* -3 0.768 33600 >> >> Processing with mosflm or HKL2000 managed to index but failed pretty bad >> in integration and scaling. >> >> >> Phaser: >> >> SOLU SET RFZ=27.5 TFZ=24.2 PAK=0 LLG=1711 RF++ TFZ=64.6 PAK=0 LLG=3610 >> LLG=4865 >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> > > > -- > Paul Adams > Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley > Lab > Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley > Lab > Adjunct Professor, Department of Bioengineering, U.C. Berkeley > Vice President for Technology, the Joint BioEnergy Institute > Laboratory Research Manager, ENIGMA Science Focus Area > > 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: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 > ] >

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DNA basepairing restraint refinement
by 李翔 18 Apr '14

18 Apr '14

Hi, I am working my low resolution data (6A) by MR and met a problem about DNA basepairing during refinement. I think so far everything looks OK except the bases flipped during the refinement. I added basepairing restraint for all bases, however, seems not help too much. Does anyone have experience on that? Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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Stalled refinement
by Yarrow Madrona 17 Apr '14

17 Apr '14

Hello, I using the latest stable build of phenx.refine (1.8.4) I recently collected data, processed and obtained an MR solution using phaser. I am stuck trying to refine with an Rfree sitting at 40% I really want to know if the high Rfree is due to poor data quality or if non-crystallographic symmetry involving a near perfect two fold rotation between the two molecules in the ASU could somehow impede refinement. Stats and other information is below. Thank you for any help you can give. -Yarrow Visually, the quality of the data is marginal at best (streaky/ice rings in many frames) despite good processing stats from XDS. Processing with mosflm or HKL2000 managed to index but failed pretty bad in integration and scaling. Phaser gave high TFZ scores for 2 molecules in the asu (see below). Density for a cholesterol like ligand shows up even though not present in the search model. MolRep Self rotation shows rotational symmetry. https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf The 2 molecules in the ASU are related by almost a 2 fold rotation: Rotation matrix for chain A to chain B: new_ncs_group rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 center_orth 15.2016 0.5245 33.7070 rota_matrix -0.9860 -0.1636 -0.0309 rota_matrix -0.1659 0.9511 0.2605 rota_matrix -0.0132 0.2620 -0.9650 tran_orth 34.3310 -24.0033 107.0457 center_orth 15.7607 7.2426 77.7512 RMSD, B onto A = 0.0007 after phaser RMSD, B onto A = 0.347 after one round of refinement in phenix Refinement using aniostropically corrected data (ucla web server: Services.mbi.ucla.edu/anisoscale) did not improve the Rfree in refinement. Statistics are listed below: UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21 RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 5.99 8280 1927 2087 92.3% 3.1% 3.3% 8246 35.09 3.5% 99.8* 20* 0.909 1296 4.30 14606 3401 3487 97.5% 3.3% 3.5% 14580 33.37 3.8% 99.9* 11* 0.843 2273 3.53 17961 4244 4445 95.5% 3.8% 3.9% 17944 31.11 4.4% 99.8* -2 0.789 2721 3.06 21954 5068 5221 97.1% 4.9% 5.1% 21933 24.81 5.6% 99.7* -2 0.780 3455 2.74 25741 5830 5933 98.3% 7.6% 7.6% 25713 18.88 8.6% 99.5* -2 0.782 4165 2.51 27859 6311 6483 97.3% 10.8% 10.8% 27824 14.06 12.3% 99.1* -2 0.774 4385 2.32 31336 6979 7084 98.5% 14.9% 15.3% 31296 10.49 16.8% 98.5* -4 0.748 5095 2.17 32396 7347 7567 97.1% 22.3% 22.7% 32341 7.46 25.4% 97.3* -7 0.728 5055 2.05 32254 7339 8047 91.2% 33.1% 33.5% 32075 5.06 37.5% 94.8* -6 0.724 5155 total 212387 48446 50354 96.2% 7.8% 7.9% 211952 16.57 8.8% 99.7* -3 0.768 33600 Processing with mosflm or HKL2000 managed to index but failed pretty bad in integration and scaling. Phaser: SOLU SET RFZ=27.5 TFZ=24.2 PAK=0 LLG=1711 RF++ TFZ=64.6 PAK=0 LLG=3610 LLG=4865

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geometry_regularization
by jp d 15 Apr '14

15 Apr '14

hi, the geometry_regularization option is gone from pdbtools in 1.8.4-1496 it looks like it works in 1.8.1, is that version ok to use ? thanks jpd

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homology models in sculptor
by "Weiergräber, Oliver H." 15 Apr '14

15 Apr '14

Hello, I am using phenix.sculptor for modification of a homology model in a challenging case of molecular replacement. The input model is complete (except at the termini), i.e. it exactly matches the target sequence as defined in the alignment file. In this scenario, are there any caveats to consider with individual options in sculptor? Specifically, a quick test seems to indicate that the Schwarzenbacher algorithm for side chain pruning does not work, i.e. not a single atom is removed from the model, whereas the alternative "similarity" option leads to deletion of a few hundred atoms. I'm using sculptor from the command line, and the log file indicates my input is interpreted correctly. Best regards Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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recovering the files from project directory
by Bishwa Subedi 14 Apr '14

14 Apr '14

Hi, I tried to use phenix in my personal computer for small checks and convenient use. I accidentally happened to make my project directory /user/XXX/Documents. Even though it was not the intended folder for running Phenix and later changed it to some other folders, I noticed that all my documents in that folder has disappeared (folder is empty). I do not see the files in trash folder as well. I assume this happened because of selecting documents as the project directory and phenix empties the folder before use, am I correct? If so is there any way to recover those files? Thanking you in advance. Best regards, Bishwa

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PhD position in Structural Biology in Norway
by Hans Petter Hersleth 11 Apr '14

11 Apr '14

Dear all, A 4-year PhD position in Structural Biology starting August 2014 is available at University of Oslo, Department of Biosciences, Section for Biochemistry and Molecular Biology. The position is funded by the Research Council of Norway and the University of Oslo. The project is dealing with different redox proteins (haem, flavin, iron-sulfur, and di-metal proteins) with a focus on flavodoxins, ferredoxins, ferredoxin/flavodoxin reductases and redox partner enzymes. The project is in the field of structural biology and biochemistry with a strong focus on protein crystallography in combination with other biochemical and biophysical methods including single-crystal spectroscopy. More information about the project, position and application procedure is found on the website: http://uio.easycruit.com/vacancy/1149343/96323?iso=no Applicants must hold a Master’s degree or equivalent in protein crystallography, structural biology, biochemistry or molecular biology. The successful applicant should have skills and experience in working with proteins. It would be advantageous with hands-on experience within topics like cloning, protein expression, purification, crystallisation, protein crystallography, spectroscopy, protein-protein interactions, enzyme kinetics, redox- and co-factor proteins and teaching. Candiates without a Master's Degree have until 30 June, 2014 to complete the final exam. Application deadline is 20th April 2014 through the website: http://uio.easycruit.com/vacancy/1149343/96323?iso=no For further information please contact: Dr. Hans-Petter Hersleth, (h.p.hersleth(a)ibv.uio.no) ---------------------------------------------------------------------------------------------- Hans-Petter Hersleth, PhD Department of Biosciences, University of Oslo Section for Biochemistry and Molecular Biology P.O.Box 1066 Blindern, NO-0316 Oslo, Norway http://www.mn.uio.no/ibv/personer/vit/hphersle/index.html -----------------------------------------------------------------------------------------------

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enforce ncs on ligand
by Garboczi, David (NIH/NIAID) [E] 10 Apr '14

10 Apr '14

I am not able to enforce ncs on two copies of a ligand. The ligand is largish, flavin-like. How do I use the information that the two ligands are identical in Phenix-refine. thanks, Dave

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fwd: 2nd Australian Advanced Methods in Crystallography Workshop
by Nathaniel Echols 10 Apr '14

10 Apr '14

---------- Forwarded message ---------- From: Sofia Caria <S.Caria(a)latrobe.edu.au> To: undisclosed-recipients:; Date: Wed, 9 Apr 2014 23:04:50 +0000 Subject: 2nd Australian Advanced Methods in Crystallography Workshop Dear all, The Australian Synchrotron is pleased to announce the *2nd Australian Advanced Methods in Crystallography Workshop*. This workshop will explore the state of the art in macromolecular crystallography. It will combine lectures on advanced topics in data collection, processing and structure determination with hands-on tutorials using both MX beamlines at the Australian Synchrotron. International experts will present their experience in solving crystal structures, model and ligand building, twinning and refinement. Associated with this workshop there will also be a day for Lipid Cubic Phase Crystallisation Satellite (LCP). Registration as part of the main event or separately is possible (see details in programme and registration). *Confirmed speakers: *Kay Diederichs, Harry Powell, Viviane Richter, Santosh Panjikar, Navraj Pannu, Daniele de Sanctis, Paul Adams, Joana Pereira, Paul Emsley, Tom Caradoc-Davies, David Aragão and Wei Liu. Workshop dates: 22-25th June 2014 Registration deadline: 22th May 2014 Website: https://events.synchrotron.org.au Contact: xtalworkshop2014(a)synchrotron.org.au Best regards, Sofia Caria (by the organising committee) *Organising committee:* Daniel Eriksson- Australian Synchrotron David Aragão - Australian Synchrotron Jade Forwood - Charles Sturt University Mihwa Lee - La Trobe University Sofia Caria - La Trobe University Stephanie Gras - Monash University

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AssertionError at asking for kicked maps
by Jorge Iulek 09 Apr '14

09 Apr '14

Dear all, It would be nice to have kicked maps for a structure I am working with now. When I set then to True, I get in my log: " ... shake map coefficients cycles: 0 1 2 3 4 5 6 7 8 9 shake f_model cycles: approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.231506183818 approx_equal ERROR 0.235167389229 approx_equal ERROR Traceback (most recent call last): File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py", line 177, in run map_manger.write_files() File "/usr/local/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py", line 1780, in write_files map_coeff_dataset=self.write_mtz_file(), File "/usr/local/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py", line 1766, in write_mtz_file pdb_hierarchy=self.refine_object.model.pdb_hierarchy()) File "/usr/local/phenix-1.8.4-1496/cctbx_project/mmtbx/maps/__init__.py", line 515, in __init__ pdb_hierarchy = pdb_hierarchy) File "/usr/local/phenix-1.8.4-1496/cctbx_project/mmtbx/maps/__init__.py", line 439, in map_coefficients_from_fmodel map_type = params.map_type).map_coefficients File "/usr/local/phenix-1.8.4-1496/cctbx_project/mmtbx/maps/__init__.py", line 650, in __init__ assert approx_equal(fmodel.r_work(), fmodel_dc.r_work()) AssertionError " I see a previous problem like this at http://www.phenix-online.org/pipermail/phenixbb/2009-July/013517.html , but I cannot find a follow up concerning how to solve it. I am using the latest stable version, phenix-1.8.4-1496 , under openSuSE 12.3. When I set kicked maps to false, everything goes fine. Can this be solved? Also, a point to a former version that can "kick" would be enough. Thanks, Jorge

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fwd: Deadline is approaching: CCP4 crystallographic summer school in USA, at APS, June 24-July 2
by Nathaniel Echols 08 Apr '14

08 Apr '14

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Date: Tue, 8 Apr 2014 15:46:36 +0000 Subject: Deadline is approaching: CCP4 crystallographic summer school in USA, at APS, June 24-July 2 Dear Colleagues, We would like to remind you that the application deadline for the annual CCP4/APS Crystallographic Summer School in at the end of this week. The original announcement with some useful details is below. With best wishes, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ------------------------------ Dear Colleagues, We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2014/index.php *Title:*"CCP4 crystallographic school: From data collection to structure refinement and beyond" *Dates*: June 24 to July 2. *Site:* Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA *The school content: *Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is April 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.php<http://www.ccp4.ac.uk/schools/APS-2013/index.php> *Fees: *There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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GRC on Diffraction Methods: end July 2014
by Anastassis Perrakis 08 Apr '14

08 Apr '14

Dear all, We are getting closer and closer to the 2014 edition of my favorite Gordon Research Conference (https://www.grc.org/programs.aspx?year=2014&program=diffrac ) on Diffraction Methods in Structural Biology "Faster, Smaller, Better: Novel Technologies for Diffraction Experiments in Molecular Biology and Drug Discovery" , which this year will also feature before it starts the Gordon Research Seminars "Towards Integrative Structural Biology" (https://www.grc.org/programs.aspx?year=2014&program=grs_diff), targeting young scientists! Thanks to INSTRUCT (http://www.structuralbiology.eu) there will be four fellowships for young European researchers coming originally from an INSTRUCT member country or working in an INSTRUCT member country (http://www.structuralbiology.eu/resources/countries). Each fellowship will amount to 750 Euro, covering registration for both the GRC and the GRS, and all local expenses. It is a condition that you have to attend both the GRS and the GRC and submit a poster for both events. If you want to apply for such a fellowship, please send me an email reply (maintain the subject line please), including a single-page PDF file, a very short CV, an equally short abstract of your research, and a motivation statement explaining why you think this event is crucial for your career. Please include the email of your direct supervisor in the end of this letter, and a statement that she/he has agreed to cover the travel expenses for you to attend, if your fellowship application comes through. The deadline for receiving these letters is Wednesday 16 April at 12:CET (yes, thats less than a week from now! get writing!). The letters will be reviewed by an INSTRUCT panel, and the chosen four candidates will get a notification by the 8th of May! And, of course, I do take this opportunity to remind to everyone that the (almost) final program is on-line, we have an absolutely amazing group of speakers lined up, and the available places are filling up fast! So please remember to register on time! Looking forward to see you all at Bates College for what I trust you can make an exciting and memorable meeting! Best regards, Tassos PS If the file is not PDF, if its more than one page, if the characters you use are too small to read, etc etc, don't be too surprised if you do not get the travel fellowship award! Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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fix part of structure during refinement
by Jorge Iulek 08 Apr '14

08 Apr '14

Dear all, I want to test a refinement in which I fix part of my structure (say, residues 1 to 244 in chains C and D, and chains A and B completely) while the rest is to be refined with annealing. From the manual and http://www.phenix-online.org/pipermail/phenixbb/2009-June/013358.html, I have in my parameter file: " ... refine { strategy = *individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls *occupancies group_anomalous sites { individual = ( chain C and resseq 245:259 ) or ( chain D and resseq 245:259 ) torsion_angles = None rigid_body = None } ... " I thought atoms out of the selection in the output structure (chains A and B + residues 1 to 244 in chains C and D) would keep the same coordinates as they were input. But I see all structure atoms changed coordinates. I also tried to turn off tls and ncs usage, but the picture is the same. What do I miss here, to be able to fix some atoms during refinement? Thanks, Jorge

4 4

Tenure track junior Group Leader positions at IEO, Milan, Italy
by Sebastiano Pasqualato 04 Apr '14

04 Apr '14

Dear all, please find enclosed the details to apply for junior Group Leader positions in Experimental and Computation Cancer Biology, open at the European Institute of Oncology, in Milan, Italy. -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit

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calculating anomalous differences from a model
by Jonathan Grimes 04 Apr '14

04 Apr '14

Given a refined protein structure, is there an straightforward way to calculate the anomalous differences as a function of resolution, at wavelength X. many thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer DIAMOND Research Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

5 7

determining molprobity version?
by Pete Meyer 01 Apr '14

01 Apr '14

Hi, I may be missing something obvious, but how do I determine which version of molprobity is being used for generating the clash scores reported by phenix.model_vs_data ? Pete

2 1

error estimates on coordinates
by Benoît Masquida 27 Mar '14

27 Mar '14

Hello, Can someone shed light on the way coordinates errors are obtained in REMARK 3 using maximum of likelihood as compared to Luzzati or sigmaa? What article can be cited in this respect? Thanks in advance. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr

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phenix.pdbtools model_statics=true
by Maehigashi, Tatsuya 26 Mar '14

26 Mar '14

Hi all, What would be the best way to define the "selection" to show average B factors using phenix.pdbtools from command line? I've tried several ways using something like... phenix.pdbtools XXXXX.pdb stop_for_unknown=false model_statistics=true selections="chain QA or chain RA" However, the output always contain the standard/default "ADP statistics" table only (not for the selection I specified). Yes, I'm aware of the GUI option (under other tools) and it works great. However, I'm trying to compute average b for 9 coordinates under 4 separate categories (protein, RNA, ligands... and such), and I think it'll be a lot easier from the command line (using some quick script, for example). Any input will be appreciated! "T" ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Obtaining just the Wilson B with Xtriage
by Morten Grøftehauge 26 Mar '14

26 Mar '14

Hi guys, Is there a way to just have phenix.xtriage compute and output the Wilson B factor and not do everything else? I want to run it on a lot of files and that would simplify things. Cheers Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

3 3

2014 workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 25 Mar '14

25 Mar '14

Second announcement Fifth Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 16 - June 20, 2014 Application deadline: April 18, 2014 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization may not be able to offer travel or accommodation support. The number of participants will be limited to 15. There is no registration fees for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 18, 2014. Detailed information can be found on the course web page: http://neutrons.ornl.gov/conf/gcnb2014/ Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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xtriage reindexing suggestions
by Todd Jason Green 24 Mar '14

24 Mar '14

Hello all- I am trying to merge a few partial Se datasets. I am certain that I will have to reindex one or more to make sure that + and - reflections are not jumbled up. Can someone confirm that xtriage take this into account in suggesting to reindex one dataset in relation to a reference dataset? ie. does it use something like maximizing the anomalous signal in suggesting whether or not reindexing is necessary? I think the below suggests as much but I wanted confirmation: Automatic re-indexing For each data set supplied (other than the first data set given), all possible re-indexing matrices are derived as described by Grosse-Kunstleve et al. (2005). Each data set isautomatically re-indexed using the matrix that maximizes the correlation of amplitudes Have a good weekend. -Todd My Example: Reference analyses The following reindexing operators have been found: ------------------------------------------------- | Operator | Correlation | matches (%) | choice | ------------------------------------------------- | -k,h,l | 0.874 | 70.1 | <--- | | h,k,l | 0.032 | 76.7 | | ------------------------------------------------- If the data is reindexed with operator (-k,h,l), the correlation of the intensities to the reference data is maximized. sx205b_anom.sca This can be done for instance with: phenix.reflection_file_converter sx205b_anom.sca --change_of_basis="-k,h,l" <output_options>

4 4

Multiprocessor refine
by Kenneth A. Satyshur 23 Mar '14

23 Mar '14

The FAQ on the web says that phenix.refine uses multiprocessors, yet only phenix.autobuild seems to use MP. Do I need a special version of Phenix? I am using GUI 1.8.4-1496 >How can I use multiple processors to run a job? >Only AutoBuild(http://www.phenix-online.org/documentation/autobuild_gui.htm), LigandFit(http://www.phenix-online.org/documentation/ligandfit_gui.htm), phaser.MRage(http://www.phenix-online.org/documentation/MRage.htm), phenix.refine(http://www.phenix-online.org/documentation/refine_gui.htm), the structure comparison GUI(http://www.phenix-online.org/documentation/structure_comparison.htm), and phenix.find_tls_groups support runtime >configuration of parallel processing. In most cases this is done by adding the "nproc" keyword, for instance: etc RHEL6 x86_64 thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

2 1

Fwd: Reminder: CCP4 crystallographic summer school in USA, at APS, June 24-July 2
by Nathaniel Echols 17 Mar '14

17 Mar '14

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Date: Mon, 17 Mar 2014 21:13:27 +0000 Subject: Reminder: CCP4 crystallographic summer school in USA, at APS, June 24-July 2 Dear Colleagues, This is a reminder for approaching deadline to apply for the CCP4 Crystallographic Summer School to be held in June at the APS, near Chicago. Please see the original announcement below for more details. We hope to see you at APS in June. With best wishes, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ------------------------------ Dear Colleagues, We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2014/index.php *Title:*"CCP4 crystallographic school: From data collection to structure refinement and beyond" *Dates*: June 24 to July 2. *Site:* Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA *The school content: *Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is April 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.php<http://www.ccp4.ac.uk/schools/APS-2013/index.php> *Fees: *There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov __._,_.___ Reply via web post<https://groups.yahoo.com/group/cnsbb/post;_ylc=X3oDMTJwdmJpN3JlBF9TAzk3MzU5…> Reply to sender <[email protected]?subject=Re%3A%20Reminder%3A%20CCP4%20crystallographic%20summer%20school%20in%20USA%2C%20at%20APS%2C%20June%2024-July%202> Reply to group <[email protected]?subject=Re%3A%20Reminder%3A%20CCP4%20crystallographic%20summer%20school%20in%20USA%2C%20at%20APS%2C%20June%2024-July%202> Start a New Topic<https://groups.yahoo.com/group/cnsbb/post;_ylc=X3oDMTJldnZiMm5wBF9TAzk3MzU5…> Messages in this topic<https://groups.yahoo.com/group/cnsbb/message/2257;_ylc=X3oDMTM0dDhrM2VpBF9T…>(1) -------------------------------------------------------- List information at http://groups.yahoo.com/group/cnsbb. Posting is only allowed for members of this list. Visit Your Group<https://groups.yahoo.com/group/cnsbb;_ylc=X3oDMTJlazc1ZTluBF9TAzk3MzU5NzE0B…> [image: Yahoo! Groups]<https://groups.yahoo.com/;_ylc=X3oDMTJkZGZ1bzZpBF9TAzk3NDc2NTkwBGdycElkAzMw…> * Privacy <https://info.yahoo.com/privacy/us/yahoo/groups/details.html> * Unsubscribe <cnsbb-unsubscribe(a)yahoogroups.com?subject=Unsubscribe> * Terms of Use <https://info.yahoo.com/legal/us/yahoo/utos/terms/> . __,_._,___

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MRage run
by Jobichen Chacko 17 Mar '14

17 Mar '14

Dear All, I am running a molecular replacement using MRage program for almost 1 week with 4 threads, but yet to finish the run. I am using Phenix Version dev-1549 I am having a pretty big protein (around 100 KDa). I gave data file, sequence file, one model pdb and output from HHpred as input. Is there anyway to to find out when it is going to finish the run, or I can extract any information from the current run, if I manually end the run? Thank you. Jobi

2 1

phasing high(er) resolution anomalous difference maps with low resolution phases
by Todd Jason Green 13 Mar '14

13 Mar '14

Hello all- I am working on a huge protein assembly(monomer is ~3000 amino acids, large cell ~200, ~200, ~520) that has between 200 and 300 Se-met residues in the asymmetric unit(depending on the number of molecules I pick in the a.u.). I believe I have low resolution phasing from another heavy atom with limits to ~ 6.2 angstrom. Density modified FOMs dip below 0.6 at that point. I can see many tubes that have the diameter of model alpha helices. I ran phenix.find_helices_strands with the helices_before_trace=True option and got a series of helices encompassing about 3400 residues. Assuming that the phasing on the low resolution derivative is true, is it better to use phasing from the lower resolution derivative or phasing from the helical models to fish out the Se-Met sites via an anomalous difference Fourier? I assume I'm stuck at 6.2 for the derivative phasing though i guess i could extend phasing from the map a little further. How far is too far? How high of resolution can I phase from the helices (or from the derivative map for that matter) and still get accurate enough phasing to yield reliable difference peaks to find the Se sites. I have a couple Se-met datasets between 3 and 2.5 angstroms. What sigma levels should I expect for the difference peaks? also, what is the best way to pick the highest difference peaks in the anomalous difference fourier? I didn't see a tool in phenix. "find difference peaks and holes" seems like a logical choice but it seems to want to structure. I've just created maps and used the very old and reliable peakmax in ccp4. I have solved structures like this before but with a lot more info on ncs, envelopes, ncs averaging and a much much smaller protein. I remember getting sites and plugging them into resolve with scripts where you could fix them/or not and phase without looking for more sites, no build etc. Can i just enter sites and phase followed by density modification with one of the gui programs. any comments would be appreciated? and thanks in advance. -Todd

4 3

Postdoctoral position available
by Peter Zwart 11 Mar '14

11 Mar '14

Dear All, The Berkeley Center for Structural Biology at Lawrence Berkeley National Lab is looking for a postdoctoral fellow to work on the development of computational methods aimed at improving the overall quality of crystallographic data and its resulting atomic models. The results of this work will be integrated into the Berkeley Center for Structural Biology (BCSB) crystallography beam lines at the Advanced Light Source. Please have a look at the job posting and contact me for more information: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=77796 Regards Peter Zwart -- ----------------------------------------------------------------- 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 0

phenix error
by SD Y 04 Mar '14

04 Mar '14

Hi, Could you please tell me why am I getting this error " No atom selected: "name O and chain W and resname HOH and resseq 69". Log file ends as follows: ============================= Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 7 Type Number sf(0) Gaussians Zn2+ 1 27.88 1 S 10 15.96 2 P 2 14.95 2 Mg2+ 3 9.96 1 O 635 7.97 2 N 523 6.97 2 C 1983 5.97 2 sf(0) = scattering factor at diffraction angle 0. ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ======================== Summary of geometry restraints ======================= Number of disulfides: simple=0, symmetry=0 Custom bonds:Sorry------------------------------ Thanks a lotSDY

3 3

project not displayed
by SD Y 03 Mar '14

03 Mar '14

Hi, When I open phenix (1.8.4-1496), I dont see my project. If I import it, it appears. If I close and reopen I disappear again. I have the folders and jobs everything and nothing is lost. Though its not a serious problem, I am wondering if I could get some solution. ThanksSDY

2 1

Rwork/Rfree by resolution shell
by Ursula Schulze-Gahmen 03 Mar '14

03 Mar '14

Where can I found the values for Rwork/Rfree by resolution shell in phenix refinement or analysis. I ran phenix.model_vs_data which provides a list of Rwork by resolution, but no Rfree. Any helpful suggestions? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 642 8766

2 1

fwd: Post-doctoral Fellowship at the University of Texas
by Nathaniel Echols 01 Mar '14

01 Mar '14

---------- Forwarded message ---------- From: "Rudenko, Gabrielle" <garudenk(a)utmb.edu> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Date: Sat, 1 Mar 2014 20:36:00 +0000 Subject: Post-doctoral Fellowship at the University of Texas * Macromolecular Crystallography, Biophysics and Biochemistry* A post-doctoral fellowship position is available at the University of Texas Medical Branch (UTMB) located in the greater Houston area in the research team of Dr. Gabrielle Rudenko. We study molecules that mediate the formation, maintenance and plasticity of synapses, the contact and communication point between neurons. Our proteins of interest organize and regulate protein interaction networks in the synaptic cleft and impact how neurons communicate with each other at synapses. Many of the proteins we study are implicated in neurological disease and serve as potential novel therapeutic targets. We are looking for highly motivated, enthusiastic, hard working individuals who are interested in combining the fields of structural biology and neuroscience. Research projects involve protein over-expression and purification, x-ray crystallography, biochemical and biophysical techniques, proteomics, chemical biology and in collaboration electron microscopy and NMR. Our laboratory is part of the endowed Sealy Center for Structural Biology and Molecular Biophysics and the Department of Pharmacology/Toxicology at UTMB. The Sealy Center provides access to exceptional facilities, training and experimental assistance. *X-ray facilities* include a high-brilliance FR-E Superbright x-ray generator, a Rigaku R-AXIS-IV dual 30cm Imaging Plate detector, a Bruker SMART 2K CCD and a Rigaku BioSAXS-1000 2D-Kratky camera (for solution scattering data). *Biophysics facilities* include equipment for analytical ultracentrifugation, fluorescence, MALDI-TOF mass spectrometry, dynamic light scattering, surface plasmon resonance, titration micro-calorimetry, and high throughput screening with the ThermoFluor HTS apparatus. In addition, the *Electron Microscopy facilities*house three modern JEOL cryo-electron microscopes (a 200 keV JEOL 2200FS cryo-EM with in-column electron energy filter and field emission gun, a 200 keV JEOL 2100 EM, and a 120 keV JEM1400 microscope) and the *NMR facilities*include three NMR spectrometers (Bruker Avance III 800, 750 and 600 MHz with cryoprobes). See http://www.scsb.utmb.edu/resources/ UTMB is part of the Texas Medical Center, the world's largest medical center located in greater Houston. UTMB has research facilities situated on Galveston Island offering a pleasant subtropical climate and miles of relaxing beaches. UTMB is located within commuting distance of Houston, the fourth largest city in the United States and a leader in the arts, education, and health care. *Qualifications:* Applicants should have received a Ph.D. degree in a field relevant to structural biology within in the last three years and have a strong publication record. Applicants with experience in cloning, bacterial/insect cell culture, protein purification and crystallization, and macromolecular structure determination are preferred. However, recent graduates with a strong background in protein over-expression and purification, and an exceptional interest in learning crystallography are also encouraged to apply. Good written and oral communication skills in English are essential as well as the ability and desire to work as part of a highly motivated, collaborative team. To apply please e-mail the following to *rudenkolab.application(a)gmail.com*<rudenkolab.application(a)gmail.com>: CV, contact information for three references (address, phone and e-mail), a list of your experimental expertise and skills relevant to this position and a research statement describing your past research experience and future goals (1-2 pages). Visa sponsorship is available for non-US nationals. For questions, please contact Dr. Gabrielle Rudenko at gabrielle.rudenko(a)utmb.edu For more information please visit http://scsb.utmb.edu/labgroups/rudenko/ The University of Texas is a non-discriminatory, affirmative action employer. Gabrielle Rudenko, PhD Dept of Pharmacology and Toxicology Sealy Center for Structural Biology & Biophysics University of Texas Medical Branch 301 University Boulevard Basic Sciences Building Rm. 5.114B Galveston Texas 77555

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Ligands: a BCSB nano-workshop
by Peter Zwart 28 Feb '14

28 Feb '14

Dear All, On May 2, 2014 the BCSB will be hosting a full day event dedicated to ligands in the life sciences. Access is free, but is limited to 30 participants. The lectures will be streamed allowing remote participation to this event. For onsite and remote attendance, please register to receive further instructions. The registration for on-site participation will be on a first come, first serve basis. The program will cover structural science associated with ligands in the life sciences. Viewpoints from macromolecular crystallography, quantum chemistry, small molecule crystallography and solution scattering will provide the participants with a 360-degree perspective of the role of and technology associated with ligands in structural biology. Please have a look at https://sites.google.com/a/lbl.gov/ligands/home for more information. Regards Peter Zwart -- ----------------------------------------------------------------- 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 -----------------------------------------------------------------

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observed reflections error?
by Joel Tyndall 28 Feb '14

28 Feb '14

Hi all, I have a minor issue with phenix reporting the number of observed reflections in the output pdb file where it appears to be roughly double (120080 ) to what is actually in an mtz file (~65000) from scala. Any suggestions where this number might originate from? Joel _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

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Re: [phenixbb] ERRASER location within rosetta
by Terwilliger, Thomas C 28 Feb '14

28 Feb '14

________________________________ From: Terwilliger, Thomas C Sent: Friday, February 28, 2014 8:42 AM To: Benoît Masquida Cc: Terwilliger, Thomas C Subject: RE: [phenixbb] ERRASER location within rosetta Hi Benoit, I'm sorry for the trouble! The error message, "Sorry, Rosetta version 3.5 or later is needed for ERRASER" is printed if erraser cannot find the file erraser_option.py which should be located in $PHENIX_ROSETTA_PATH/rosetta_tools/ERRASER or $PHENIX_ROSETTA_PATH/tools/ERRASER If you don't have PHENIX_ROSETTA_PATH defined then that would fix it as well. Let me know if this doesn't help! All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Benoît Masquida [b.masquida(a)unistra.fr] Sent: Friday, February 28, 2014 8:27 AM To: PHENIX user mailing list Subject: [phenixbb] ERRASER location within rosetta Hello all, I just built rosetta on my Mac OS 10.8.5 and now try to configure ERRASER within the phenix GUI. I correctly indicated the location of the rosetta build and I specified the same location for ERRASER. However when I start an ERRASER job, an error tells me that "ERRASER works with rosetta3.5 or later version". This is strange because i downloaded one of the latest version of rosetta. I don't know if I gave a wrong locate or if my build is corrupted. Any idea from anyone that could have experienced the same problem? pwd outputs this: /Users/benoit1/share/rosetta_2014wk05_bundle/main, where I find database/ and source/ Thanks. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr<mailto:[email protected]>

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ERRASER location within rosetta
by Benoît Masquida 28 Feb '14

28 Feb '14

Hello all, I just built rosetta on my Mac OS 10.8.5 and now try to configure ERRASER within the phenix GUI. I correctly indicated the location of the rosetta build and I specified the same location for ERRASER. However when I start an ERRASER job, an error tells me that "ERRASER works with rosetta3.5 or later version". This is strange because i downloaded one of the latest version of rosetta. I don't know if I gave a wrong locate or if my build is corrupted. Any idea from anyone that could have experienced the same problem? pwd outputs this: /Users/benoit1/share/rosetta_2014wk05_bundle/main, where I find database/ and source/ Thanks. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr

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Challenging Refinement at 5 A Resolution
by Erik Walinda 28 Feb '14

28 Feb '14

Dear community, This is my first adventure in crystallography and it seems a rather challenging one. I obtained at dataset at 5.06 A resolution of a 600 residue protein. 3 domains of the protein are already solved by earlier x-ray crystallographic studies. While trying to grow better diffracting crystals and waiting for the next chance to shoot crystals at the synchrotron, I am trying to fit the already solved domains into the electron density of the low data set. Although I tried phaser using the solved structures, I never got a TFZ higher than ~ 6.4. Interestingly, Balbes constructed a model which does not contain any of the already solved domains, but, when using the Balbes output in Phaser, I obtain a TFZ score of 11 and an LLG of 330. (4 molecules / ASU; P2221) If this solution is correct, then in principle it should be possible to fit the already known domains into the structure (I am dreaming of something like a electron-microscopy-type fitting or the early ribosome structures). Phenix refinement however raises the Rfree, instead of lowering it. From my limited knowledge in the field I figured this may be that a) this kind of refinement doesnt work at this resolution or 2) the MR-solution was not really a solution. So I was very excited, when I found the recent papers about DEN refinement and Phenix-Rosetta. I am trying DEN refinement first, using the already solved structures as a reference. The den_refine program nicely creates 2760 DEN restraints. However, after 1 cycle (about 6 h of CPU time at 30 processors), the Rfree goes up (Initial: 0.49; final: 0.57). Indeed, the grid search seems not to be successful, since in the grid search for gamma/w, all Rfree values are rather similar and the lowest Rfree is 0.54. So I would like to ask the community, if ... 1) I shouldn't trust the phaser TFZ score too much and maybe it is just no solution after all? 2) the DEN parameters of phenix.den_refine can be optimized to allow to refine a super-low resolution structure? (I am using the standard parameters from the example: https://www.phenix-online.org/documentation/den_refine.htm) 3) 1 cycle is simply not enough and I should let the computation run for a few days to see, if the Rfree drops down later in the run? 4) Even though Phaser gave me the solution in P2221, may it be that I am trying to refine it in the wrong spacegroup and that's why I fail? Sincerely, Erik

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Re: [phenixbb] unusually high B-factors for selected -heavier- atoms
by Kay Diederichs 27 Feb '14

27 Feb '14

Jan, could it be radiation damage? - that would affect the heavier atoms first/most ... To prove/disprove, use zero-dose extrapolation and re-refine. Kay Am 27.02.14 20:13, schrieb phenixbb-request(a)phenix-online.org: > Date: Thu, 27 Feb 2014 09:50:31 -0800 > From: Jan <jan.abendroth(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] unusually high B-factors for selected -heavier- > atoms > Message-ID: <D87628CC-A657-4B4C-B14F-C230C0C2EF00(a)gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I am refining a pretty high resolution structure (1.65?, P1) with two tetramers of the protein in the ASU using Phenix dev 1630. > Refinement statistics looks really good, R=0.16 Rf=0.18, maps are very clear. However, several sulphur atoms of the protein, and in particular the phosphorous atoms of its cofactor NAD have inflated B-factors, along with distinct FoFc peaks. For instance B-factors for a Met with very well defined density: CB=19.7, CG=27.5, SD=62.2, CE=38.4 > > For some of the residues it is comparable when I refine with or without TLS groups. I used one group per chain of this compact protein, the cofactor is part of each TLS group. Restraints for NAD were generated via eLBOW. When I refine the structure in refmac, using either the standard cif file or the eLBOW generated one, B-factors remain low. > > Any ideas? I am happy to share the data. It is a SSGCID target and will be in the PDB shortly anyway. > > Thanks, > Jan > > > > -- > Jan Abendroth > Emerald BioStructures > Seattle / Bainbridge Island WA, USA > home: Jan.Abendroth_at_gmail.com > work: JAbendroth_at_embios.com > http://www.emeraldbiostructures.com >

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unusually high B-factors for selected -heavier- atoms
by Jan 27 Feb '14

27 Feb '14

Hi all, I am refining a pretty high resolution structure (1.65Å, P1) with two tetramers of the protein in the ASU using Phenix dev 1630. Refinement statistics looks really good, R=0.16 Rf=0.18, maps are very clear. However, several sulphur atoms of the protein, and in particular the phosphorous atoms of its cofactor NAD have inflated B-factors, along with distinct FoFc peaks. For instance B-factors for a Met with very well defined density: CB=19.7, CG=27.5, SD=62.2, CE=38.4 For some of the residues it is comparable when I refine with or without TLS groups. I used one group per chain of this compact protein, the cofactor is part of each TLS group. Restraints for NAD were generated via eLBOW. When I refine the structure in refmac, using either the standard cif file or the eLBOW generated one, B-factors remain low. Any ideas? I am happy to share the data. It is a SSGCID target and will be in the PDB shortly anyway. Thanks, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

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FAQ high res refinement
by Eike Schulz 27 Feb '14

27 Feb '14

> > Dear all, > > I am currently refining a rather well resolved protein at 0.97Å. However, even > after many cycles of refinement the R-factors are stuck at around Rwork/Rfree > 14.5/16.5. Considering number of aa, Rmerge (3.5%) and resolution this seems > to be too high. I assume 10 25 macrocycles should be enough for effective > weight refinement in phenix, however no improvement of the R-factors. > > A quick run with default settings in competitor software 'R' yields >2% better > R-factors. > > I would appreciate suggestion how to improve my refinement protocol, values > differing from default are listed below. > > Thank you very much in advance > > Eike > > > > > > > refine { > adp { > individual { > isotropic = element H > anisotropic = not element H > } > group_adp_refinement_mode = one_adp_group_per_residue \ > *two_adp_groups_per_residue group_selection > } > } > main { > apply_overall_isotropic_scale_to_adp = False > nqh_flips = False > ordered_solvent = True > place_ions = True > number_of_macro_cycles = 10 > hydrogen_bonds = True > use_convergence_test = True > target = auto *ml mlhl ml_sad ls > random_seed = 3326496 > wavelength = 0.885611 > nproc = 4 > } > hydrogens { > refine = individual *riding Auto > } > tls { > find_automatically = False > one_residue_one_group = False > } > ordered_solvent { > mode = second_half filter_only every_macro_cycle \ > *every_macro_cycle_after_first > h_bond_min_mac = 1 > h_bond_min_sol = 1 > h_bond_max = 6 > refine_occupancies = True > new_solvent = isotropic *anisotropic > b_iso_min = 0 > } > peak_search { > max_number_of_peaks = 1303 > } > target_weights { > optimize_xyz_weight = True > optimize_adp_weight = True > wxc_scale = 0.2 > wxu_scale = 0.2

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Option for renumber the pdb
by Rojan Shrestha 27 Feb '14

27 Feb '14

Hello, I have found the program phenix.pdbtools. Maybe, it can renumber residues of pdb. I have found the options renumber_residues options but I am unable to see the options for starting residues. I have pdb starts from 1 and want to renumber 1 into 250. Can somebody tell me how to put the option for starting residue? Regards, Rojan

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scaling in phenix.fobs_minus_fobs_map
by Michael Thompson 27 Feb '14

27 Feb '14

Hello, I have a very simple question about phenix.fobs_minus_fobs_map, and it's implementation in the GUI. I just want to make sure I am not skipping an important step in generating my isomorphous difference map. I'm trying to create an Fo-Fo map for two data sets at pretty different resolutions, using phases from a model. I truncated the higher-res data so the high resolution limit matches the lower-res data set. Are these 2 mtz files sufficient for input into phenix.fobs_minus_fobs_map, or do I need to use another utility to scale the two data sets together prior to calculating the map coefficients? I suppose another way to ask my question would be, does phenix.fobs_minus_fobs_map perform scaling of the two Fobs arrays before calculating the new map? Thanks for clarifying, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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problem phenix ensemble
by Firas FADEL 25 Feb '14

25 Feb '14

Hello, I am using phenix ensemble to refine an X-ray structure of a protein (40kDa) at 1.05 A in complex with a ligand. The occupancy of the ligand is 73%. After refining the structure, I found out that the program confused the position of the ligand and put some water molecules. Do you have any suggestion or a command to avoid this problem. If you need details I can send you the mtz and pdb files. Thanks in advance. Firas Fadel Firas FADEL Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC Equipe Alberto PODJARNY, 1 Rue Laurent Fries, 67404 Illkirch-France Email : fadel(a)igbmc.fr<mailto:[email protected]> Tel: + 33 (0) 3 88 65 33 13<tel:%2B%2033%20%280%29%203%2088%2065%2033%2013>

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Announcement: QuantumBio Release of QM-based X-ray Crystallography Plugin v1.0 for Phenix
by Lance Westerhoff 25 Feb '14

25 Feb '14

Hello All- We are pleased to announce the release of our linear scaling, quantum mechanics DivCon Discovery Suite plug-in v1.0 for the Phenix, x-ray crystallography platform. As was detailed in the recent Phenix Newsletter, when this plugin is installed, the conventional refinement functional along with the stereochemical restraints or CIFile for the ligand(s) and for the surrounding active site(s) are replaced with QM data in "real time" during the refinement in order to increase structural accuracy and decrease artificial strain. To see the full press release along with references and links for further information, please take a look at the following website: http://www.quantumbioinc.com/news/show/PhenixAnnouncement To encourage adoption, we have waived the license fee for non-profit, academic use and we have posted our commercial evaluation license as well. These licenses are available at the following link: http://www.quantumbioinc.com/products/software_licensing Certainly, let me know if you have any questions or if you would like to try out the technology on your own structures. -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com

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revisiting "Problem with loop fitting "
by Alejandro Buschiazzo 24 Feb '14

24 Feb '14

Dear phenix community I am attempting to use phenix.fit_loops for the first time and getting an error message: "No suitable gap found matching residues" I found a short exchange exactly about this (Jan 2011), but eventually Tom Terwilliger asked for the files directly to see if he could solve it. I can't seem to find a later summary of the solution. (apparently, the most probable reason was some kind of mismatch between PDB numbering and sequence file...which I shouldn't have... I'm probably missing some silly here - I have been fiddling around with the sequence file in many ways...with no success) many thanks for any help! alejandro -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Questions about phenix.mr_rosseta
by Yonglin Hu 24 Feb '14

24 Feb '14

Hello List, I am very new to using Phenix/Rosetta to solve MR. I just finished a job by following the procedures described on phenix-online.org using Phenix GUI. The program reported that no solution was found, but when I went through the RUN_FILE_*.log, I found that despite all the log files ended with the following sentences: Stage to relax: refined_rescored_rosetta_solution No solutions to relax No autobuilt solutions to iterate... Finishing up mr_rosetta... one solution had a Rfree of 0.48 with correct number of molecules in ASU. When I refined that solution using phenix, Rfree went down further, proving to be a correct one. So my question is: why phenix.mr_rosetta did not report this solution as a good one? My second question is regarding model rebuild using phenix/rosetta. No matter I used the GUI or command lines copied from phenix-online like the following: phenix.mr_rosetta \ seq_file=~/MA/Mpa.pir \ data=~/MA/MA.mtz \ search_models=~/MA/refine_6.pdb \ already_placed=True \ fragment_files = ~/MA/MA-3mer \ fragment_files = ~/MA/MA-9mer \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=6 \ space_group="C 1 2 1" \ use_all_plausible_sg=False \ nproc=4 the program always fails. The log files have the following messages: Sorry, a subprocess has failed... ...... Sorry: Failed to run REBUILD...see log file in MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/rebuild.log They pointed to rebuild.log files, but these files don't contain error message and they ended with the following seemingly innocuous lines: protocols.relax.FastRelax: CMD: accept_to_best -3682.86 0.994359 0.994359 0.44 core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 402 requested but only 401 protein CA atoms found. core.scoring.rms_util: WARNING: In CA_rmsd, residue range 1 to 402 requested but only 401 protein CA atoms found. protocols.relax.FastRelax: CMD: endrepeat -3682.86 0.994359 0.994359 0.44 protocols::checkpoint: Deleting checkpoints of FastRelax protocols::checkpoint: Deleting checkpoints of FastRelax protocols.jd2.JobDistributor: S_MA_R_0005 reported success in 4573 seconds protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 5 jobs considered, 5 jobs attempted in 20716 seconds I would appreciate it if you could tell me what could be the causes of the failures. Thank in advance, Yonglin

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stop_for_unknowns=False in new version ?
by Michaela Renner-Schneck 19 Feb '14

19 Feb '14

Hi, I haven’t been running phenix.refine for a couple of weeks and meanwhile we have updated to the latest version. Now I need to re-run an old job but unfortunately the pdb-interpretation option "stop_for_unknowns=False“ which I needed for this seems to be no longer valid. Is there a way to get this option work again ? thx in advance Michaela

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New position
by Gillette, William (NIH/NCI) [C] 19 Feb '14

19 Feb '14

Dear colleagues, We have an opening for a structural biologist here in Frederick, MD. If not interested, please forward this email to those who might be. Thank you. Best regards, Bill <http://jobs.leidos.com/job/Frederick-Lead-Structural-Biology-603181-%28NCI%…> http://jobs.leidos.com/job/Frederick-Lead-Structural-Biology-603181-%28NCI%… ______________________________________________________ Bill Gillette, Ph.D. (Contractor) Sr. Scientist, Protein Expression Laboratory Cancer Research Technology Program Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research (FNL) P.O. Box B, Frederick, MD 21702 Phone: 301-846-1029 William.Gillette(a)nih.gov<gillettew(a)mail.nih.gov> Notice: This communication may contain privileged or other confidential information. If you are not the intended recipient, or believe that you have received this communication in error, please do not print, copy, retransmit, disseminate or otherwise use the information. Please indicate to the sender that you have received this email in error and delete the copy you received.

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phenix.composite-omit-map and PBScluster
by Mark A Saper 19 Feb '14

19 Feb '14

Hi, This is a technical question for cluster experts. I tried to run phenix.composite-omit-map which can divide the calculations into separate jobs, on a very large cluster controlled by the PBS system. I used this command of which the first 2 lines specify to divide the work up into 16 processes, and each process will use 1 of the CPU's in the cluster. phenix.composite_omit_map nproc=16 background=False technology=pbs \ qsub_command="qsub -V -l procs=1,walltime=00:30:00,mem=2000mb,qos=flux -j oe -M saper(a)umich.edu -q flux -m abe " \ omit_type=anneal map_type=2mFo-Dfc output.file_name=composite_omit_map9.mtz \ reflections3_5percent.mtz Refine_122.pdb This is the end of the log file before it aborted: ----------Calculating individual omit maps---------- |-----------------------------------------------------------------------------| | target_work(ml) = 4.65539 r_work = 0.1750 r_free = 0.2066 | |-----------------------------------------------------------------------------| And this is the error log: Traceback (most recent call last): File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 238, in <module> run(sys.argv[1:]) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 166, in run out=out) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/phenix/phenix/automation/composite_omit_map.py", line 395, in __init__ preserve_exception_message=True) File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/easy_mp.py", line 502, in parallel_map display_stderr = not preserve_exception_message, File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/queuing_system_utils/processing/__init__.py", line 405, in PBS raise RuntimeError, "PBS does not support synchronous submission" RuntimeError: PBS does not support synchronous submission I know that PBS doesn't support synchronous submission. Perhaps each job (or map region) requires more than one processor? Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan c/o Biophysics, Chem 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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list policy change: Reply-To header
by Nathaniel Echols 18 Feb '14

18 Feb '14

Hi all-- Since the current practice of directing all replies to the entire phenixbb seems to cause confusion, we've changed this so the reply will be sent to the original sender. Because we rely on the list archives as a form of ongoing "live" documentation, we encourage everyone to use "reply to all" unless you are really certain that you do not want your message to go to the list. (This especially applies to my colleagues: if you don't copy the entire list, the rest of us have no way of knowing if a question has been answered or not.) thanks, Nat

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