Re: [ccp4bb] cell discrepancies and stuck refinement using different XDS-versions
Dear Sabine, I would first take a look at the respective log-files for differences in parameter settings, in particular SPOT_RANGE / DATA_RANGE, INCLUDE_RESOLUTION_RANGE. Start with IDXREF.LP, then proceed to COLSPOT.LP. The relevant parameters are always listed in the header of the log-files. Programms like xxdiff or vimdiff are very useful to highlight the differences. Best, Tim On Monday, August 6, 2018 4:50:56 PM CEST Sabine Schneider wrote: > Dear all, > > We are encountering a differences in indexing using different XDS > versions, which results in either 2 or 4 mols/asu (SG P1; structure > determination via MR (30% seq ID model)) and either successful > refinement or stuck R/Rfree > > - the data were collected at ESRF ID30A3 (Aiger detector) and extend to > about 2.3A resolution (CC1/2 ~50%) > > The XDS version build 20180126 (and or autoprocessing at the ESRF via > autoproc, dials, xdsapp or grenade -> here also xds version from > 20180126 used) gives us: > > P1 38.6550.7661.11 110.057 99.945 90.197 > XDS complains and I need to use "DEFPIX INTEGRATE CORRECT" > -> 2mols/asu, structure refines to R/Rfree of 22/25 > > In contrast the actual XDS-Version BUILT=20180409 results in: > P1 39.2 51.3 116.8 86.3 82.3 89.8 > but XDS runs smoothly. > -> 4mols/asu, tNCS, R/Rfree stuck at 28/32 > If I feed XDS with the smaller cell above, it fails. > > (The smaller cell is also found by Xia2/dials via the CCP4i2 interface.) > > Thus I am wondering, what are the differences between the two > XDS-versions? (I remember vaguely that there was a tread about different > XDS-versions, but couldn't find it..) > > Cheers Sabine -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OSUA/204 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 signature.asc Description: This is a digitally signed message part.
[ccp4bb] cell discrepancies and stuck refinement using different XDS-versions
Dear all, We are encountering a differences in indexing using different XDS versions, which results in either 2 or 4 mols/asu (SG P1; structure determination via MR (30% seq ID model)) and either successful refinement or stuck R/Rfree - the data were collected at ESRF ID30A3 (Aiger detector) and extend to about 2.3A resolution (CC1/2 ~50%) The XDS version build 20180126 (and or autoprocessing at the ESRF via autoproc, dials, xdsapp or grenade -> here also xds version from 20180126 used) gives us: P1 38.65 50.76 61.11 110.057 99.945 90.197 XDS complains and I need to use "DEFPIX INTEGRATE CORRECT" -> 2mols/asu, structure refines to R/Rfree of 22/25 In contrast the actual XDS-Version BUILT=20180409 results in: P1 39.2 51.3 116.8 86.3 82.3 89.8 but XDS runs smoothly. -> 4mols/asu, tNCS, R/Rfree stuck at 28/32 If I feed XDS with the smaller cell above, it fails. (The smaller cell is also found by Xia2/dials via the CCP4i2 interface.) Thus I am wondering, what are the differences between the two XDS-versions? (I remember vaguely that there was a tread about different XDS-versions, but couldn't find it..) Cheers Sabine -- -- Dr. Sabine Schneider Research Group Leader Technical University of Munich Department of Chemistry Chair of Biochemistry Lichtenbergstr. 4 85748 Garching Germany Tel.: +49 (0) 89 289 13759 Fax: +49 (0) 89 289 13363 http://www.biochemie.ch.tum.de/index.php?id=919 -- -- Dr. Sabine Schneider Research Group Leader Technical University of Munich Department of Chemistry Chair of Biochemistry Lichtenbergstr. 4 85748 Garching Germany Tel.: +49 (0) 89 289 13759 Fax: +49 (0) 89 289 13363 http://www.biochemie.ch.tum.de/index.php?id=919 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] HTS Specialist Position at St. Jude
The High Throughput Biosciences (HTB) Center is recruiting a senior-level scientist to serve as our in-house protein expert and to join our efforts in using high-throughput screening (HTS) for structure/target-based small molecule discovery (Job title: HTS Specialist). The HTS Specialist reports to the Director of the High Throughput Bioscience (HTB) Center and is expected to independently lead and implement collaborative projects; present and publish research results; and assist the Center Director in managing the daily operations of the Center. The successful candidate will have extensive experience in molecular biology, protein biochemistry, and structural biology and a strong interest in learning, developing, and implementing new techniques related to high-throughput small-molecule drug discovery. Experience in the following areas is a plus: protein purification, protein crystallography, docking, and biochemical and biophysical assay development, along with a strong publication record. Please direct your questions, cover letter, current CV, and 3 letters of reference to Dr. Taosheng Chen (taosheng.c...@stjude.org). The *High Throughput Bioscience Center* at St. Jude consists of members with advanced training in biology, chemistry, and engineering. We have professional experience in target identification and validation, assay development, high-throughput screening, laboratory automation, and management of scientific collaborations. *Minimum Education* Bachelor's or Master's degree in biology, chemistry, or a related field required. PhD in biological sciences with relevant postdoctoral training preferred. *Minimum Experience * Seven (7) years of relevant experience is required with a Bachelor’s degree. Six (6) years of relevant experience is acceptable with a Master’s degree. At least two (2) years of relevant experience is acceptable with a PhD. *Contact* Taosheng Chen, PhD Member, Department of Chemical Biology and Therapeutics Director, High Throughput Bioscience Center St. Jude Children's Research Hospital Memphis, TN, 38105-3678, USA https://www.stjude.org/chen http://www.stjuderesearch.org/site/lab/chen *Link to Ad* https://careers-stjude.icims.com/jobs/3973/hts-specialist/job To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
