# Latest

**URL:** https://discourse.rs-station.org/latest.md

[Latest](https://discourse.rs-station.org/latest.md) · [Categories](https://discourse.rs-station.org/categories.md) · [Tags](https://discourse.rs-station.org/tags.md)

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## [Welcome to Reciprocal Space Station! 👋](https://discourse.rs-station.org/t/welcome-to-reciprocal-space-station/5)

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**Author:** [@system](https://discourse.rs-station.org/u/system)\
**Replies:** 0\
**Last updated:** [December 6, 2024, 4:56am UTC](https://discourse.rs-station.org/t/welcome-to-reciprocal-space-station/5 "2024-12-06T04:56:55Z")

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We are so glad you joined us. Reciprocal Space Station Structural biology community administered by the reciprocalspaceship developers Here are some things you can do to get started: :speaking\_head: Introduce yourse…

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## ["UnitCell" has no attribute "fractionalization\_matrix". Laue-Dials help](https://discourse.rs-station.org/t/unitcell-has-no-attribute-fractionalization-matrix-laue-dials-help/228)

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**Author:** [@tbonzon1](https://discourse.rs-station.org/u/tbonzon1)\
**Replies:** 2\
**Last updated:** [October 29, 2026, 8:06pm UTC](https://discourse.rs-station.org/t/unitcell-has-no-attribute-fractionalization-matrix-laue-dials-help/228 "2026-10-29T20:06:32Z")

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Hello all, I am trying to index some images I collected at BioCARS and I am running into the following warning/error: Indexing imageset id 0 (1/31) Using max\_cell: 213.7 Angstrom 'UnitCell' object has no attribute 'f…

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## [Cell File Syntax](https://discourse.rs-station.org/t/cell-file-syntax/217)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 6\
**Last updated:** [August 23, 2026, 8:33am UTC](https://discourse.rs-station.org/t/cell-file-syntax/217 "2026-08-23T08:33:08Z")

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I swear I found a page describing the .cell file syntax before, but for the life of me I can’t find it anymore. Can someone help me locate the docs for this?

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## [LLM Tips and Tricks Leaderboard](https://discourse.rs-station.org/t/llm-tips-and-tricks-leaderboard/174)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 6\
**Last updated:** [August 22, 2026, 5:33pm UTC](https://discourse.rs-station.org/t/llm-tips-and-tricks-leaderboard/174 "2026-08-22T17:33:15Z")

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Submit tips and tricks for coding with LLMs like snippets you like to include in prompts or features you find helpful.

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## [ESRF ID29 Bandwidth Benchmarks](https://discourse.rs-station.org/t/esrf-id29-bandwidth-benchmarks/216)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 6\
**Last updated:** [August 13, 2026, 9:11pm UTC](https://discourse.rs-station.org/t/esrf-id29-bandwidth-benchmarks/216 "2026-08-13T21:11:01Z")

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ID29 has two modes, 0.4% and 1.0% bandwidth. There is some uncertainty about which mode is better for data quality and, to what extent, this is due to software vs sample. Naively, the 1.0% should be better because there …

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## [CARELESS on MacOS GPU/Metal](https://discourse.rs-station.org/t/careless-on-macos-gpu-metal/189)

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**Author:** [@aaronfinke](https://discourse.rs-station.org/u/aaronfinke)\
**Replies:** 8\
**Last updated:** [August 12, 2026, 1:48pm UTC](https://discourse.rs-station.org/t/careless-on-macos-gpu-metal/189 "2026-08-12T13:48:04Z")

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Is it possible to use the TensorFlow Apple SIlicon GPU implementation for mac with CARELESS?

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## [Classic Papers (Indexing)](https://discourse.rs-station.org/t/classic-papers-indexing/211)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 2\
**Last updated:** [July 22, 2026, 10:40pm UTC](https://discourse.rs-station.org/t/classic-papers-indexing/211 "2026-07-22T22:40:51Z")

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This topic is meant for sharing and discussing classic papers about the indexing problem in crystallography. The scope includes both rotation method and stills, monochromatic and Laue. I’ll start us off with some of my f…

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## [Partialator Reflection Filtering](https://discourse.rs-station.org/t/partialator-reflection-filtering/203)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 4\
**Last updated:** [June 24, 2026, 4:31pm UTC](https://discourse.rs-station.org/t/partialator-reflection-filtering/203 "2026-06-24T16:31:30Z")

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I’m curious about prediction in idexamajig and outlier rejection in partialator. I’m working on a dataset from CXIDB (CXIDB - Coherent X-ray Imaging Data Bank) to benchmark my merging code. Here are the indexamajig para…

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## [crystFEL 0.12.0 xsphere -- CC statistics don't go to zero as a function of resolution](https://discourse.rs-station.org/t/crystfel-0-12-0-xsphere-cc-statistics-dont-go-to-zero-as-a-function-of-resolution/196)

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**Author:** [@tjlane](https://discourse.rs-station.org/u/tjlane)\
**Replies:** 4\
**Last updated:** [June 16, 2026, 12:57pm UTC](https://discourse.rs-station.org/t/crystfel-0-12-0-xsphere-cc-statistics-dont-go-to-zero-as-a-function-of-resolution/196 "2026-06-16T12:57:26Z")

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I’ve recently been working on some TR-SFX data taken at Alvra, and was testing different merging options. I discovered that the CC1/2 or CC\* plots for data merged using the xsphere model don’t nicely approach zero as on…

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## [Output in unmerged batch mtz](https://discourse.rs-station.org/t/output-in-unmerged-batch-mtz/197)

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**Author:** [@aaronfinke](https://discourse.rs-station.org/u/aaronfinke)\
**Replies:** 3\
**Last updated:** [June 15, 2026, 4:18pm UTC](https://discourse.rs-station.org/t/output-in-unmerged-batch-mtz/197 "2026-06-15T16:18:49Z")

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Can 1/(spaceship) output unmerged mtz files in batches? I can’t seem to figure out how to do that if so. Gemmi can, but it’s messy: cell = ds\_corr.cell sg = ds\_corr.spacegroup ds\_corr = rs.DataSet(whatever) mtz\_out = …

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## [Dials error model overestimation](https://discourse.rs-station.org/t/dials-error-model-overestimation/191)

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**Author:** [@rbauer](https://discourse.rs-station.org/u/rbauer)\
**Replies:** 9\
**Last updated:** [May 29, 2026, 8:43am UTC](https://discourse.rs-station.org/t/dials-error-model-overestimation/191 "2026-05-29T08:43:24Z")

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I’m trying to process some diffraction data, but the error model is refining to poor values, a=10 b=0.01. CC1/2 and CCano are both good, but the sigma dependent statistics are very poor. When disabling the error model th…

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## [Spotfinding DIALS \`.expt\` Files with Many Stills](https://discourse.rs-station.org/t/spotfinding-dials-expt-files-with-many-stills/170)

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**Author:** [@rahewitt](https://discourse.rs-station.org/u/rahewitt)\
**Replies:** 2\
**Last updated:** [May 28, 2026, 4:22pm UTC](https://discourse.rs-station.org/t/spotfinding-dials-expt-files-with-many-stills/170 "2026-05-28T16:22:57Z")

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I have a dataset with 5332 still images. I can run dials.import on them and get 5332 stills, but am routinely running into Out-Of-Memory errors even with 120 GB of memory during spotfinding. Are there any tips for dealin…

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## [AI Applications in Structural Biology](https://discourse.rs-station.org/t/ai-applications-in-structural-biology/190)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 3\
**Last updated:** [May 5, 2026, 4:54pm UTC](https://discourse.rs-station.org/t/ai-applications-in-structural-biology/190 "2026-05-05T16:54:59Z")

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Let’s catalogue applications of artificial intelligence and machine learning in structural biology spanning the whole ecosystem from experiment to data reduction to structure modeling and deposition. If you’ve got an app…

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## [Double Wilson Prior for Anomalous Signal in SFX Data](https://discourse.rs-station.org/t/double-wilson-prior-for-anomalous-signal-in-sfx-data/188)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 1\
**Last updated:** [May 1, 2026, 6:00pm UTC](https://discourse.rs-station.org/t/double-wilson-prior-for-anomalous-signal-in-sfx-data/188 "2026-05-01T18:00:57Z")

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I’m analyzing some moderate size SFX datasets with anomalous scattering, and I would like to use the multivariate Wilson prior and optimize r as in figure S13 of the paper. I’m wondering if there is a simple example some…

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## [Introduction to Command Line / Cluster Computing](https://discourse.rs-station.org/t/introduction-to-command-line-cluster-computing/74)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 7\
**Last updated:** [April 23, 2026, 7:28am UTC](https://discourse.rs-station.org/t/introduction-to-command-line-cluster-computing/74 "2026-04-23T07:28:18Z")

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What are some great resources for getting students up to speed on using computing clusters? This includes topics like: bash ssh / rsync slurm git python

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## [Running ABISMAL on NERSC](https://discourse.rs-station.org/t/running-abismal-on-nersc/187)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 0\
**Last updated:** [April 16, 2026, 1:39am UTC](https://discourse.rs-station.org/t/running-abismal-on-nersc/187 "2026-04-16T01:39:54Z")

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This short tutorial will cover running ABISMAL on NERSC in order to process time-resolved crystallography data. @kmdalton maintains an ABISMAL install on NERSC for LCLS use: source /global/common/software/lcls/abismal/…

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## [Resources for CrystFEL Processing at MFX](https://discourse.rs-station.org/t/resources-for-crystfel-processing-at-mfx/185)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 0\
**Last updated:** [April 15, 2026, 2:39pm UTC](https://discourse.rs-station.org/t/resources-for-crystfel-processing-at-mfx/185 "2026-04-15T14:39:49Z")

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A recent user group at LCLS MFX had a very successful time-resolved crystallography experiment using CrystFEL for data processing. They have put together some documentation of their workflow over on the Desy GitLab. This…

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## [Scattering Correlations in Python (SCORPY)](https://discourse.rs-station.org/t/scattering-correlations-in-python-scorpy/182)

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**Author:** [@YellowSub17](https://discourse.rs-station.org/u/YellowSub17)\
**Replies:** 2\
**Last updated:** [April 15, 2026, 7:36am UTC](https://discourse.rs-station.org/t/scattering-correlations-in-python-scorpy/182 "2026-04-15T07:36:01Z")

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Hello! I’d like to share with you a python package I wrote during my PhD for calculating scattering correlations in python (SCORPY). In fluctuation x-ray scattering (FXS), the distribution of pairs of intensity points in…

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## [Call for abstracts for NeXus meeting at NOBUGS](https://discourse.rs-station.org/t/call-for-abstracts-for-nexus-meeting-at-nobugs/181)

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**Author:** [@phyy-nx](https://discourse.rs-station.org/u/phyy-nx)\
**Replies:** 0\
**Last updated:** [April 8, 2026, 5:23pm UTC](https://discourse.rs-station.org/t/call-for-abstracts-for-nexus-meeting-at-nobugs/181 "2026-04-08T17:23:32Z")

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Hi all, the NeXus International Advisory Committee (NIAC) is soliciting user talks as part of its biennial meeting at NOBUGS on Sept 25th, 2026 in Hamburg, Germany. We’d like to invite general users of NeXus from a vari…

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## [Groupby symmetry equivalent reflections in a rs.DataSet?](https://discourse.rs-station.org/t/groupby-symmetry-equivalent-reflections-in-a-rs-dataset/180)

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**Author:** [@aaronfinke](https://discourse.rs-station.org/u/aaronfinke)\
**Replies:** 2\
**Last updated:** [April 7, 2026, 2:19pm UTC](https://discourse.rs-station.org/t/groupby-symmetry-equivalent-reflections-in-a-rs-dataset/180 "2026-04-07T14:19:46Z")

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Fairly simple question here: let’s say I have a DataSet of h,k,l for a particular unmerged list of reflections with a unit cell and spacegroup (no intensities). Is there a simple way to groupbysymmetry-related reflection…

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## [Recover Intensity without Background Subtraction](https://discourse.rs-station.org/t/recover-intensity-without-background-subtraction/175)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 4\
**Last updated:** [March 5, 2026, 4:42pm UTC](https://discourse.rs-station.org/t/recover-intensity-without-background-subtraction/175 "2026-03-05T16:42:50Z")

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I have a reflection table from stills\_process (source: CXIDB ID 81) with the following columns. Can I recover an estimate of the intensity prior to background subtraction? Should it be a simple arithmetic transform invol…

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## [LLM Prompting for Crystallographic Software Generation](https://discourse.rs-station.org/t/llm-prompting-for-crystallographic-software-generation/173)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 2\
**Last updated:** [March 5, 2026, 4:10am UTC](https://discourse.rs-station.org/t/llm-prompting-for-crystallographic-software-generation/173 "2026-03-05T04:10:14Z")

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I am interested in people’s tips and tricks for getting the most of LLMs when working on technical projects. My own work is at the intersection of crystallography and machine learning, and I frequently combine variationa…

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## [Dials.stills\_process for ID-29 data](https://discourse.rs-station.org/t/dials-stills-process-for-id-29-data/160)

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**Author:** [@kzielinski](https://discourse.rs-station.org/u/kzielinski)\
**Replies:** 4\
**Last updated:** [March 4, 2026, 8:54pm UTC](https://discourse.rs-station.org/t/dials-stills-process-for-id-29-data/160 "2026-03-04T20:54:18Z")

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I summarized my dials.stills\_process processing pipeline for ID-29 data and presented to the SLAC Computational Crystallography Group Meeting slides are here: ID-29 MISC Data Processing.pdf (1.1 MB) I share some dials.…

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## [Added ORCID Support](https://discourse.rs-station.org/t/added-orcid-support/159)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 4\
**Last updated:** [February 26, 2026, 9:12pm UTC](https://discourse.rs-station.org/t/added-orcid-support/159 "2026-02-26T21:12:00Z")

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I’ve just added support for ORCID authentication on this forum. Happy to hear any feedback about this feature here or over in the Site Feedback category. Thanks!

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## [Creation of multi-block sf-cif files for VALDO deposition](https://discourse.rs-station.org/t/creation-of-multi-block-sf-cif-files-for-valdo-deposition/157)

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**Author:** [@Doeke\_Hekstra](https://discourse.rs-station.org/u/Doeke_Hekstra)\
**Replies:** 5\
**Last updated:** [December 29, 2025, 10:05pm UTC](https://discourse.rs-station.org/t/creation-of-multi-block-sf-cif-files-for-valdo-deposition/157 "2025-12-29T22:05:19Z")

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In preparing VALDO output for PDB deposition, we are thinking of following the following convention for deposition: a multi-block sf-cif file with the following blocks: extrapolated structure factor amplitudes as used …

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## [Planned Outage Wednesday November 19th](https://discourse.rs-station.org/t/planned-outage-wednesday-november-19th/155)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 0\
**Last updated:** [November 18, 2025, 7:56pm UTC](https://discourse.rs-station.org/t/planned-outage-wednesday-november-19th/155 "2025-11-18T19:56:55Z")

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The rs-station forum will be down for maintenance on Wednesday, November 19th at 5:00am UTC for an expected duration of 60 minutes.

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## [DIALS Stills Process Resources](https://discourse.rs-station.org/t/dials-stills-process-resources/140)

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**Author:** [@kzielinski](https://discourse.rs-station.org/u/kzielinski)\
**Replies:** 1\
**Last updated:** [November 1, 2025, 3:59pm UTC](https://discourse.rs-station.org/t/dials-stills-process-resources/140 "2025-11-01T15:59:42Z")

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http://viper.lbl.gov:8080/cctbx.xfel/index.php/2017\_dials.stills\_process

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## [CrystFEL 0.12.0 released](https://discourse.rs-station.org/t/crystfel-0-12-0-released/143)

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**Author:** [@taw](https://discourse.rs-station.org/u/taw)\
**Replies:** 1\
**Last updated:** [October 22, 2025, 9:29am UTC](https://discourse.rs-station.org/t/crystfel-0-12-0-released/143 "2025-10-22T09:29:04Z")

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Hi everyone, In case you haven’t heard already, CrystFEL version 0.12.0 has been released! This version adds enforcement of lattice type restrictions (e.g. 90° cell angles) during indexing, which substantially improves…

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## [Converting merged intensity to amplitude](https://discourse.rs-station.org/t/converting-merged-intensity-to-amplitude/146)

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**Author:** [@anonymous1](https://discourse.rs-station.org/u/anonymous1)\
**Replies:** 1\
**Last updated:** [September 27, 2025, 2:49pm UTC](https://discourse.rs-station.org/t/converting-merged-intensity-to-amplitude/146 "2025-09-27T14:49:01Z")

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Given a set of merged intensities (e.g. downloaded via the “Structure Factors (CIF)” tab on PDB), what is the best practice to convert to amplitude? I see that reciprocalspaceship has this function rs.algorithms.scale\_me…

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## [Extending Free R Flags](https://discourse.rs-station.org/t/extending-free-r-flags/141)

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**Author:** [@kmdalton](https://discourse.rs-station.org/u/kmdalton)\
**Replies:** 1\
**Last updated:** [September 23, 2025, 6:55pm UTC](https://discourse.rs-station.org/t/extending-free-r-flags/141 "2025-09-23T18:55:08Z")

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I have a phenix refine output mtz which has an R-free flag column, but it is not complete and it doesn’t extend to the resolution range I’d like. How can I use rs to make a new mtz with r-free flags that are complete out…

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