Influence of pump laser fluence on ultrafast myoglobin structural changes

DESCRIPTION OF TAR ARCHIVE CONTENTS the folder SCRIPTS contains two subfolders: ANALYZE and REFINE ANALYZE contains python3 scripts for analysis.There are three files:-analyze_pdb.py which contains functions, and-make_figures.py which calls these functions. In make_figures.py one needs to change the directories at thebeginning of the script so the script can find the files it needs.Moreover, one needs to have numpy, scipy, and matplotlib installed. As the functions in analyze_pdb cannot handle altlocs, there is a third file: extract_Bloc.py which takes the B altloc atoms out of a pdb file and makes a new file containing only these. In this way, the photolyzed structures, which are stored als altloc B by the refinement script (see below), can be analyzed. REFINE contains the files needed for multi-copy refinement. There are several files: -multicopy_refine performs the multicopy refinement (duh...); it needs to be edited to conform to your file names/directory structure. Instructions are at the top of the file. The script requires python2.7 and phenix. This version will use the automatically determined occupancy for final refinement. The file needs to be adapted when another, preset occupancy is required. -refine_par.in contains parameters for phenix.refine that are called by multicopy_refine, and needs to be in the same directory. -the pdb files are the starting structures for multicopy refinement. The "4 and 18 uJ" starting structures are for the 23- and 101 mJ/cm2 case (and the power titration), for the low-fluence data the other dark structures ("1 uJ") need to be substituted. Details of the multicopy refinement scheme are in the publication. Back in the top folder, the subfolder GEOMETRY contains the .cif file which describes the heme geometry usedfor all refinements. In it, the prior ESDs for the planarity of the heme have been increasedfrom 0.02 to 0.2 The STREAMS folder contains the CrystFEL stream files used for Monte Carlo integration. There are four subdirectories, one for each time series, and a separate one for the power titration. DARKS contains the refined dark structures as well as the MTZ files with the dark data. POWERTITRATION contains the power titration multicopy refinement results, as well as the MTZ files with the integrated data. TIMESERIES contains the time series multicopy refinement results.TAR归档内容说明 SCRIPTS文件夹包含两个子文件夹：ANALYZE与REFINE。 ANALYZE文件夹存放用于数据分析的Python3脚本，共3个文件：一是包含各类功能函数的`analyze_pdb.py`，二是调用上述函数的`make_figures.py`。使用`make_figures.py`时，需修改脚本开头的目录路径，使其能正确检索所需文件；此外，运行该脚本需预先安装numpy、scipy与matplotlib库。 由于`analyze_pdb.py`中的函数无法处理替代位点（altlocs），因此提供第三个文件`extract_Bloc.py`：该脚本可从PDB文件中提取B位点的原子，并生成仅包含这些原子的新文件，借此可对通过精修脚本存储为B替代位点的光解结构（详见下文）进行分析。 REFINE文件夹存放多拷贝精修所需的相关文件，包含以下内容： - `multicopy_refine`：用于执行多拷贝精修的脚本（字面含义即为多拷贝精修），需根据实际文件名与目录结构进行编辑，脚本顶部附有详细使用说明。该脚本需依托Python2.7与phenix环境运行，默认采用自动确定的占有率进行最终精修；若需使用预设占有率，则需对该脚本进行适配调整。 - `refine_par.in`：存放phenix.refine的配置参数，供`multicopy_refine`调用，需与脚本置于同一目录下。 - PDB格式初始结构文件：作为多拷贝精修的起始结构。其中标注“4和18 uJ”的初始结构对应23 mJ/cm²与101 mJ/cm²的辐照条件（亦适用于功率滴定实验）；针对低通量数据，需替换为标注“1 uJ”的暗态初始结构。多拷贝精修方案的详细细节已发表于相关学术论文。 回到顶层目录，其子文件夹GEOMETRY存放用于所有精修流程的血红素几何构型描述文件（.cif格式），该文件中血红素平面性的先验估计标准偏差（estimated standard deviations, ESDs）已从0.02调整至0.2。 STREAMS文件夹存放用于蒙特卡洛积分的CrystFEL stream文件，包含4个子目录：分别对应4个时间序列数据集，另有一个独立子目录用于功率滴定实验。 DARKS文件夹存放已精修完成的暗态结构，以及包含暗态衍射数据的MTZ文件。 POWERTITRATION文件夹存放功率滴定实验的多拷贝精修结果，以及包含积分衍射数据的MTZ文件。 TIMESERIES文件夹存放时间序列实验的多拷贝精修结果。