conformational dynamics of the transcription bubble in RNAP-promoter open complex - FPS analysis - input - input data

These files include the following input for the FPS procedure:<br>1. dye_positions.txt - a table that lists the unique name of the dye attachment point, the structure subunit (template or nontemplate strand, pdb files) to which the dye is conjugated, if it is an acceptor or a donor (A/D), the coarse-grained model used to calculate the dye AV, the dye coarse-grained dimensions (Linker length and width and ellipsoidal radii of fluorophore) and the atom ID (in the PDB file of the subunit) to which the dye is conjugated.2. distances_1_dwells.txt - a table that lists the D-A pairs and their distances, for the distance set classified as <i>RPo state</i>: the unique name of the acceptor attachment point, the unique name of the donor attachment point, the experimental mean D-A distance, the experimental D-A distance error lower boundary and the experimental D-A distance error upper boundary3. distances_2_dwells.txt - a table that lists the D-A pairs and their distances, for the distance set classified as <i>scrunched RPo state</i>The experimental mean D-A distances are shown in Fig. 4

本数据集包含FPS流程所需的以下输入文件：<br>1. dye_positions.txt：该表格记录了染料结合位点的唯一标识、染料结合的结构亚基（对应模板链或非模板链的PDB（Protein Data Bank）文件）、染料类型（受体/供体，即A/D）、用于计算染料各向异性值（AV）的粗粒度模型、染料粗粒度尺寸参数（包括连接子的长度、宽度以及荧光团的椭球半径），以及染料所结合的亚基PDB文件中的原子ID。<br>2. distances_1_dwells.txt：该表格记录了被归类为<i>RPo状态</i>的距离数据集对应的供体-受体（Donor-Acceptor, D-A）对及其距离参数，具体包含受体结合位点唯一标识、供体结合位点唯一标识、实验测得的供体-受体平均距离、供体-受体距离的实验误差下限以及实验误差上限。<br>3. distances_2_dwells.txt：该表格记录了被归类为<i>紧缩型RPo状态</i>的距离数据集对应的供体-受体对及其距离参数。实验测得的供体-受体平均距离详见图4。