SEQADV:PDB与其它记录的出入 SEQRES:给出了每条链的残基序列 MODRES:对标准残基的修饰(此文件没有进行残基修饰) 三、杂因子 HET:非标准残基(缩写)、所属链、残基号、所含原子数目 HETNAM:非标准残基的全称 FORMUL:非标准残基化学式(那个数字我也不知道是什么!) 四、二级结构 HELIX:螺旋,每个螺旋一条记录,...
数据库从PDB中下载: ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt 用cd-hit处理去冗余(解压后加变量后就能用) 代码语言:javascript 代码运行次数:0 运行 AI代码解释 $:cd-hit-i/path/pdb_seqres_simp.fasta-o PDB_simp.fasta-c0.9 ...
数据库从PDB中下载: ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt 用cd-hit处理去冗余(解压后加变量后就能用) $: cd-hit -i /path/pdb_seqres_simp.fasta -o PDB_simp.fasta -c 0.9 格式化数据库: $: makeblastdb –in PDB_simp.fasta –dbtype prot –out PDB -in:待格式化...
cat {protein_id}/{protein_id}.tar.gz.part* > {protein_id}/{protein_id}.tar.gz cd ${Your Storage Root} mkdir dynamicPDB # ignore if directory exists tar -xvzf dynamicPDB_raw/{protein_id}/{protein_id}.tar.gz -C dynamicPDB Finally, the dataset should be organized as follows: ./dyn...
Fixed bug pertaining to SEQRES parsing when chain ID is numeric. Changed format of residue IDs to include colon. Considerable speed improvements in .mmcif parsing. Release 0.11.0 22 August 2018 Added .mmcif parsing. Changed how parsing in general is done under the hood. ...
Merge the split-volume compression into one file and then unzip the.tar.gzfile: cat {protein_id}/{protein_id}.tar.gz.part*>{protein_id}/{protein_id}.tar.gzcd${Your Storage Root}mkdir dynamicPDB#ignore if directory existstar -xvzf dynamicPDB_raw/{protein_id}/{protein_id}.tar.gz -C...