显示MRC数据
目录 |
显示MRC数据
目标为读入电镜三维数据，MRC格式，并有效的渲染它。
转换格式
--大鸟
来不及查怎么直接读取MRC格式了，刚好看到eman的proc3d命令可以将mrc格式转化为amira的am格式，所以就直接做了，利用之前的基础命令，就可以得到一个初步的显示结果，果然比chimera和iris漂亮很多（当然，也是因为没有好好研究chimera和Iris的缘故）
按照如下步骤来做：
- 使用onefilenew命令将icos5f.map转化为mhv5f.mrc
- 使用proc3d命令将mhv5f.mrc转化为mhv5f.am
- 进入amira用户界面，打开mhv5f.am，在pool窗口会出现mhv5f.am的绿色数据模块图标，点击pool窗口上方的快捷模块按钮：Boundingbox和Isosurface，点击Isosurface，在property窗口中修改Colormap的参数范围（在颜色条上右击弹出菜单，选择Adjust Range），同时修改threshlod的参数(改成2或者3)，最后点击右下角的绿色Apply按钮，在viewer窗口中观察效果。
直接读取
昨天问了CLP，用Amira直接读取MRC的方法是选择数据格式为“raw data”，打开后会弹出一个input对话框让你输入一些参数，如果所示：
Image:Mhv5f18A.jpg
之后按照基本操作里面所讲的方法去做即可。
基本配置
硬件和软件的配置
硬件配置
软件配置
读入MRC格式的文件需要ResolveRT Pack附件。
MRC is a file format for the exchange of electron microscopy data.
With this reader you can import and export files in the MRC file format into amira. Recognized file extensions for the reader are .mrc and .rec.
Note that this reader expects the file header to be in little endian encoding.
显示PDB数据
PDB is a file format for storing structures of biomolecules. The format is used for archiving molecules in the online protein data base. [1]
- Supported records
amira uses most, but not all, information supplied in a PDB file. The following record types will be parsed:
HELIX SHEET TURN SITE MODEL ENDMDL ATOM HETATM TER CONECT END
The rest will be skipped.
When saving a structure, the following record types will be written:
HEADER TITLE AUTHOR SEQRES HELIX SHEET TURN SITE SSBOND ATOM HETATM TER CONECT MASTER END
amira supports PDB files that follow the conventions of PDB format version 2.0 or higher.
- How to identify PDB groups in amira
In amira all levels (atoms, residues, bonds , ...) contain a set of information fields called attributes. Every level contains the field `index' which is an internal identifier that does not necessarily correspond to the succession of the groups in the file.
If the molecule has been read from a PDB file then the atom 'name' field is composed of the chain name and the sequence number (columns 7 - 11) of the respective ATOM records. The field 'index' only corresponds to the sequence number if the enumeration of pdb atoms is continuous.
The `type' field contains the information of the field named `atom name' (columns 13 - 16) in the PDB file.
The `name' field of chains contains the chainID (column 22) of the respective ATOM record. HETATM records whose chainID field is empty will not belong to any chain in amira. The chain name of atoms belonging to ATOM records whose chainID field is empty will be set to `NIL'.
The `name' field of residiues is composed of the chain name and the residue sequence number (columns 23 - 26). If the residue is a het-group, the name will start with `HET'.
The field `type' contains the residue names (columns 18 - 20). If none is given, the field will be set to `UNK' (for unknown).
- Example:
ATOM 441 CB VAL L 58 21.025 37.362 -2.515 1.00 8.15 1IGM 562
The atom will be known with name 'L441' and comment `CB'. It will belong to the residue with name `L58' and of type `VAL' which is sited on the chain with name `L'.
It is possible to save trajectories in the PDB format. Note, however, that this is inefficient due to the redundancy of information of the atom records in each model entry.
- Possible problems
Some molecular modelling packages use slightly altered conventions for saving PDB files. If you encounter any problems in reading such files please check the following section and adjust your files as necessary.
amira can read several models of one molecule as a trajectory if the different versions are separately declared between MODEL and ENDMDL records. If there are several possible conformations in one model (by using alternate location identificators), amira will read only the first version (that one with the altLocId `A').
Molecules that are declared as models need to have the same number of atoms as amira will only read the topology once. Only the coordinates are read in for each timestep. If you have several different molecules in one PDB file, you can separate them by END records. amira will load every molecule ended by an END record separately, creating its own data object.
The automatic creation of bonds of peptide and RNA/DNA residues is done by comparing the atoms of the residues with a residue database. The method requires the atom names and the residue names to follow the PDB standard. Sometimes third party programs write atoms like O3* as O3'. This will prevent amira from recognizing the atoms in the database. Connections between consecutive residues is done by checking the sequence of residues of each chain. Bonds of non-standard residues must be declared in the connect records. Columns 77-78 should contain the element name of the atom. In some PDB files, this field is empty or contains other information. In this case, amira uses the first two letters of the atom name to determine the atom type. However, in special cases this is not unequivocal. The field is not allowed to contain non-numerical information.
All information in columns 79-80 is interpreted as the charge of the atom. Thus, line numbers in this field will lead to strange charge values. You can get complete documentation of the file format at http://www.rcsb.org/pdb/.