Question

目标：我想比较计算相同残基的RMSD，例如131Thr，来自相同目标的2个pdb文件。使用pymol，我计算了一个5个残基的滑动窗口以进行局部比对，然后选择该残基并计算两个残基之间的均方根值，其灵感来自此处的帖子https://pymolwiki.org/index.php/RmsdByResidue。唯一的区别是：我预先定义了一个5个残基的滑动窗口以进行局部比对。

代码段（Python / Pymol接口）：

  referenceProteinChain = cmd.fetch(pbdstructure1)
  targetProteinChain = cmd.fetch(pdbstructure2)
  sel = referenceProteinChain
  list_atoms = [[133, 133]] # example list, I want to calculate the rmsd between residue 133 and residue 133 of two pdb structures

for j in list_atoms:
   # I formulate my sliding window of 5 residues, my residue of interest is in the middle
    ref_begin = int(j[0])-2
    ref_end = int(j[0])+2
    target_begin = int(j[1])-2
    target_end = int(j[1])+2

    # I create a selection for the reference protein and the target protein 
    cmd.create("ref_gzt", referenceProteinChain+" and polymer and not alt B and not Alt C and not alt D  and resi %s-%s" 
    cmd.alter("ref_gzt", "chain='A'")
    cmd.alter("ref_gzt", "segi=''")
    cmd.create("target_gzt", targetProteinChain+" and polymer and  not alt B and not Alt C and not alt D  and resi %s-%s" %(target_begin,target_end) )
    cmd.alter("target_gzt", "chain='A'")
    cmd.alter("target_gzt", "segi=''")

    # I align my selected 5 residues for a local alignment window
    cmd.align("target_gzt","ref_gzt",object="align", cycles =5) 


   # select alpha carbon of in reference structure to loop over
    calpha=cmd.get_model(sel+" and name CA and not alt B and not Alt C and not alt D  and resi %s-%s" %(ref_begin,ref_end) )

   ## here I loop over all residues in the sliding window and calculte the rmsd for my residues of interest.
    for g in calpha.atom : I loop over the slinding window
        if g.resi == str(j[0]): ## we select only our residue of interest within the sliding window
            if cmd.count_atoms("ref_gzt and polymer and resi "+g.resi)==cmd.count_atoms("target_gzt and polymer and resi "+g.resi):

                ## calculte the pairwise RMSD between the residues I specified in list_atoms 
                rmsdRes=cmd.rms_cur("ref_gzt and polymer and resi "+g.resi,"target_gzt and polymer and resi "+g.resi)

我的问题： 我选择的残基得到的原子数不同，因此无法计算我的RMSD

我需要一个Pymol函数，通过它我可以查看正在比较的残基，例如我是否实际上在两个pdb文件中都比较131Thr。有这样的功能吗？
是否有更好的方法为滑动窗口创建两个选择？
cmd.alter-我用它来确保两个结构的残基匹配，但是有没有办法保留我的原始注释？

注意：我检查了原始pdb文件中的残基是否匹配。他们是这样。我如何选择残留物似乎是Pymol问题。

作为Pymol的新手-如果有人可以给我一个建议，将不胜感激！我检查了pymol邮件列表并尝试了其他功能，例如使用cmd.select，但没有任何进一步的内容。

Pymol-关于创建对象并为滑动窗口选择特定残基的问题

0 个答案: