应《网络安全法》要求，自2017年10月1日起，未进行实名认证将不得使用互联网跟帖服务。为保障您的帐号能够正常使用，请尽快对帐号进行手机号验证，感谢您的理解与支持！

24小时热门版块排行榜    

CyRhmU.jpeg
小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » DS/Sybyl/Autodock » modeller multiple templates求助
南方科技大学公共卫生及应急管理学院2025级博士研究生招生报考通知
121/2返回列表12下一页
查看: 1438  |  回复: 11
只看楼主@他人 存档 新回复提醒 (忽略) 收藏    在APP中查看

nufang19a

金虫 (正式写手)

[求助] modeller multiple templates求助

from modeller import *

log.verbose()
env = environ()
env.io.atom_files_directory = './:../atom_files/'

aln = alignment(env)
for (code, chain) in (('2mdh', 'A'), ('1bdm', 'A'), ('1b8p', 'A')):
    mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain))
    aln.append_model(mdl, atom_files=code, align_codes=code+chain)

for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True),
                                    ((1., 0.5, 1., 1., 1., 0.), False, True),
                                    ((1., 1., 1., 1., 1., 0.), True, False)):
    aln.salign(rms_cutoff=3.5, normalize_pp_scores=False,
               rr_file='$(LIB)/as1.sim.mat', overhang=30,
               gap_penalties_1d=(-450, -50),
               gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0,
               dendrogram_file='fm00495.tree',
               alignment_type='tree', # If 'progresive', the tree is not
                                      # computed and all structues will be
                                      # aligned sequentially to the first
               feature_weights=weights, # For a multiple sequence alignment only
                                        # the first feature needs to be non-zero
               improve_alignment=True, fit=True, write_fit=write_fit,
               write_whole_pdb=whole, output='ALIGNMENT QUALITY')
aln.write(file='fm00495.pap', alignment_format='PAP')
aln.write(file='fm00495.ali', alignment_format='PIR')

aln.salign(rms_cutoff=1.0, normalize_pp_scores=False,
           rr_file='$(LIB)/as1.sim.mat', overhang=30,
           gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3),
           gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree',
           alignment_type='progressive', feature_weights=[0]*6,
           improve_alignment=False, fit=False, write_fit=True,
           write_whole_pdb=False, output='QUALITY')
这一段中，粗体字部分看不懂，期待得到解答，先谢谢了
回复此楼

» 猜你喜欢

» 本主题相关价值贴推荐，对您同样有帮助:
1楼2012-02-28 16:56:35
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

nufang19a

金虫 (正式写手)
顶上去，求解答
回复此楼
2楼2012-02-29 09:20:25
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

nufang19a

金虫 (正式写手)
对于gap_penalties_1d明白了，在modeller网站上查到这样一句话
The gap initiation and extension penalties are specified by gap_penalties_1d. The default values of -900 -50 for the 'as1.sim.mat' similarity matrix were found to be optimal for pairwise alignments of sequences that share from 30% to 45% sequence identity (RS and AŠ, in preparation).
赞一下 回复此楼
3楼2012-02-29 10:39:13
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

nufang19a

金虫 (正式写手)
rr_file 也明白了
rr_file is the residue-residue substitution matrix to use when calculating the position-specific scoring matrix (PSSM).
赞一下 回复此楼
4楼2012-02-29 15:02:49
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

nufang19a

金虫 (正式写手)
write_fit 明白了
If write_fit is True, the fitted atom files are written out in their final fitted orientations
赞一下 回复此楼
5楼2012-03-03 16:36:22
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

nufang19a

金虫 (正式写手)
write_whole_pdb
明白了
If write_whole_pdb is True, the whole PDB files are written out; otherwise only the parts corresponding to the aligned sequences are output.
赞一下 回复此楼
6楼2012-03-03 16:40:30
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

nufang19a

金虫 (正式写手)
fit 明白了
If fit is False, the initial alignment is not changed. This is useful when all the structures have to be superimposed with the initial alignment (fit = False and write_fit = True).
赞一下 回复此楼
7楼2012-03-03 16:42:06
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

nufang19a

金虫 (正式写手)
write_whole_pdb 明白了
If write_whole_pdb is True, the whole PDB files are written out; otherwise only the parts corresponding to the aligned sequences are output.
赞一下 回复此楼
8楼2012-03-03 16:53:56
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

nufang19a

金虫 (正式写手)
gap_penalties_3d ，算是懂一点了：
This optimal alignment is obtained by an iterative procedure as follows (the same as in alignment.align3d()). The average structures for both sub-alignments are calculated for all sub-alignment positions with at least one defined selected atom. This calculation is straightforward because the structures within the two sub-alignments are already superposed with each other (see below). Then, the distance matrix for dynamic programming with affine gap penalties is calculated as the matrix of Euclidean distances between the two averages. The dynamic programming results into a new alignment, dependent also on the gap initiation and extension penalties gap_penalties_3d (a reasonable setting is (0, 3)). gap_penalties_3d[0] is a gap creation penalty (usually 0), and gap_penalties_3d[1] is a gap extension penalty, say 3. When the gap initiation penalty is 0, pairs of positions are identified as equivalent when they have their selected atoms at most 2 times gap_penalties_3d[1] angstroms apart in the current superposition, as described for the alignment.align3d() command. The new alignment is then used to generate the new superposition of the two averages, and the iteration of the distance matrix calculation, alignment and superposition is repeated until there are no changes in the number of equivalent positions and in the rotation matrix relating the two averages.
赞一下 回复此楼
9楼2012-03-03 20:33:20
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

nufang19a

金虫 (正式写手)
two structures：
If you wish such a superposition, you can use alignment.malign3d() with fit = False and write_fit = True (the meaning of fit is different between alignment.salign() and alignment.malign3d()).
赞一下 回复此楼
10楼2012-03-03 20:36:05
 已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖
相关版块跳转 我要订阅楼主 nufang19a 的主题更新
121/2返回列表12下一页
普通表情 龙 兔 虎 猫
信息提示
关闭
请填处理意见
关闭