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xuxm03

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#vmdĬÈÏʹÓÃstride¼ÆËãµ°°×¶þ¼¶½á¹¹£¬ÕâÀï¸ø³övmdÌá³ödssp¼ÆËãµÄ¶þ¼¶½á¹¹²¢Êä³öµ½Ò»¸öÎļþÖÐÓÃÓÚ×÷ͼ£¬ÎļþÊä³ö¸ñʽÀàËÆAmberµÄÊä³ö¸ñʽ£¬ÆäÖÐX´ú±í²»¹æÔò¾íÇú»òÕßloop£¬½«ÒÔÏ´úÂë±£´æÎªtest.tcl¿ÉÒÔÖ±½ÓÔÚÖÕ¶ËÏÂÔËÐÐÒÔÏÂÃüÁ
#vmd test.psf test.dcd -dispdev text -e test.tcl
#Èç¹ûÊÇamberµÄÍØÆËÎļþºÍ¹ì¼£ÔòΪ
#vmd -parm7 test.prmtop -crdbox test.mdcrd -dispdev text -e test.tcl
#Êä³öµÄÎļþΪsec4traj.txt
1 # dealing with data in DSSP file
2 proc myproc1 {a b framei} {
3 # creat a empty list
4 set newsecdata

    5 set linenumber 0
    6 foreach a $b {
    7 incr linenumber
    8 if {[string equal [string index $a 2] #]} {
    9 puts "The line number is $linenumber"
    10 set secdata [lrange $b $linenumber end]
    11 # puts $secdata
    12 foreach secinfo $secdata {
    13 set sectype [string index $secinfo 16]
    14 if {[string is space $sectype]} then {
    15 lappend newsecdata X
    16 } else {
    17 lappend newsecdata $sectype
    18 }
    19 }
    20 }
    21 }
    22 set mynewsecdata [join $newsecdata \t]
    23 set secdataframe [linsert $mynewsecdata 0 $framei]
    24 puts $secdataframe
    25 set sectraj [open sec4traj.txt a]
    26 puts $sectraj $secdataframe
    27 close $sectraj
    28 }
    29
    30 # generate each frame pdb file and analyze secondary structure with dssp
    31 set n [molinfo top get numframes]
    32 puts "===Analysis number of frames: $n"
    33 set myprotein [atomselect top protein]
    34 #write resids
    35 set myresids [lsort -integer -unique [$myprotein get resid]]
    36
    37 set sectraj [open sec4traj.txt w]
    38 puts $sectraj $myresids
    39 close $sectraj
    40
    41 #analysis of frames
    42 for { set i 0 } { $i < $n } { incr i } {
    43 $myprotein frame $i
    44 $myprotein update
    45 $myprotein writepdb myptrotein_$i.pdb
    46 exec mkdssp -i myptrotein_$i.pdb -o myptrotein_$i.dssp
    47
    48 set dsspfile [open myptrotein_$i.dssp r]
    49 set dsspline [read $dsspfile ]
    50 set dsspdata [split $dsspline \n]
    51 close $dsspfile
    52 myproc1 splitdata $dsspdata $i
    53
    54
    55 file delete myptrotein_$i.pdb
    56 file delete myptrotein_$i.dssp
    57 }
7Â¥2013-08-01 18:10:33
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emrecoba

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jiaoyixiong: ½ð±Ò+2, ¹ÄÀø½»Á÷ 2013-07-27 08:39:28
lingogo: ½ð±Ò+15, ¡ï¡ï¡ïºÜÓаïÖú 2013-07-30 18:48:58
Â¥Ö÷¿ÉÒÔ¿¼ÂÇDSSP. ÕâÀïÊÇÁ´½Óhttp://swift.cmbi.ru.nl/gv/dssp/
2Â¥2013-07-27 02:00:28
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caozx

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lingogo: ½ð±Ò+10, ¡ï¡ï¡ïºÜÓаïÖú 2013-08-01 16:11:15
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childsliu

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¶þµ±¼ÒµÄ

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lingogo: ½ð±Ò+5, ¡ï¡ï¡ïºÜÓаïÖú 2013-08-01 16:11:13
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