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nufang19a

½ð³æ (ÕýʽдÊÖ)


[½»Á÷] ¡¾ÌÖÂÛ¡¿ÔÚ´´½¨¼ØÀë×ÓͨµÀµ°°×ËľÛÌåʱ³öÏÖÎÊÌâ ÒÑÓÐ3È˲ÎÓë

ÔÚ´´½¨¼ØÀë×ÓͨµÀµ°°×ËľÛÌåʱ³öÏÖÎÊÌ⣬ÎÒ°´ÕÕtutorial²Ù×÷µÄ¹ý³ÌÈçÏ£º
ÔÚ01-BUILDĿ¼Ï£º
vmd
Extensions ¡ª¡ª¡·Tk Console
mol load pdb 1K4C.pdb
set all [atomselect top all]
$all set segname A
$all writepdb KCSA-A.pdb
$all delete

set sel [atomselect top "all and not name K"]
$sel set segname B
$sel move {{-1.0 0.0 0.0 310.66} {0.0 -1.0 0.0 310.66}
{0.0 0.0 1.0 0.0} {0.0 0.0 0.0 1.0}}
$sel writepdb KCSA-B.pdb
$sel delete

mol delete top
mol load pdb 1K4C.pdb
set sel [atomselect top "all and not name K"]
$sel set segname C
$sel move {{0.0 -1.0 0.0 310.66} {1.0 0.0 0.0 0.0}
{0.0 0.0 1.0 0.0} {0.0 0.0 0.0 1.0}}
$sel writepdb KCSA-C.pdb
$sel delete

mol delete top
mol load pdb 1K4C.pdb
set sel [atomselect top "all and not name K"]
$sel set segname D
$sel move {{0.0 1.0 0.0 0.0} {-1.0 0.0 0.0 310.66}
{0.0 0.0 1.0 0.0} {0.0 0.0 0.0 1.0}}
$sel writepdb KCSA-D.pdb
$sel delete

Exit VMD

cat KCSA-A.pdb KCSA-B.pdb KCSA-C.pdb KCSA-D.pdb
> KCSA.pdb

gedit KCSA.pdb£¬È»ºó
delete the lines:
END
CRYST1 155.330 155.330 76.270 90.00 90.00 90.00 P 1 1
Ôٴ洢ΪKCSA-ALL.pdb

ÔÙ´ÎÔÚÔÚ01-BUILDĿ¼Ï´ò¿ªVMD£¬·¢ÏÖKCSA-ALL.pdb²»ÊÇËľÛÌå¹¹Ïó

¶ø01-BUILDĿ¼µÄexample-outÀïµÄKCSA-ALL.pdbÓÃvmd´ò¿ªºóÊÇËľÛÌå¹¹Ïó£º


ÎҲ鿴ÁËÎÒµÄKCSA-A.pdb  KCSA-B.pdb   KCSA-C.pdb   KCSA-D.pdb ×ø±ê£¬·¢ÏÖ×ø±êûÓÐÖØ¸´µÄ°¡¡£È»ºóÓÃVMDÒÀ´Î´ò¿ª·¢ÏÖÕýºÃ¿ÉÒÔ¹¹³ÉÒ»¸öËľÛÌåµÄ¹¹Ï󣬶øÇÒºÍexample-outÀïµÄKCSA-ALL.pdbÒ»Ñù¡£ÕâÊÇÒÀ´Î´ò¿ªºóËù¹¹³ÉµÄͼÇë¿´£º

»Ø¸´´ËÂ¥

» ²ÂÄãϲ»¶

» ±¾Ö÷ÌâÏà¹Ø¼ÛÖµÌùÍÆ¼ö£¬¶ÔÄúͬÑùÓаïÖú:

ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

nufang19a

½ð³æ (ÕýʽдÊÖ)


ÎÒÓÖ¶Ô±ÈÁËexample-outputÀïµÄKCSA-ALL.pdbºÍ×Ô¼ºÉú³ÉµÄKCSA-ALL.pdb,Ã»Ê²Ã´Çø±ð°¡£¿£¿ÕâÊÇÔõô»ØÊ°¡£¿£¿
3Â¥2010-11-10 15:49:36
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû
²é¿´È«²¿ 6 ¸ö»Ø´ð

nufang19a

½ð³æ (ÕýʽдÊÖ)


¸ßÊÖ°ïæÕï¶ÏÒ»ÏÂÊDz»ÊÇÎÒµÄVMD³öÏÖÁËbug£¿£¿ÎÒÐèÒª»»°æ±¾Â𣿣¿
2Â¥2010-11-10 15:45:33
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

wally8962

ľ³æ (ÖøÃûдÊÖ)

¡ï
Сľ³æ(½ð±Ò+0.5):¸ø¸öºì°ü£¬Ð»Ð»»ØÌû½»Á÷
END
CRYST1 155.330 155.330 76.270 90.00 90.00 90.00 P 1 1

ÕâÑùµÄÎÄ×ÖÄãɾµôÁ˼¸·Ý£¿

ºÜÆæ¹ÖtutÀïÃæ½ÌµÄ×ö·¨
4Â¥2010-11-10 17:28:12
ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû

nufang19a

½ð³æ (ÕýʽдÊÖ)


Òѽâ¾ö£¬¾ÍÊÇ´¦ÓÚsegementAÓëB BÓëC CÓëDÖ®¼äµÄ
END
CRYST1 155.330 155.330 76.270 90.00 90.00 90.00 P 1 1
ÎÒûÊÕɾ³ý¡£ÕâÑùVMD¶ÁÈ¡·Ö×Óʱ¶Áµ½END¾Í»áÍ£Ö¹£¬¶øµ¼Ö³öÀ´µÄ²»ÊÇËľÛÌå¹¹Ïó¡£
×Ô¼ºÌ«´ÖÐÄÁË£¬Ã»ºÃºÃÀí½âÕâ¾ä»°£º
Using a text editor open the file KCSA.pdb, search for END and delete the
lines:
END
CRYST1 155.330 155.330 76.270 90.00 90.00 90.00 P 1 1
that are between segments A and B, B and C, as well as those found
between segments C and D.
ÖÕÓÚ¿Ë·þÁË¡£
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ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû
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