pymol½Ì³Ì-09.7.23 - ͼÎÄ ÏÂÔØ±¾ÎÄ

¡·¡·¡·PyMOLÓû§Ö¸ÄÏ¡¶¡¶¡¶ 09.7.23

Çø±ðÓÚ¶ÔÏó£¨objects£©¡£¿ØÖÆÃæ°åµÄ²Ëµ¥Ñ¡Ïî¶ÔÔ­×ÓÑ¡ÔñºÍ¶ÔÏóÊDz»Í¬µÄ£¬ÒòΪÁ½ÕߵŦÄÜÓÐ

΢СµÄ²î±ð¡£Ñ¡ÔñÊǽ¨Á¢ÔÚ¶ÔÏóϵÄÒ»×éÊý¾ÝµÄÖ¸Ïò£¬µ±É¾³ý¶ÔÏó£¬Êý¾Ý¾Í²»ÔÙ¿ÉÓã¬ÈκÎÖ¸ÏòÕâЩÊý¾ÝµÄÑ¡ÔñÒ²¶¼²»ÔÙ¿ÉÓᣵ«Êǵ±É¾³ýÑ¡Ôñ£¬Êý¾ÝÈÔÈ»¿ÉÓá£Disable¶ÔÏóÊÇ´ÓviewerÏÔʾÖÐɾ³ýËü£¬¶ødisableÑ¡Ôñ½öÊǹرÕviewerÖиßÁÁÏÔʾѡÔñµÄ·Ûºìµã¡£

Ô­×ÓÑ¡ÔñÎÞÂÛÃüÃûÓë·ñ£¬¶¼ÄÜ¿çÔ½¶à¸ö¶ÔÏó£º PyMOL>load fc.pdb PyMOL>load pept.pdb

PyMOL>select alpha_c,name ca #Ñ¡Ôñ°üÀ¨ÁËÁ½¸ö¶ÔÏóÖеÄÔ­×Ó PyMOL>color red,name ca

Ô­×ÓÑ¡ÔñÔÚ·Ö×ӽṹ¸Ä±äºóÈÔÈ»×àЧ£º PyMOL>load pept.pdb

PyMOL>select bb,name c+n+o+ca

PyMOL>count_atoms bb #bbÖÐÊýÓÐ52¸öÔ­×Ó

PyMOL>remove resi 5 #´Ó¶ÔÏóÖÐɾ³ý²Ð»ù5ÖеÄËùÓÐÔ­×Ó PyMOL>count_atoms bb #ÏÖÔÚbbÖÐÊýÓÐ48¸öÔ­×Ó

Ô­×ÓÑ¡ÔñÊǾ²Ì¬µÄ£¨static£©£¬Ñ¡ÔñËù°üº¬µÄÔ­×Ó½ö½öÊÇÑ¡Ôñ±»¶¨Òåʱ¿Ì´æÔÚµÄÔ­×Ó£¬¶ø²»°üÀ¨ÆäËû£¬¼´Ê¹ÊÇÔÚÑ¡Ôñ·¶Î§ÄÚºóÀ´±»ÔØÈëµÄÔ­×ÓÒ²²»ÐÐ:

PyMOL>load pept.pdb

PyMOL>select 007,pept #´´½¨Ñ¡Ôñ¡°007¡±°üÀ¨ËùÓеÄÔ­×Ó PyMOL>count_atoms 007 #¡°007¡±ÖÐÊýÓÐ107¸öÔ­×Ó PyMOL>h_add #PyMOLÔÚºÏÊʵÄλÖüÓÇâ PyMOL>count_atoms 007 #¡°007¡±ÖÐÊýÓÐ107¸öÔ­×Ó

PyMOL>count_atoms #¶ø¡°pept¡±ÖÐÈ´ÊýÓÐ200¸öÔ­×Ó

Ô­×ÓÑ¡ÔñÄܹ»±»ºóÃæµÄÔ­×ÓÑ¡ÔñÀûÓãº

PyMOL>select bb,name n #Ñ¡Ôñ¡°bb¡±°üº¬ËùÓеªÔ­×Ó

PyMOL>select cc,bb or name o #Ñ¡Ôñ¡°cc¡±°üº¬ËùÓеªÔ­×ÓºÍÑõÔ­×Ó ×¢Ò⣺Âß¼­ÔËËã·û¡°or¡± ¡°and¡±µÄº¬ÒåµÈͬÓÚ´úÊýÖеġ°»ò¡±¡°ÇÒ¡±¡£

3) µ¥×Ö£¨single-word£©Ñ¡Ôñ·û

×î¼òµ¥µÄselection-expressionÊǵ¥×ÖÑ¡Ôñ·û£¬ÕâЩѡÔñ·ûûÓбêʶ·û¡£ µ¥×ÖÑ¡Ôñ·û ËõÂÔÑ¡Ôñ·û ÃèÊö all * µ±Ç°ÔØÈëPyMOLµÄËùÓÐÔ­×Ó none none ûÓÐÔ­×Ó,¿ÕÑ¡Ôñ hydro h. µ±Ç°ÔØÈëPyMOLµÄËùÓÐÇâÔ­×Ó É½¶«´óѧ ÉúÃü¿ÆÑ§Ñ§Ôº lswang lab

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¡·¡·¡·PyMOLÓû§Ö¸ÄÏ¡¶¡¶¡¶ 09.7.23

´ÓProtein Data Bank HETATM recordsÖÐÔØÈëµÄËùÓÐÔ­×Ó visible v. ÖÁÉÙÓÐÒ»Öֿɼû±íʾÐÎʽµÄenabled¶ÔÏóÖеÄËùÓÐÔ­×Ó present pr. µ±Ç°×´Ì¬ÏÂÓÐÈ·¶¨×ø±êµÄËùÓÐÔ­×Ó£¨ÓÃÓÚ´´½¨¶¯»­£© Ñ¡Ôñ·ûnoneÔÚÏòPyMOLÖ±½ÓÊäÈëÃüÁîʱ²»»á³öÏÖ£¬µ«ÔÚ³ÌÐò½Å±¾ÖÐÊ®·ÖÓÐÓᣠµ¥×ÖÑ¡Ôñ·ûÓÐËõÂÔÐÎʽ£¬Ò»Ð©ËõÂԴʺó±ØÐë¸ú×ÅÔ²µã»ò¿Õ¸ñ£¬ÓÃÀ´½ç¶¨×Ö·û¡£ËõÂԴʺͳ¤×Ö·ûµÈЧ£¬Ñ¡ÔñÄã×Ô¼ºÏ²»¶µÄÐÎʽ¼´¿É£º

PyMOL>color blue,all

PyMOL>color blue,* #ËùÓÐÔ­×Ó±ä³ÉÀ¶É«

PyMOL>hide hydro

PyMOL>hide h. #ËùÓеÄÇâÔ­×ӵıíʾÐÎʽ±»Òþ²Ø

PyMOL>show cartoon,hetatm #PDBÊäÈëÎļþÖб»¶¨ÒåΪHETATMµÄ PyMOL>show cartoon,het #ËùÓÐÔ­×ÓÏÔʾΪcartoon

4) ÊôÐÔÑ¡Ôñ·û

PyMOLÄܹ»¶ÁÈ¡PDB,MOL/SDF,Macromodel,ChemPy ModelºÍTinker XYZ¸ñʽµÄÊý¾ÝÎļþ¡£ÕâЩ¸ñʽÎļþµÄijЩÊý¾ÝÇøÔÊÐíPyMOLΪԭ×ÓÖ¸¶¨ÊôÐÔ¡£¸ù¾ÝÕâЩÊôÐÔ£¬Äã¿ÉÒÔÓ¦ÓÃÊôÐÔÑ¡Ôñ·ûºÍ±êʶ·û¶ÔÔ­×Ó½øÐзÖ×éºÍÑ¡Ôñ£ºÑ¡Ôñ·û¶ÔÓ¦ÓÚÊý¾ÝÎļþµÄÕâЩÊý¾ÝÇø£¬±êʶ·û¶ÔÓ¦ÓÚÆ¥ÅäµÄÄ¿±ê´Ê»òÄ¿±êÊý×Ö¡£

ÔÚ±êʶ·ûÁбíÖв»Í¬µÄÏîÄ¿½öÓá°+¡±Á¬½Ó£¬²»ÒªÓпոñ£¬Á¬ÐøµÄÑ¡ÔñÓá°-¡±Á¬½Ó£º PyMOL>select boy,resi 1+2+3 #²Ð»ù1¡¢2ºÍ3±»Ñ¡Ôñ PyMOL>select 007,resi 1-10 #²Ð»ù1µ½10±»Ñ¡Ôñ ½÷¼ÇÔÚͬһ±êʶ·ûºó²»¿Éͬʱ³öÏÖ¡°+¡±¡°-¡±£¬Èç¡°select bad£¬resi 1-4+9¡±¡£

¶ÔÓÚ¿Õ°×Êý¾ÝÇø£¬±êʶ·ûÊÇÒ»¶Ô¿ÕµÄË«ÒýºÅ£º

PyMOL>select blank,ss ¡°¡± #blank°üº¬·Ç¶þ¼¶½á¹¹µÄËùÓÐÔ­×Ó

´ó¶àÊýµÄÊôÐÔÑ¡Ôñ·ûÆ¥ÅäËüµÄ±êʶ·û£º ÊôÐÔÑ¡Ôñ·û ËõÂÔÐÎʽ ±êʶ·ûºÍ¾ÙÀý symbol e. Chemical-symbol-list µ¥×Öĸ»òË«×ÖĸµÄ»¯Ñ§ÔªËØ·ûºÅ PyMOL>select polar,symbol o+n name n. Atom-name-list µ°°×ºÍºËËáÖÐÖÁ¶à4×ÖĸµÄÔ­×Ó·ûºÅ PyMOL>select carbons,name ca+cb+cg resn r. Residue-name-list hetatm het ɽ¶«´óѧ ÉúÃü¿ÆÑ§Ñ§Ôº lswang lab

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¡·¡·¡·PyMOLÓû§Ö¸ÄÏ¡¶¡¶¡¶ 09.7.23

3×ÖĸµÄ°±»ùËá·ûºÅ PyMOL>select aas,resn asp+glu+asn+gln »òÖÁ¶à2×ÖĸµÄºËÜÕËá·ûºÅ PyMOL>select bases,resn a+g resi i. Residue-identifier-list ÖÁ¶à4λÊýµÄ²Ð»ùºÅ PyMOL>select boy,resi 1+10+100+1000 Residue-identifier-range PyMOL>select boy,resi 1-10 alt alt Alternate-conformation-identifier-list µ¥×Öĸ PyMOL>select altconf,alt a+¡¯¡® chain c. Chain-identifier-list µ¥×Öĸ»òÓÐʱÊÇÊý×Ö PyMOL>select 007,chain a segi s. Segment-identifier-list ÖÁ¶à4×Öĸ PyMOL>select ligand,segi lig flag f. Flag-number ´Ó0µ½31µÄµ¥ÕûÊý PyMOL>select f1,flag 0 numeric_type nt. Type-number µ¥ÕûÊý PyMOL>select f1,nt. 5 text_type tt. Type-string ÖÁ¶à4×Öĸ PyMOL>select subset,text_type HA+HC id id External-index-number µ¥ÕûÊý PyMOL>select idno,id 23 index idx. Internal-index-number µ¥ÕûÊý PyMOL>select intid,index 11 ss ss Secondary-structure-type µ¥×Öĸ PyMOL>select allstrs,ss h+s+l+¡¯¡® ÆäËûµÄÑ¡Ôñ·û¶ÔÓ¦ÓÚÊý×Ö±êʶ·û£º Êý×ÖÑ¡Ôñ·û ËõÂÔÐÎʽ Óï¾äºÍ¾ÙÀý b b Comparison-operator b-factor ¨Cvalue ʵÊý PyMOL>select fuzzy,b>10 Comparison-operator occupancy-value ʵÊý 19 / 39

q q ɽ¶«´óѧ ÉúÃü¿ÆÑ§Ñ§Ôº lswang lab

¡·¡·¡·PyMOLÓû§Ö¸ÄÏ¡¶¡¶¡¶ 09.7.23

formal_charge fc. partial_charge pc. PyMOL>select lowcharges,q<0.5 Comparison-operator formal charge-value ÕûÊý PyMOL>select doubles,fc.=-1 Comparison-operator partial charge-value ʵÊý PyMOL>select hicharges,pc.>1

5) Ñ¡Ôñ´úÊý

ͨ¹ýÂß¼­ÔËËã·ûµÄ×éºÏ£¬Ñ¡Ôñ¸ü¸»Óо«È·ÐÔ»ò°üº¬ÐÔ£¬ÕâЩËã·û¼´²¼¶ûËã·û°üÀ¨and£¬orºÍnot£¬ËüÃǵĺ¬ÒåºÍ´úÊýÖеġ°ÇÒ¡±¡°»ò¡±¡°·Ç¡±Í¬Òå¡£

ÔËËã·û£º

Ñ¡ÔñÔËËã·ûºÍ±êʶ·ûÁбíÈçÏ¡£ÐéÉèµÄ±äÁ¿s1ºÍs2´ú±íselection-expressions. ÔËËã·û ËõÂÔÐÎʽ Ч¹û Ñ¡Ôñ²»ÔÚs1ÖеÄÔ­×Ó not s1 ! s1 PyMOL>select sidechains,! bb Ñ¡Ôñs1ºÍs2Öй²ÓеÄÔ­×Ó s1 and s2 s1 & s2 PyMOL>select far_bb,bb&farfrm_ten s1¦òs2 Ñ¡Ôñs1ºÍs2ÖеÄËùÓÐÔ­×Ó s1 or s2 PyMOL>select all_prot,bb¦òsidechain Ñ¡Ôñs1Öбêʶ·ûname,resi,resn,chain,segiȫƥs1 in s2 s1 in s2 Åäs2µÄÔ­×Ó PyMOL>select same_atms,pept in prot Ñ¡Ôñs1Öбêʶ·ûnameºÍresiÆ¥Åäs2µÄÔ­×Ó s1 like s2 s1 l. s2 PyMOL>select similar_atms,pept like prot Ñ¡Ôñ·¶µÂ»ª°ë¾¶Óës1µÄ·¶µÂ»ª°ë¾¶ s1 gap x s1 gap x ÒÔ×îС¾àÀëx°£·ÖÀëµÄËùÓÐÔ­×Ó PyMOL>select farfrm_ten,resi 10 gap 5 Ñ¡ÔñÖÐÐÄÔÚÒÔs1ÈκÎÔ­×ÓΪÖÐÐÄ£¬ÒÔx°£Îª°ë¾¶µÄs1 around x s1 a. x ·¶Î§ÄÚµÄËùÓÐÔ­×Ó PyMOL>select near_ten,resi 10 around 5 ͨ¹ýÔÚÒÔs1ÈκÎÔ­×ÓΪÖÐÐÄ£¬ÒÔx°£Îª°ë¾¶µÄ·¶Î§s1 expand x s1 e. x ÄÚµÄËùÓÐÔ­×ÓÀ©³äs1 PyMOL>select near_ten_x,near 10 expand 3 s1 within x of s2 s1 w. x of Ñ¡Ôñs1ÖÐÔÚs2 x°£·¶Î§ÄÚµÄÔ­×Ó É½¶«´óѧ ÉúÃü¿ÆÑ§Ñ§Ôº lswang lab

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