A very old fashioned hands on way to do it.. Run distang Find those H2O which contact two protein molecules.. 5od5.pdb has 3 chains..
distang xyzin CCP4_DOWNLOADED_FILES/5od5.pdb > d You get a list like this Atom I Atom J Dij Sym TX TY TZ occ(i)*occ(j) av_bi+bj M 23 SD A S 40 OG A 2.954 X,Y,Z 1.00 69.64 I 26 N A N 148 OD1 A 2.702 X,Y,Z 1.00 39.22 S 27 N A K 38 O A 2.911 X,Y,Z 1.00 41.32 S 27 O A K 38 N A 2.789 X,Y,Z 1.00 38.33 S 29 N A L 36 O A 2.817 X,Y,Z 1.00 42.18 .... then for the HOH O 502 O A I 231 O A 2.282 X,Y,Z 1.00 49.74 O 502 O A G 32 CA B 2.710 X,Y,Z [-1 0+1] 1.00 53.59 O 503 O A D 39 CG A 2.973 X,Y,Z 1.00 42.27 O 503 O A D 39 OD1 A 2.470 X,Y,Z 1.00 39.89 Here HOH all labelled 501 on A B or C I cut out the HOH from d got rid of HOH to HOH checked for any with more than one link to protein * O 502 O A I 231 O A 2.282 X,Y,Z 1.00 49.74* * O. 502 O A G 32 CA B 2.710 X,Y,Z [-1 0+1] 1.00 53.59* O 503 O A D 39 CG A 2.973 X,Y,Z 1.00 42.27 O 503 O A D 39 OD1 A 2.470 X,Y,Z 1.00 39.89 O 503 O A D 39 OD2 A 2.782 X,Y,Z 1.00 39.34 O 503 O A Y 123 OH A 2.823 X,Y,Z 1.00 41.69 * O 504 O A D 62 OD1 A 2.520 X,Y,Z 1.00 32.93 O 504 O A K 52 NZ C 2.886 X,Y,Z 1.00 28.56* O 505 O A D 248 OD2 A 2.526 X,Y,Z 1.00 38.18 O 506 O A I 189 N A 2.723 X,Y,Z 1.00 40.59 O 507 O A D 248 N A 2.919 X,Y,Z 1.00 30.24 * O 510 O A D 65 OD2 A 2.636 X,Y,Z 1.00 32.75 O 510 O A D 111 OD2 C 2.795 X,Y,Z 1.00 34.55* .... O 505 O C K 306 NZ A 2.896 X,Y,Z [0+1 0] 1.00 50.02 O 505 O C D 264 OD2 C 2.542 X,Y,Z 1.00 51.45 ..... * O 526 O C N 90 N A 2.854 X,Y,Z 1.00 28.44 O 526 O C N 90 ND2 A 2.928 X,Y,Z 1.00 30.82 O 526 O C Z 407 O3 C 2.744 X,Y,Z 1.00 34.91* On Thu, 7 Nov 2024 at 10:38, Jon Cooper < 0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > Is it possible to extract this info from pdbepisa? > > Best wishes, Jon Cooper. > Emeritus at UCL. > > jon.b.coo...@protonmail.com > Sent from Proton Mail Android > > > -------- Original Message -------- > On 07/11/2024 09:31, Italo Carugo Oliviero wrote: > > Dear Tommi, > you could write a program (perhaps with ChatGPT) that (i) stores water > molecules, (ii) stores protein atoms, and (iii) searches, among the water > molecules, for those that are close to two protein atoms that belong to > different chains. > Oliviero > > Il giorno mer 6 nov 2024 alle ore 16:43 Kajander, Tommi A < > tommi.kajan...@helsinki.fi> ha scritto: > >> Dear all, >> >> >> >> Is there a something available to automatically >> analyse/identifiy/quantify bound (“bridging”) water molecules at >> protein-protein interfaces? Could not find anyting right away. >> >> >> >> Thanks in advance, >> >> Best, >> >> >> >> Tommi >> >> >> >> >> >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
