From: <ang...@ua...> - 2006-10-28 18:17:51
|
I found a funny behaviour of "rockets" on 2hhd.pdb, chain C Try this:=20 load 2hhd.pdb; restrict *:C; select all; spacefill off; select hetero and not solvent; spacefill on; select protein; cartoons on; rockets on; =20 There are two stretches of alpha helix separated by a turn around = residue nr. 74. Jmol (both 10.2 and 10.9.87) is assigning an alpha = secondary structure to the turn. As a consequence, instead of two = rockets one gets only one, avoiding the full path of the two helices and = crossing right through the heme group.=20 I know rockets are not meant to be too faithful to structure, but this = is extreme. Very unpedagogical! =20 |
From: Bob H. <ha...@st...> - 2006-10-29 13:18:53
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Herr=E1ez S=E1nchez Angel wrote: >I found a funny behaviour of "rockets" on 2hhd.pdb, chain C > >Try this:=20 > >load 2hhd.pdb; > >restrict *:C; > >select all; spacefill off; > >select hetero and not solvent; spacefill on; > >select protein; cartoons on; rockets on; > > =20 > I'm not seeing what you want me to see. load 2hhd.pdb;display *:C;center visible; restrict none;select hetero and not solvent;wireframe on select protein;cartoons on;rockets on select 74;color yellow moveto 1.0 { 494 537 684 93.7} 200.0 {-0.3075999 23.937828 48.634956} 52= .4; This looks perfectly fine to me. The turn at 74 is there. I got my 2hhd.pdb file from the AJAX connection at http:www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm Do we have the same files? Bob >=20 > >There are two stretches of alpha helix separated by a turn around residu= e nr. 74. Jmol (both 10.2 and 10.9.87) is assigning an alpha secondary st= ructure to the turn. As a consequence, instead of two rockets one gets on= ly one, avoiding the full path of the two helices and crossing right thro= ugh the heme group.=20 > >I know rockets are not meant to be too faithful to structure, but this i= s extreme. Very unpedagogical! > >=20 > > >------------------------------------------------------------------------= - >Using Tomcat but need to do more? Need to support web services, security= ? >Get stuff done quickly with pre-integrated technology to make your job e= asier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geroni= mo >http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 121642 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > =20 > |
From: <rh...@fl...> - 2006-10-29 16:28:02
|
Quoting Bob Hanson <ha...@st...>: > Herr=E1ez S=E1nchez Angel wrote: > >> I found a funny behaviour of "rockets" on 2hhd.pdb, chain C > I'm not seeing what you want me to see. > > load 2hhd.pdb;display *:C;center visible; > restrict none;select hetero and not solvent;wireframe on > select protein;cartoons on;rockets on > select 74;color yellow > moveto 1.0 { 494 537 684 93.7} 200.0 {-0.3075999 23.937828 48.634956} 52.= 4; > > This looks perfectly fine to me. The turn at 74 is there. > > I got my 2hhd.pdb file from the AJAX connection at > > http:www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm > > Do we have the same files? > If I use the PDB format file provided by the RCSB FTP server for the =20 asymmetric unit I observe the same as Angel. If I use the PDB format =20 file of the biological unit the helix is split up into 3 helices. Comparison of the files shows that the asymmetric unit file doesn't =20 contain any secondary structure records but the biological unit file =20 does. Regards, Rolf ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
From: Bob H. <ha...@st...> - 2006-10-29 23:33:25
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Ah, yes, using AJAX I would have been using the CIF file. As Rolf points out, the PDB file does not have secondary structure=20 information, so Jmol is assigning it. Jmol is inappropriately assigning a SINGLE=20 helix to what is either a helix-turn-helix or helix-helix-helix sequence. I'll look into why Jmol assigned one single helix to that run. Bob rh...@fl... wrote: >Quoting Bob Hanson <ha...@st...>: > > =20 > >>Herr=E1ez S=E1nchez Angel wrote: >> >> =20 >> >>>I found a funny behaviour of "rockets" on 2hhd.pdb, chain C >>> =20 >>> > > =20 > >>I'm not seeing what you want me to see. >> >>load 2hhd.pdb;display *:C;center visible; >>restrict none;select hetero and not solvent;wireframe on >>select protein;cartoons on;rockets on >>select 74;color yellow >>moveto 1.0 { 494 537 684 93.7} 200.0 {-0.3075999 23.937828 48.634956} = 52.4; >> >>This looks perfectly fine to me. The turn at 74 is there. >> >>I got my 2hhd.pdb file from the AJAX connection at >> >>http:www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm >> >>Do we have the same files? >> >> =20 >> > >If I use the PDB format file provided by the RCSB FTP server for the =20 >asymmetric unit I observe the same as Angel. If I use the PDB format =20 >file of the biological unit the helix is split up into 3 helices. > >Comparison of the files shows that the asymmetric unit file doesn't =20 >contain any secondary structure records but the biological unit file =20 >does. > >Regards, >Rolf > >---------------------------------------------------------------- >This message was sent using IMP, the Internet Messaging Program. > > >------------------------------------------------------------------------= - >Using Tomcat but need to do more? Need to support web services, security= ? >Get stuff done quickly with pre-integrated technology to make your job e= asier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geroni= mo >http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 121642 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > =20 > |
From: Bob H. <ha...@st...> - 2006-10-30 00:42:52
|
This is going to be an interesting challenge, and I will need the help=20 of some biomolecular scientist types. Someone explain to me how psi and phi are related to helix structure. The problem is, I think, that Jmol is two-fold: 1) Jmol is using a very simplistic idea of what a helix is 2) Jmol does not recognize that although there is a broad range of=20 possibilities for phi and psi, a given helix should only have a certain=20 subset of that range. 3) Once a residue is assigned "helix" it doesn't matter what subtype it i= s. Bob rh...@fl... wrote: >Quoting Bob Hanson <ha...@st...>: > > =20 > >>Herr=E1ez S=E1nchez Angel wrote: >> >> =20 >> >>>I found a funny behaviour of "rockets" on 2hhd.pdb, chain C >>> =20 >>> > > =20 > >>I'm not seeing what you want me to see. >> >>load 2hhd.pdb;display *:C;center visible; >>restrict none;select hetero and not solvent;wireframe on >>select protein;cartoons on;rockets on >>select 74;color yellow >>moveto 1.0 { 494 537 684 93.7} 200.0 {-0.3075999 23.937828 48.634956} = 52.4; >> >>This looks perfectly fine to me. The turn at 74 is there. >> >>I got my 2hhd.pdb file from the AJAX connection at >> >>http:www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm >> >>Do we have the same files? >> >> =20 >> > >If I use the PDB format file provided by the RCSB FTP server for the =20 >asymmetric unit I observe the same as Angel. If I use the PDB format =20 >file of the biological unit the helix is split up into 3 helices. > >Comparison of the files shows that the asymmetric unit file doesn't =20 >contain any secondary structure records but the biological unit file =20 >does. > >Regards, >Rolf > >---------------------------------------------------------------- >This message was sent using IMP, the Internet Messaging Program. > > >------------------------------------------------------------------------= - >Using Tomcat but need to do more? Need to support web services, security= ? >Get stuff done quickly with pre-integrated technology to make your job e= asier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geroni= mo >http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 121642 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > =20 > |
From: Bob H. <ha...@st...> - 2006-10-30 01:30:09
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ah, and I notice that cartoonRockets don't display/hide properly. Herr=E1ez S=E1nchez Angel wrote: >I found a funny behaviour of "rockets" on 2hhd.pdb, chain C > >Try this:=20 > >load 2hhd.pdb; > >restrict *:C; > >select all; spacefill off; > >select hetero and not solvent; spacefill on; > >select protein; cartoons on; rockets on; > >=20 > >There are two stretches of alpha helix separated by a turn around residu= e nr. 74. Jmol (both 10.2 and 10.9.87) is assigning an alpha secondary st= ructure to the turn. As a consequence, instead of two rockets one gets on= ly one, avoiding the full path of the two helices and crossing right thro= ugh the heme group.=20 > >I know rockets are not meant to be too faithful to structure, but this i= s extreme. Very unpedagogical! > >=20 > > >------------------------------------------------------------------------= - >Using Tomcat but need to do more? Need to support web services, security= ? >Get stuff done quickly with pre-integrated technology to make your job e= asier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geroni= mo >http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 121642 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > =20 > |