Subject: [PyMOL] Superimpoition problem Use first structure for reference and then align rest of them to first one.
--- pymol-users-requ...@lists.sourceforge.net wrote: > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, > visit > > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body > 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ad...@lists.sourceforge.net > > When replying, please edit your Subject line so it > is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. Lists vs Tuples inconsistency in > cmd.load_cgo() (Terry Jones) > 2. problems with pymol installation (Savvas N. > Savvides) > 3. (no subject) (O. J. Ganesh) > 4. Superimpoition problem (chiradip chatterjee) > > --__--__-- > > Message: 1 > Date: Mon, 29 May 2006 10:01:24 +0200 > From: Terry Jones <tc...@cam.ac.uk> > To: pymol-users@lists.sourceforge.net > CC: djs...@cam.ac.uk > Reply-To: tc...@cam.ac.uk > Subject: [PyMOL] Lists vs Tuples inconsistency in > cmd.load_cgo() > > I spent quite a bit of time last night chasing down > the following. This: > > cmd.load_cgo([SPHERE, 0.0, 0.0, 0.0, 1.0], 'a') > > puts a sphere on the screen as expected. But this: > > cmd.load_cgo((SPHERE, 0.0, 0.0, 0.0, 1.0), 'a') > > seemingly has no effect at all. I.e., if you pass a > tuple instead of a > list, your CGO is not displayed. It's an easy > mistake to make (supposing it > should be called a mistake), and it's not easy to > figure out why your CGO > does not appear. > > The reason seems to be an if(PyList_Size(pycgo) test > on line 440 of > layer2/ObjectCGO.c in the 0.99 release - at least > that's as far as I went > in tracing this. > > Is there any reason why a tuple cannot be used here > too? > > Regards, > Terry > > > --__--__-- > > Message: 2 > Reply-To: <savvas.savvi...@ugent.be> > From: "Savvas N. Savvides" > <savvas.savvi...@ugent.be> > To: <pymol-users@lists.sourceforge.net> > Date: Mon, 29 May 2006 12:36:08 +0200 > Organization: Ghent University > Subject: [PyMOL] problems with pymol installation > > This is a multi-part message in MIME format. > > ------=_NextPart_000_0036_01C6831C.78CBC160 > Content-Type: text/plain; > charset="us-ascii" > Content-Transfer-Encoding: 7bit > > Dear colleagues, > I am trying to install pymol v0.99 on a new laptop > running windows XP > but the installer keeps giving an error message that > my specified path > does not exist. This is quite striking to me because > the extracted files > do indeed have the path that the installer is > complaining about! So the > path does exist! Upon restarting the computer > hoping to solve the > problem with path recognition, I get a system error > about the ntvdm.exe > emulator. Is this a related problem? Would that also > be a sign that I > should reinstall the operating system from scratch? > I just got the > computer and this may be the most appropriate time > to do it. > > Thanks in advance for any input > Savvas > > ----- > Savvas N. Savvides > Professor of Structural Biology > Ghent University > Laboratory for Protein Biochemistry > K.L.Ledeganckstraat 35 > 9000 Ghent, BELGIUM > Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 > FAX: +32-(0)9-264.53.38 > Email: savvas.savvi...@ugent.be > > > ------=_NextPart_000_0036_01C6831C.78CBC160 > Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"> > <HTML> > <HEAD> > <META HTTP-EQUIV=3D"Content-Type" > CONTENT=3D"text/html; = > charset=3Dus-ascii"> > <META NAME=3D"Generator" CONTENT=3D"MS Exchange > Server version = > 6.0.4630.0"> > <TITLE>problems with pymol installation</TITLE> > </HEAD> > <BODY> > <!-- Converted from text/rtf format --> > > <P><FONT SIZE=3D2 FACE=3D"Arial">Dear > colleagues,</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">I am trying to > install pymol v0.99 on = > a new laptop running windows XP but the installer > keeps giving an error = > message that my specified path does not exist. This > is quite striking to = > me because the extracted files do indeed have the > path that the = > installer is complaining about! So the path does > exist! Upon = > restarting the computer hoping to solve the problem > with path = > recognition, I get a system error about the > ntvdm.exe emulator. Is this = > a related problem? Would that also be a sign that I > should reinstall the = > operating system from scratch? I just got the > computer and this may be = > the most appropriate time to do it.</FONT></P> > > <P><FONT SIZE=3D2 FACE=3D"Arial">Thanks in advance > for any input</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">Savvas</FONT> > </P> > > <P><FONT SIZE=3D2 FACE=3D"Arial">-----</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">Savvas N. > Savvides</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">Professor of > Structural Biology</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">Ghent > University</FONT> > > <BR><FONT SIZE=3D2 FACE=3D"Arial">Laboratory for > Protein = > Biochemistry</FONT> > > <BR><SPAN LANG=3D"nl"><FONT SIZE=3D2 > FACE=3D"Arial">K.L.Ledeganckstraat = > 35</FONT></SPAN> > > <BR><SPAN LANG=3D"nl"><FONT SIZE=3D2 > FACE=3D"Arial">9000 Ghent, = > BELGIUM</FONT></SPAN> > > <BR><SPAN LANG=3D"nl"><FONT SIZE=3D2 > FACE=3D"Arial">Phone: = > +32-(0)9-264.51.24 ; > +32-(0)472-92.85.19</FONT></SPAN> > > <BR><SPAN LANG=3D"fr"><FONT SIZE=3D2 > FACE=3D"Arial">FAX: = > +32-(0)9-264.53.38</FONT></SPAN> > === message truncated === __________________________________________________ Do You Yahoo!? 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