Hi Zuben, I think I “solved” the problem. Converting “closed.py” to “closed.pse” does the trick.
Many thanks for your suggestions George > On 14 Oct 2021, at 22:26, Brown, Zuben <zb2...@cumc.columbia.edu> wrote: > > Hi George, > > The image came through. > > I think the problem is that it is assigning the same chain ID to multiple > chains. Can you give each protein (open, closed) unique chain IDs and see if > the problem persists? > > best, > Zuben > From: Brown, Zuben <zb2...@cumc.columbia.edu> > Sent: Thursday, October 14, 2021 4:42 PM > To: George Tzotzos <gtzot...@me.com> > Cc: pymol-users@lists.sourceforge.net <pymol-users@lists.sourceforge.net> > Subject: Re: [PyMOL] [EXTERNAL] Superposition of native pdb to scripted pdb. > > Hi George, > > It seems that image can't be loaded, possibly due to security settings with > my email. > > Anyway, if the issue only occurs after running closed.py then that must be > the issue. I assume loading open.pdb and closed.pdb without that script > shows no issue. > > Without knowing what closed.py is doing, it will be hard to troubleshoot. > If it isn't a long script, then perhaps you could post it? > > Best wishes, > Zuben > From: George Tzotzos <gtzot...@me.com> > Sent: Thursday, October 14, 2021 2:29 PM > To: Brown, Zuben <zb2...@cumc.columbia.edu> > Cc: pymol-users@lists.sourceforge.net <pymol-users@lists.sourceforge.net> > Subject: Re: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb. > > Zuben, thank you for the prompt response. > > Perhaps, I didn’t describe well the problem. I’m attaching a snapshot showing > the loaded scripted structure (“closed.py". It shows anti-correlated movement > of backbone atoms of my protein in “closed” conformation. The same protein > also adopts an “open” conformation, say “open.pdb”. I know want to load > open.pdb in the same pymol session with closed.py. Upon opening/loading > open.pdb, the protein can be seen in the pymol window but it is total > garbled. Somehow, it seems that the script of closed.py affects the > appearance of open.pdb. That is before I even attempt to align the two > conformations. > > Once again, many thanks > > George > > <PastedGraphic-1.tiff> > > > >> On 14 Oct 2021, at 18:34, Brown, Zuben <zb2...@cumc.columbia.edu >> <mailto:zb2...@cumc.columbia.edu>> wrote: >> >> Have a look here to see if this is what you want: >> >> https://pymolwiki.org/index.php/Align >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Align&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=vRK3AvbEVUrswd78pyC5leKAJSWaMy8peponXB8jGzc&e=> >> Align - PyMOLWiki >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Align&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=vRK3AvbEVUrswd78pyC5leKAJSWaMy8peponXB8jGzc&e=> >> align performs a sequence alignment followed by a structural superposition, >> and then carries out zero or more cycles of refinement in order to reject >> structural outliers found during the fit.align does a good job on proteins >> with decent sequence similarity (identity >30%).For comparing proteins with >> lower sequence identity, the super and cealign commands perform better. >> pymolwiki.org >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__pymolwiki.org_&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=NCPUIQ7K4-QE9iT6xoqQh9_jfNLffrKYQEF65SyxhnE&s=G-DVox001clYfvlqDJi_SO3fjxMwUnWEXG1mDewzLoA&e=> >> >> best wishes, >> Zuben >> From: George Tzotzos via PyMOL-users <pymol-users@lists.sourceforge.net >> <mailto:pymol-users@lists.sourceforge.net>> >> Sent: Thursday, October 14, 2021 12:06 PM >> To: pymol-users@lists.sourceforge.net >> <mailto:pymol-users@lists.sourceforge.net> >> <pymol-users@lists.sourceforge.net >> <mailto:pymol-users@lists.sourceforge.net>> >> Subject: [EXTERNAL] [PyMOL] Superposition of native pdb to scripted pdb. >> >> Apologies if this is trivial but I’m rather new to Pymol. >> >> I’m loading a script (x.py) that allows me to visualise correlations in the >> atomic movements of my protein. I have no problems with this. >> >> My next task is to load the native pdb file (e.g y.pdb) of the same protein >> but in a different conformation. Once I do this, y.pdb comes out garbled. My >> goal is to superimpose the y to x to check if the atomic correlations >> correspond to the conformation of y. >> >> Many thanks in advance for any suggestions >> >> George >> >> >> >> >> _______________________________________________ >> PyMOL-users mailing list >> Archives: >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=V3QCdoTZnZUiJepLeIuFTYhGOyNdEmY0slebFRPGECw&e= >> >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=V3QCdoTZnZUiJepLeIuFTYhGOyNdEmY0slebFRPGECw&e=> >> >> Unsubscribe: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=FZ0aDkzSeZUxYs9UfM3YoG-Hj9tSNmJ-Zk8QG0Cq1Rc&e= >> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=N22QT8CBWdjggQkEdjgQ18HPQz9mEkU4Y-Y3TZtJ_cs&s=FZ0aDkzSeZUxYs9UfM3YoG-Hj9tSNmJ-Zk8QG0Cq1Rc&e=>
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