Re: [PyMOL] [EXTERNAL] Superposition of native pdb to scripted pdb.

[George T. <gtz...@me...>]

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 <zb...@cu...> 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 <zb...@cu...>
> Sent: Thursday, October 14, 2021 4:42 PM
> To: George Tzotzos <gtz...@me...>
> Cc: pym...@li... <pym...@li...>
> 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 <gtz...@me...>
> Sent: Thursday, October 14, 2021 2:29 PM
> To: Brown, Zuben <zb...@cu...>
> Cc: pym...@li... <pym...@li...>
> 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 <zb...@cu... <mailto:zb...@cu...>> 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 <pym...@li... <mailto:pym...@li...>>
>> Sent: Thursday, October 14, 2021 12:06 PM
>> To: pym...@li... <mailto:pym...@li...> <pym...@li... <mailto:pym...@li...>>
>> 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
>> 
>> 
>> 
>> 
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