IFP-generation

[haoxuanluo731]

I use the pycharm,this is my .py

this is where is my problem happen

I check the traject.py,I think my problem is happen in this way

but my xtc is ok,so I want to know what happened

[StefanGIT]

Can you print out more information on the exception?
eg:
except Exception as inst:
print(type(inst)) # the exception type
print(inst.args) # arguments stored in .args
print(inst) # str allows args to be printed directly,
This would give more details on what goes wrong.

https://docs.python.org/3/tutorial/errors.html

[haoxuanluo731]

thank you very much，I use this method I find I have differernt number between topol and xtc ， I will check it ，if I have problem，I will tell you，thank you so much

[haoxuanluo731]

I also have question that I have generate dissociation pathways graph,and I also genertion IFp,so I want to know how to generate this picture in the article

[AegithalosCaudatus]

I myself had never done a picture like this, but it looks like they used pymol and put multiple frames of ligand in a surface representation (with some transparency and color).

[haoxuanluo731]

I myself had never done a picture like this, but it looks like they used pymol and put multiple frames of ligand in a surface representation (with some transparency and color).我自己从来没有画过这样的图片，但看起来他们使用了 pymol 并将多个配体框架放入表面表示中（具有一定的透明度和颜色）。

我在他们的文章中看到了他们是说将他映射到3Dmap上得到这个图，我在实例中找到了这段代码，

但我运行的时候显示错误

[StefanGIT]

The method Map_3D_grid is saving a trajectory data frame in a grid format. However it seems that your data frame does not contain data. You will need to check where this is lost in your code. It is impossible to overlook this from this small sample.

[haoxuanluo731]

I have get the dx file，how can i use this file to generate picture

[StefanGIT]

I think there are many tutorials on the internet on how to visualize volume data in pymol. Eg.: https://pymol.org/dokuwiki/doku.php?id=media:volumevisualization Kind regards

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________________________________ Von: haoxuanluo731 ***@***.***> Gesendet: Dienstag, 10. September 2024 03:51:52 An: HITS-MCM/MD-IFP Cc: Richter, Stefan; Comment Betreff: Re: [HITS-MCM/MD-IFP] IFP-generation (Issue #15) Diese E-Mail stammt von einem externen Absender. Bitte prüfen Sie den Absender genau, bevor Sie Anhänge oder Links öffnen! I have get the dx file，how can i use this file to generate picture — Reply to this email directly, view it on GitHub<#15 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABRB7RR7Z7ERVDTHSCW3XODZVZGDRAVCNFSM6AAAAABNSFSKBCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZZGQ2TENRVGM>. You are receiving this because you commented.Message ID: ***@***.***>

[haoxuanluo731]

thank you very much

[haoxuanluo731]

I have a question. I indeed opened this file in PyMOL. For example, my trajectory is divided into 8 categories, and the last 4 were obtained with 3Dcom. However, when I open it individually, it only appears as a plane. I'm wondering how I can combine this 3D surface with the ligand-protein that I need to achieve a figure similar to the one in your article. Another question is about the isosurface; I used different values, such as 1.5 and 2, to obtain different sizes of isosurfaces. What role does this isosurface play in this context?