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Author Topic: A small issue on capping interactions  (Read 7224 times)

Offline Luigi

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A small issue on capping interactions
« on: March 16, 2015, 11:16:42 am »
Hello Xiang-Jun,

following your reply about the problem we had on capping interactions, we standardly use the option --polygon-offset=0 with DSSR. Anyway I came across an issue with the structure 4V9P (E. coliribosome, a mmCIF file), on the residue 488 in chain AA. As you can see in the attached picture, OP2 atom of the capping PO4 is slightly outside the guanine ring. Can you please have a look at it?

Thank you very much in advance,

Luigi

Offline xiangjun

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Re: A small issue on capping interactions
« Reply #1 on: March 16, 2015, 11:47:10 am »
Hi Luigi,

I am aware of such 'small issue' and that why I introduced the --polygon-offset option. It may not a bad idea to use a small number (e.g., 0.05 instead of zero) to avoid such surprises.

I will look into detail for your case when I have a more time, and follow back here. To verify for yourself, reset the two nucleotides in the base reference of G488 on chain AA, manually change the z-coordinate of the OP2 atom in question to 0.000, and see what you get in PyMOL/Jmol.

Xiang-Jun
« Last Edit: March 16, 2015, 02:28:05 pm by xiangjun »

Offline xiangjun

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Re: A small issue on capping interactions
« Reply #2 on: March 16, 2015, 02:40:33 pm »
Hi Luigi,

I realized that you are using PyMOL for visualization in its default mode. Simply do the following in PyMOL:

Code: [Select]
set orthoscopic, on
and regenerate the figure.

Also as I suggested previously, set the z-coordinate of the OP2 atom of G491 (chain AA) to zero when the two nts are set to the base reference frame of G488. In this case, no matter whether orthoscopic view is on or off, you will get the 'expected' result.

Please contribute a follow-up post with requested figures and the original PDB file, for future reference and the benefit of other users.

Best regards,

Xiang-Jun

Offline Luigi

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Re: A small issue on capping interactions
« Reply #3 on: March 17, 2015, 07:53:03 am »
Hi Xiang-Jun,

after many tests, I realized the result of this particular contact being included in our output was due to the absence of --polygon-offset=0 option which didn't apply weirdly for this structure. Re-running DSSR specifying the option excluded this from results. So in fact it was my mistake, I apologize for pointing it out. If it is not a big issue, I would like to have all the options used launching DSSR listed in the output, because for example --polygon-offset isn't listed even when I used it.

As a side note, the attached figure was already generated with orthoscopic view on and for that reason I showed it to you.

Thank you very much for your answers,

Luigi

Offline xiangjun

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Re: A small issue on capping interactions
« Reply #4 on: March 17, 2015, 08:24:43 am »
Quote
If it is not a big issue, I would like to have all the options used launching DSSR listed in the output, because for example --polygon-offset isn't listed even when I used it.

There are dozens of additional options in DSSR which are undocumented, some experimental, and several directly added for your purpose. DSSR aims for simplicity and the general audience at this stage, before a formal paper is published. I do respond to any questions users have, including unpublished results.

Quote
As a side note, the attached figure was already generated with orthoscopic view on and for that reason I showed it to you.

It seems different from my testing ... Any way, including the original PDB file for the image would help to clarify the issue.

Xiang-Jun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.