Messages

1

RNA structures (DSSR) / Re: Water molecules in DSSR

« on: August 18, 2015, 01:09:28 pm »

Hello Xiang-Jun,

I tried running DSSR on tRNAPhe 1EHZ and ribosome 1VQ8 with the option --water and I do not see differences from the standard DSSR output.
Just for information I used the command: x3dna-dssr --water --i=1EHZ.py.pdb -o=1EHZ.py.dssr.out.
I do not attach the output file as it is the same of a run without the --water option.

Luigi

2

RNA structures (DSSR) / Water molecules in DSSR

« on: August 17, 2015, 01:09:41 pm »

Hi Xiang-Jun,

is there an option in DSSR to obtain hydrogen bonds with nucleic acid atoms for crystallographic water molecules?

Best regards,

Luigi

3

RNA structures (DSSR) / Re: Issue with lattice contacts

« on: August 17, 2015, 01:03:34 pm »

Hi Xiang-Jun,

I apologize for the delay in the answer. I tried the new version and it works perfectly!

Thank you,

Luigi

4

RNA structures (DSSR) / Re: Issue with lattice contacts

« on: July 28, 2015, 05:26:12 am »

Hi Xiang-Jun,

thanks for the answer. Here's the "3HTS.py.pdb" file used as DSSR input.
Measuring the distance from the B000.A.DG.1. and ..A.DC.12. we get around 40 Å and not 2.84 Å as reported in the output in this line

1 sugar      O4'@.B000.A.DG.1.    ..A.DC.12.     2.84

Best regards,

Luigi

5

RNA structures (DSSR) / Issue with lattice contacts

« on: July 27, 2015, 01:56:54 pm »

Hello Xiang-Jun and congratulations for the NAR paper!
I came into a problem using DSSR on several small structures, I will show you 3HTS as example. The input is the following:

x3dna-dssr -i=/home//3HTS.py.pdb --segid --idstr=long --u-turn --more --non-pair --po4 --nested -o=3HTS.py.dssr.out

Here the fragment of the output file which causes me troubles:

****************************************************************************
List of 3 atom-base capping interactions
    dv: vertical distance of the atom above the nucleotide base
    -----------------------------------------------------------
     type       atom                 nt             dv
   1 sugar      O4'@.B000.A.DG.1.    ..A.DC.12.     2.84
   2 sugar      O4'@..A.DG.1.        .A00Z.A.DC.12. 2.84
   3 sugar      O4'@.B000.A.DG.1.    .B00A.A.DC.12. 2.84

****************************************************************************
I attached the output file "dssr-a2bases" to show you better the issue. In fact it seems that in the capping contact between the DG 1A and DC 12A there are some troubles related to the symmetry codes. If I open the file with PyMol generating symmetry mates, I find that the residue DG 1A with symmetry A00A is stacked over DC 12A, while in the dssr output the symmetric B000 is reported. I know it's a quite tricky matter and occurs only in small structures, but I still wanted to show it to you.

Thank you in advance for your answer

Luigi

6

RNA structures (DSSR) / Re: A small issue on capping interactions

« 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

7

RNA structures (DSSR) / 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