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Messages - febos

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1
RNA structures (DSSR) / Re: DSSR multiplets
« on: October 08, 2017, 02:25:35 pm »
Dr. Lu,

That's it! Thank you!

Respectfully,
Eugene

2
RNA structures (DSSR) / Re: DSSR multiplets
« on: October 08, 2017, 12:15:49 pm »
Dr. Lu,

I'm sorry for not being clear. By "aligned" I mean that if I take several base triples from an arbitrary dssr-multiplets.pdb file and look at them in Jmol - they appear aligned. So my question is about processing coordinates of the nucleotides - the coordinates of nucleotides in dssr-multiplets.pdb are different from initial PDB entry. Could you please explain what transformation DSSR performs in there?

Respectfully,
Eugene

3
RNA structures (DSSR) / DSSR multiplets
« on: October 08, 2017, 10:57:50 am »
Dear Dr. Lu,

At the moment I study RNA base triples found in RNA-containing PDB entries using DSSR. I and my students have created a new classification of base triples with respect to secondary structure environment of their nucleotides and now we are planning to implement the classification within our database's web-interface.
We thought it would be helpful to include the 3D visualization of an arbitrary set of aligned base triples and while working on that problem I've noticed that DSSR stores aligned base triples within its output file named dssr-multiplets.pdb.
Could you please tell me how you align multiplets in DSSR? Unfortunately I couldn't have found this information in DSSR tutorials.

Thanks in advance.

Respectfully,
Eugene

4
RNA structures (DSSR) / Re: "malloc failure"
« on: February 01, 2017, 12:45:47 pm »
Good afternoon, Dr. Lu

At first i have not thought about memory since problematic entries were not the largest ones. Now I understand that when i run DSSR i have had some other heavy processes running. I tried to stop them and run DSSR on 5tgm again. It worked just fine.
Thank you and please sorry for bothering.

Eugene

5
RNA structures (DSSR) / "malloc failure"
« on: January 31, 2017, 08:33:37 am »
Good afternoon, Dr. Lu

i have found a problem with some pdb entries (around 50 different entries).
For example:
entry 5tgm:
Quote
x3dna-dssr-170122 -i=5tgm.cif1 --idstr=long --more -o=5tgm0122.out1

Processing file '5tgm.cif1'
allocate_atoms_array(): malloc failure (411589)

Time used: 00:00:00:05

this problem holds within at least three last versions of DSSR (17jan22, 16nov19, 16oct19).

Could you please explain this issue?

thanks in advance,
Eugene

6
RNA structures (DSSR) / Re: non-one-char chain identifiers
« on: January 25, 2016, 08:13:10 am »
Good afternoon, Dr. Lu

Sorry for late reply.
This fix should be great.

Just in case:
In pdb entries I saw chain identifiers up to 4 chars (I do not know if it can be longer or not, but 4 is the largest I have seen).
Does the last update of DSSR take it into consideration?

Best regards,
Eugene

7
RNA structures (DSSR) / non-one-char chain identifiers
« on: January 24, 2016, 12:45:05 pm »
Good afternoon, Dr. Lu

I've noticed an issue with long chain identifiers in the section with dot-brackets.

Example:
Entry - 1VY6

fragment from DSSR output header:
Code: [Select]
no. of DNA/RNA chains: 12 [AA=1498,AV=13,AW=2,AX=76,BA=2819,BB=120,CA=1503,CV=12,CW=2,CX=76,DA=2800,DB=120]fragments from dbn section:
Code: [Select]
>1vy6-1-A #1 nts=1498 [chain] RNA*
>1vy6-1-A #2 nts=13 [chain] RNA
>1vy6-1-A #3 nts=2 [chain] RNA
>1vy6-1-A #4 nts=76 [chain] RNA
>1vy6-1-B #5 nts=2819 [chain] RNA*
>1vy6-1-B #6 nts=120 [chain] RNA
>1vy6-1-C #7 nts=1503 [chain] RNA*
>1vy6-1-C #8 nts=12 [chain] RNA
>1vy6-1-C #9 nts=2 [chain] RNA
>1vy6-1-C #10 nts=76 [chain] RNA
>1vy6-1-D #11 nts=2800 [chain] RNA*
>1vy6-1-D #12 nts=120 [chain] RNA

I cannot recover one-to-one correspondence from these lines. I mean, of course in the given case i am able to find correspondence not from identifiers but from lengths, but this is just a lucky example.
Could you fix this, please?


Best regards,
Eugene

8
RNA structures (DSSR) / Re: Strange bp parameters in 1FFK
« on: November 06, 2015, 11:14:47 am »
Dr. Lu,

Thank you for your explanation.
I will read those blog posts and the article of Richardson.
I think I will be able to understand the difference between two sets of parameters after that.

Best regards,
Eugene

9
RNA structures (DSSR) / Strange bp parameters in 1FFK
« on: November 05, 2015, 03:33:58 am »
Good Afternoon, Dr. Lu.

I've noticed some strange numbers in the 1st bp in the 1FFK file (in pdb format):

Code: [Select]
   nt1            nt2           bp  name        Saenger    LW  DSSR
   1 .0.U.12.       .0.G.531.      U-G --          n/a       tHS  tM-m
       [-171.2(anti) ~C3'-endo lambda=8.4] [-159.4(anti) ~C3'-endo lambda=97.9]
       d(C1'-C1')=10.93 d(N1-N9)=9.76 d(C6-C8)=10.33 tor(C1'-N1-N9-C1')=-76.3
       H-bonds[1]: "O4(carbonyl)-N2(amino)[2.99]"
       interBase-angle=12  Simple-bpParams: Shear=-7.49 Stretch=3.77 Buckle=-5.4 Propeller=10.8
       bp-pars: [-7.75   -3.20   0.40    -11.69  2.97    -4.39]

in all other basepairs there is a respectivity (is it a right word?) between "Shear=" and №1 of "bp-pars"; "Stretch=" and №2; "Buckle=" and №4; "Propeller=" and №5.
But in this bp there is no such thing. Do I missing something or it is in fact a bug? And which parameters are actually real?

Best regards,
Eugene

10
RNA structures (DSSR) / exotic CIF format
« on: September 06, 2015, 07:53:49 am »
Good Afternoon!

I'd like to draw Your attention to structure 5AJ0 (http://www.rcsb.org/pdb/files/5AJ0.cif).
Its mmCIF file contains exotic row orderings in its tables and DSSR is not capable to parse it in right way.
For instance, in its "_atom_site" table words "ATOM/HETATM" are not first words in line.

Best wishes
Eugene

11
Good afternoon Dr. Xiang-Jun Lu

I want to report some unusual behaviour of DSSR (latest version - Apr 19)

If I run DSSR without option --altloc=smth on pdb-file in which this option is needed - the console ouput looks something like " no ATOM/HETATM entries found. Time used 00:00:00" and out-file isn't created. But: in the latest version in this case my script gets from DSSR returnvalue=0 (there was not any error). In previous versions (particularly jan 25) my script got returnvalue=1 in such cases (program finished with error).

I need to get returnvalue=1 in such cases so my script can identify when --altloc is needed.

Could you please fix this?

Best regards,
Eugene.

12
Related topics / Re: What other software is available?
« on: February 05, 2014, 01:21:46 am »
Thanks, Dr. Lu

13
Related topics / Re: What other software is available?
« on: February 04, 2014, 09:24:03 am »
Good Afternoon Dr. Lu.

Do you know any tools or programs which are similar to DSSR? (Especially for determining base-pairs from pdb-file).
DSSR is great for me but I need to know that it's the best and so far I could not find other programs.

Best regards,
Eugene

14
RNA structures (DSSR) / Re: Question on Multiplets
« on: January 29, 2014, 12:38:41 am »
Dr.Lu,

I looked at this file in Jmol and now I understand Your definition.

Thanks for Your help.

Best regards,
Eugene

15
RNA structures (DSSR) / Question on Multiplets
« on: January 28, 2014, 01:10:51 pm »
Good Afternoon, Dr. Lu

I found out that multiplets in DSSR (beta-r29-on-20140106) can intersect each other, example in 2RSK (model 8 ):
Code: [Select]
****************************************************************************
List of 4 multiplet(s)
   1 nts=4 GGGG [8.A.G.2.+8.A.G.5.+8.A.G.8.+8.A.G.11.]
   2 nts=4 GGGG [8.B.G.14.+8.B.G.17.+8.B.G.20.+8.B.G.23.]
   3 nts=7 GAGAGAG [8.A.G.1.+8.A.A.3.+8.A.G.4.+8.A.A.6.+8.A.G.7.+8.A.A.9.+8.A.G.10.]
   4 nts=10* AAAGAGAGAG [8.A.A.3.+8.A.A.6.+8.A.A.9.+8.B.G.13.+8.B.A.15.+8.B.G.16.+8.B.A.18.+8.B.G.19.+8.B.A.21.+8.B.G.22.]

****************************************************************************
Here nts 8.A.A.3.;8.A.A.6.;8.A.A.9. are in both №3 and №4 multiplets.

Considering this issue I'd like to know what is Your definition of Multiplet? And also what does symbol "*" in " nts=10* " mean?

I'm sorry if You already described it somewhere else.

Best regards,
Eugene

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Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.