Messages

1

General discussions (Q&As) / Re: zero or negative helical rise?

« on: March 28, 2013, 03:04:19 pm »

Hi, Xiangjun!

Thanks for the reply! Do you mean DSSR will give better results for helical/step parameters for DNA/RNA near the non-canonical bps? Have DSSR resolved the zero/negative helical rise issue?

Thanks!

Jane

2

General discussions (Q&As) / zero or negative helical rise?

« on: March 25, 2013, 01:49:52 pm »

Hi, Xiangjun!

I am a little confused about zero or even negative helical rise for some base-pair step parameter output, for example DNA in PDBID 1XVK. Do you have any comment or reference on this ? Thanks a lot!

Best,
Jane

3

General discussions (Q&As) / Re: question on +/- signs of local bp parameters

« on: January 14, 2013, 10:49:29 am »

Hi, Xiangjun!

I think my question has been pretty much covered; thank you so much!

Best,
Jane

4

General discussions (Q&As) / Re: question on +/- signs of local bp parameters

« on: January 13, 2013, 08:17:04 pm »

Sorry I have one more question to follow up:
 
based on my understanding, does the +/- sign for local base pair parameters only show the orientation differences but not the relative angle? i.e. the absolute value of opening angle/buckle/... could represent the relative angle between the two bases in a pair regardless of spatial orientations of the two? Thanks a lot!

5

General discussions (Q&As) / Re: question on +/- signs of local bp parameters

« on: January 13, 2013, 08:10:52 pm »

Hi, Xiangjun!

Thank you so much for your reply!

I am still a little confused about what the local coordinates on the purine base looks like when it adopts syn conformation. Could you please add on local coordinates (x1,y1,z1 and x2,y2,z2) to the bases in the example to show the differences between T+A and A+T? Thanks a lot!

Best,
Jane

6

General discussions (Q&As) / Re: question on +/- signs of local bp parameters

« on: January 11, 2013, 03:06:21 pm »

Thanks for your reply!

One specific case for opening is 1XVR(PDBID), in which the middle two AT and TA Hoogsteen base pair have similarly large openings and opposite signs. I am wondering what the opposite signs(+/-) actually imply in terms of structure. I could hardly tell the differences in opening by visualization through pymol. Thanks!

Cheers,
Jane

7

General discussions (Q&As) / question on +/- signs of local bp parameters

« on: January 11, 2013, 01:35:30 pm »

Hi!

I am confused with the meaning of the +/- values of the local base pair parameters, like opening, shear, ect. I noticed in a Bform DNA duplex, a AT(looking from the primary strand) pair usually have a + opening while a TA pair usually has a -opening angles. Is +/- supposed to differentiate this kind of situation? I checked the two pair in pymol and can not tell any differences between the opening the + and - opening angles(both open to the major groove side.) Thanks!