Search found 17 matches

by zhuwenkai
2018.10.30 10:25
Forum: Mixtures and Flexible Systems
Topic: interdomain linker is broken in SREFLEX
Replies: 0
Views: 9727

interdomain linker is broken in SREFLEX

Hi Alex and everyone,

when i was running SREFLEX, i found the interdomain linker is broken in the output pdbs. How can i keep the whole structure intact while only allow the

flexibility of the two two domains? Thank you.
by zhuwenkai
2018.10.24 03:57
Forum: Mixtures and Flexible Systems
Topic: Volume fractions in OLIGOMER
Replies: 2
Views: 6798

Re: Volume fractions in OLIGOMER

I have the same question with you, and did you fix it?
by zhuwenkai
2018.10.21 16:42
Forum: Mixtures and Flexible Systems
Topic: the meaning of volume fration in OLIGOMER
Replies: 0
Views: 9707

the meaning of volume fration in OLIGOMER

Hi, all I have some questions about volume fration in OLIGOMER. Is volume fraction equal to number fraction or molar fraction? Considering a multicomponent of mixture ,A, B and AB. The form factors are obtained from pdbs and no scale was performed. The volume fraction given by OLIGOMER is 0.25, 0.25...
by zhuwenkai
2017.03.15 15:13
Forum: Working with Models
Topic: CRYSOL:deal with the missing part in the pdb file?
Replies: 2
Views: 5831

Re: CRYSOL:deal with the missing part in the pdb file?

Alex wrote:
and how can i add the missing part to the structural model to make it complete?
use BUNCH and/or CORAL.
Thank you very much!
by zhuwenkai
2017.03.08 11:28
Forum: Working with Models
Topic: CRYSOL:deal with the missing part in the pdb file?
Replies: 2
Views: 5831

CRYSOL:deal with the missing part in the pdb file?

Hi,the protein involved in my project is flexible, so a 6aa linker is missing in the high-resolution model. I compare the experimental curve with the theoretical curve computed from the model by CRYSOL to prove the conformation in solution is different. However, i don't know whether the comparison i...
by zhuwenkai
2017.01.15 17:54
Forum: Primary Data Processing
Topic: help with my p(r) curves,how to get the accurate Dmax?
Replies: 1
Views: 5376

help with my p(r) curves,how to get the accurate Dmax?

Hi.i have got serval SAXS curves of my protein(apo.mutant.complex).I want to know the conformational changes from Dmax value. Here comes the question,i think the difference between the Dmax value is comparable to the uncertainy of the values(5%-10%).So i was puzzled about how to determine the Dmax v...
by zhuwenkai
2016.12.02 09:18
Forum: Primary Data Processing
Topic: How to generate the theoretical P(r) curve from pdb files?
Replies: 3
Views: 7149

How to generate the theoretical P(r) curve from pdb files?

Hi.generally, we get the theoretical scattering curves from high-resolution structures by CROSOL, but i was wondering How to generate the theoretical P(r) curve from pdb files? I know a example using CPPTRAJ in the AMBER 14 package to get the P(r) curve. By the way, one more question, i get the advi...
by zhuwenkai
2016.12.02 07:45
Forum: ATSAS Package in General
Topic: forbidden:you don't have the permission···
Replies: 2
Views: 5901

Re: forbidden:you don't have the permission···

ckerr wrote:Try again - hopefully the problem has been fixed.
Thank you very much! The problem has been solved.
by zhuwenkai
2016.11.30 08:13
Forum: ATSAS Package in General
Topic: forbidden:you don't have the permission···
Replies: 2
Views: 5901

forbidden:you don't have the permission···

Hi. sorry to ask such a question in the forum, i am a Chinese phd student from WuHan. I have visited https://www.embl-hamburg.de/biosaxs/manuals/eom.html for many times rencently. (My apology, i find the webserver very useful) But i can't visit it anymore··· I hope the administrator can solve my pro...
by zhuwenkai
2016.11.30 08:02
Forum: Rigid Body Modelling
Topic: NSD between the model by CORAL and DAMMIF is large
Replies: 0
Views: 5978

NSD between the model by CORAL and DAMMIF is large

Hi.I have used coral to build a model (5aa linker missing),then i superimposed the model to the DAMMIF model ,NSD=2.87 I also tried to build a model by sasref with nmr structure (no missing parts), when superimposed to the DAMMIF model ,NSD=3.2 so, my question is, whether the large NSD value is due ...
by zhuwenkai
2016.11.29 04:59
Forum: Mixtures and Flexible Systems
Topic: EOM-selected ensemble doesn't fit well with the curve
Replies: 3
Views: 2146

Re: Rg of your models are too small for your data

From the Guinier approximation of your experimental data I get R g = 22 A. (And you have to remove the first 60 data points because your data are from an aggregated sample.) From the p(r) function (with D max = 108 A) I get R g = 24 A. Your most extended model has R g = 18.6 A. I.e. EOM can't fit d...
by zhuwenkai
2016.11.28 17:38
Forum: Mixtures and Flexible Systems
Topic: EOM-selected ensemble doesn't fit well with the curve
Replies: 3
Views: 2146

Re: Rg of your models are too small for your data

From the Guinier approximation of your experimental data I get R g = 22 A. (And you have to remove the first 60 data points because your data are from an aggregated sample.) From the p(r) function (with D max = 108 A) I get R g = 24 A. Your most extended model has R g = 18.6 A. I.e. EOM can't fit d...
by zhuwenkai
2016.11.28 13:19
Forum: Mixtures and Flexible Systems
Topic: EOM-selected ensemble doesn't fit well with the curve
Replies: 3
Views: 2146

EOM-selected ensemble doesn't fit well with the curve

I was working with a protein of two domain in between with a flexible 16aa linker. i run the eom ,but i didn't get a good fit to the scattering data. It was supposed to populate both the closed state and open state, thus bimodal distribution, but the eom_pdb seems like a single patially closed state...
by zhuwenkai
2016.10.06 17:16
Forum: Working with Models
Topic: generate the envelop of the protein
Replies: 3
Views: 6740

Re: generate surface

AL wrote:Check this post.
If you use PyMOL - try to set solvent_radius in surface representation (careful, it may crash if the radius is too large).
Thanks a lot, i will read it carefully.
by zhuwenkai
2016.09.28 09:32
Forum: Working with Models
Topic: protein peptide complex scattering profile
Replies: 3
Views: 6568

Re: protein peptide complex scattering profile

thank you for your quick reply, i got it.It depends on the affinity of the complex, i think i know what to substract.