Search found 13 matches

by gia75
2017.08.18 12:54
Forum: Mixtures and Flexible Systems
Topic: how to fix an interface in EOM ?
Replies: 1
Views: 1356

how to fix an interface in EOM ?

Hi All

I have a 4 domains, monomeric protein (1 chain, symmetry P1).
The domain 1 and 4 interact together.
how to define such interface in EOM ? (I don't want them to move apart).

Thank you,

GIA
by gia75
2017.05.12 18:33
Forum: Rigid Body Modelling
Topic: which alm for bunch ?
Replies: 4
Views: 3860

Re: which alm for bunch ?

Hi and thank you

the problem is that it is not that flexible...
the domain probably samples several different conformations while retaining its local secondary structure, more or less like a spring ;o)
how to model something like that ?

GIA
by gia75
2017.05.12 13:35
Forum: Rigid Body Modelling
Topic: which alm for bunch ?
Replies: 4
Views: 3860

Re: which alm for bunch ?

ps:
actually what i would like to do, is to input a starting conformation for my entire protein
and then let bunch move the flexible regions only
i understand that this is not the classical way of using bunch
is it possible to that ?

Thanks
by gia75
2017.05.11 18:09
Forum: Rigid Body Modelling
Topic: which alm for bunch ?
Replies: 4
Views: 3860

which alm for bunch ?

Dear All, I have a protein with long flexible n-term and c-term which pdb should i take to calculate the .alm file for bunch ? should i take the structure generated by pre-bunch or the original structure with n-term and c-term removed ? sorry for the question but it is not clear to me (yet) Thank yo...
by gia75
2015.09.03 15:45
Forum: Primary Data Processing
Topic: autoscale ?
Replies: 0
Views: 4085

autoscale ?

Hi All,

Is there a program that perform autoscale on multiple files ? (several curves against a single background)
I have SAXS-HPLC data for an enzyme that is degrading his substrate, so the background is constantly changing over the time (decreasing than increasing).

Thank you,

GIA
by gia75
2015.05.21 14:41
Forum: Mixtures and Flexible Systems
Topic: 4 domain protein with bunch
Replies: 1
Views: 1943

4 domain protein with bunch

Hi All,

I have a protein (monomeric) that looks like the image attached.
how do I tell Bunch that the domains 1 and 4 belongs to the same fold and they should not move with respect to each other ?

Thank you for your help,

GIAX
by gia75
2015.01.08 18:39
Forum: Mixtures and Flexible Systems
Topic: hexamer making dimers SASREFMX
Replies: 1
Views: 1786

hexamer making dimers SASREFMX

Hi All, I have an hexameric protein (symmetry P32, crystal structure known) that is forming a small percentage of dodecamers, probably trough an S-S bond beetween two hexamers. I would like to model it using SASREFMX, is it possible? I would like to input the crystal structure (hexamer) and let the ...
by gia75
2014.12.17 13:24
Forum: Rigid Body Modelling
Topic: coral and hexameric particle
Replies: 3
Views: 4896

coral and hexameric particle

Hi All, i have an hexameric particle (symmetry P32, dimer of trimer, or trimer of dimer...) with known crystal structure of the hexamer. I have missing n-term (6x) and moving loops so i would like to use CORAL to model the particle. i have already tried CORAL in P1 by fixing the 6 chains and I would...
by gia75
2014.08.28 16:45
Forum: Mixtures and Flexible Systems
Topic: help with sasrefmx: dimer of hexamers
Replies: 0
Views: 4848

help with sasrefmx: dimer of hexamers

hi All, I have big problems (but I am not the only one I see ;o) to understand the input files and parameters for sasrefmx. my problem: I have a protein (40kd) that form hexamers. Now, these hexamers can associate to form dimers of hexamers (but i don't know how, meaning that I don't know if the who...
by gia75
2014.07.02 15:21
Forum: Mixtures and Flexible Systems
Topic: mixture with unknown component
Replies: 7
Views: 3706

Re: mixture with unknown component

sorry for bothering with lots of questions. i have problem to figure out the symmetries in the sasref server. if my hexamer is symmetry P32, what should be the dodecamer ? (as i can't tell -a priori- if it is a real dimer of hexamers) or should I take the problem the other way around: dodecamer that...
by gia75
2014.07.01 12:39
Forum: Mixtures and Flexible Systems
Topic: mixture with unknown component
Replies: 7
Views: 3706

Re: mixture with unknown component

if I compare it to another protein (170kDa, monomer) that
I have measured the same day, I get 440kDa for this one.
twice the MW of the hexamer (220kDa)
by gia75
2014.07.01 12:05
Forum: Mixtures and Flexible Systems
Topic: mixture with unknown component
Replies: 7
Views: 3706

Re: mixture with unknown component

hi
thank for the reply
we are already using online hplc and we get only 1 pic
the problem is that the Rg and Dmax are much bigger than what we expect
for our hexamer (max dimension 110A) ... i post data and gnom
Best
GIAX
by gia75
2014.06.30 15:21
Forum: Mixtures and Flexible Systems
Topic: mixture with unknown component
Replies: 7
Views: 3706

mixture with unknown component

Hi All, I have a 40kD protein that make nice hexamers in solution (we have the crystal structure + secmalls data). However, the SAXS data show the presence of additional component, which (we believe) could be a dodecamer. We don't understand yet how the dodecamer could be formed as we only see hexam...