Search found 11 matches

by tomas
2018.10.29 15:01
Forum: Primary Data Processing
Topic: Porod volume in Primus/Qt
Replies: 0
Views: 4571

Porod volume in Primus/Qt

Dear SAXS people, I would like to ask about two possible Porod volume estimations in primus/qt ATSAS 2.8.4 (r10552) . When clicking the Distance Distribution button, the Porod volume (36500 A 3 ) is much different than after clicking Porod Volume button (18300 A 3 ). How could be explained this dras...
by tomas
2018.05.15 14:08
Forum: Mixtures and Flexible Systems
Topic: EOM stack with no ERROR
Replies: 0
Views: 5314

EOM stack with no ERROR

Dear ATSAS people, I found problem with not complicated P2 setup of EOM (ranch). It starts with no problem, but it doesn't work. No structures for the pool are created and it stack forever with: ... starts making models ... [ 1%] The folder with all input attached. For the quick check the eom.ans fi...
by tomas
2017.08.21 15:35
Forum: Primary Data Processing
Topic: folded or not folded?
Replies: 1
Views: 2810

folded or not folded?

Dear SAXS people,
should I consider Kratky plot of attached data as folded or not?
Thank you,
Tomas
by tomas
2017.02.17 16:01
Forum: Primary Data Processing
Topic: GNOM JOBTYP=1 radius or diameter
Replies: 0
Views: 4261

GNOM JOBTYP=1 radius or diameter

Dear SAXS people,
determining size distribution of polydisperse solid spheres using GNOM, JOBTYP=1.
On the x axis is the radius of sheres as is written in the GNOM manual ?
Or diameter?
Thank you,
Doubting Tomas
by tomas
2015.02.05 17:48
Forum: Rigid Body Modelling
Topic: subunits are not fixable in coral
Replies: 4
Views: 5003

Re: subunits are not fixable in coral

Your gut feeling was right (wrong copy paste in pdb editing). This conversation could be deleted.
Than you,
Tomas
by tomas
2015.02.05 16:54
Forum: Rigid Body Modelling
Topic: subunits are not fixable in coral
Replies: 4
Views: 5003

Re: subunits are not fixable in coral

Hi Alex, thank you for your answer and sorry for unclear question. I will explain. 1. linker was set to be 5 residues long - but the proble remain (so no new files are send). 2. problem: I want to fix only ercc1-shift.pdb and xpf-shift.pdb. The orientation is known, domains were together shifted to ...
by tomas
2015.02.04 15:13
Forum: Rigid Body Modelling
Topic: subunits are not fixable in coral
Replies: 4
Views: 5003

subunits are not fixable in coral

Dear Saxiers,
I would like to ask you about coral. I am not able to fix subunits. According to coral manual, I shifted domains to origin (0,0,0) but this doesn't help. Coral always dislocated the domains in the working model. I would like to ask you for advice how to overcome this problem.
Thank you
by tomas
2013.11.15 13:06
Forum: Ab Initio Shape Determination
Topic: ab initio model volume vs POROD volume
Replies: 3
Views: 2138

Re: ab initio model volume vs POROD volume

Hi Alex, Protein 1 have big (30%) flexible/unfolded portion. We have crystal structure of protein1 with 456AMK and whole construct in solution have 644AMK. About protein 2 we don't know anything.... Question: In case of my kind of unfolded proteins you should not trust Vporod and ab initio models? T...
by tomas
2013.11.15 11:49
Forum: Ab Initio Shape Determination
Topic: ab initio model volume vs POROD volume
Replies: 3
Views: 2138

ab initio model volume vs POROD volume

Hi, trying to confirm protein complex formation with this results: protein1: Vporod=75000 complex protein1+2: Vporod=121000 from these numbers you can say, yes the complex have been formed, but DAMMIN (and GASBOR similarly) ab initio model of protein 1 is BIGGER than complex of protein 1+2. filtered...
by tomas
2013.09.05 14:02
Forum: Mixtures and Flexible Systems
Topic: how to prevent concatenation of protein chains in EOM
Replies: 3
Views: 2457

Re: how to prevent concatenation of protein chains in EOM

Hi Alex,
yes I found the topic with identical problem:
http://www.saxier.org/forum/viewtopic.p ... m+multiple
but without the advice how to solve this, just:
"With EOM 2.0 you can do that."
But how to do that?
Thank you,
Tomas
by tomas
2013.09.02 15:00
Forum: Mixtures and Flexible Systems
Topic: how to prevent concatenation of protein chains in EOM
Replies: 3
Views: 2457

how to prevent concatenation of protein chains in EOM

Working with protein complex made of several protein subunits: the EOM output model is always concatenated (the C-terminus of subunit #n is always very close to N-terminus of the subunit #n+1)... It is possible to prevent this concatenation and to force the EOM handle the domains as independent unit...