Search found 12 matches

by Pernille
2017.12.05 13:58
Forum: Rigid Body Modelling
Topic: SASREF problem in SASPy
Replies: 2
Views: 3065

SASREF problem in SASPy

Hi I am trying to model a protein hexamer from three dimers using sasref but running through pymol the program keep crashing with following error msg: Exception in thread sasref_thread: Traceback (most recent call last): File "C:\ProgramData\PyMOL\lib\threading.py", line 801, in __bootstrap_inner se...
by Pernille
2016.12.20 17:59
Forum: Rigid Body Modelling
Topic: Coral seem to change scattering data in fitting?
Replies: 1
Views: 2963

Coral seem to change scattering data in fitting?

Hi SAXS people. so we are running coral on an antibody with an arrangement like https://www.saxier.org/forum/viewtopic.php?f=9&t=1502&p=3929&hilit=coral+input+antibody#p3929. I have done this before where it has worked nicely (attached left) but now the fit looks really weird (see attached right). I...
by Pernille
2015.07.03 15:25
Forum: Working with Models
Topic: Crysol atsas 2.6
Replies: 4
Views: 2809

Re: Crysol atsas 2.6

Ok that's it then.
She uses the graphical version while I work in command prompt.
Thank you very much :)
by Pernille
2015.07.03 13:22
Forum: Working with Models
Topic: Crysol atsas 2.6
Replies: 4
Views: 2809

Re: Crysol atsas 2.6

So here is the weird thing. On my colloeagues computer who has this odd chi issue, writing crysol --version, gives: crysol v2.8.3 <r4556> Copyright <c> ATSAS Team, EMBL, Hamburg Outstation, 1995-2013 She has Atsas 2.6 installed since february this year. I only recently updated Atsas to 2.6 on my com...
by Pernille
2015.07.01 13:33
Forum: Working with Models
Topic: Crysol atsas 2.6
Replies: 4
Views: 2809

Crysol atsas 2.6

Hi Saxier A small question regarding the chi reported from Crysol, Atsas version 2.6 According to an earlier thread on this forum, the chi value from Crysol is the square root of Chi2 (squared :) ). When reading the changes implemented in Atsas 2.6 it is said that all prgrams now report chi2. When r...
by Pernille
2015.06.16 16:51
Forum: Mixtures and Flexible Systems
Topic: EOM results
Replies: 6
Views: 3541

Re: EOM results

Uhh and thank for the other article:)
by Pernille
2015.06.16 16:49
Forum: Mixtures and Flexible Systems
Topic: EOM results
Replies: 6
Views: 3541

Re: EOM results

Hi again First the Kratky plot does not show flexibilty (see att.) but as the attached protein ("peptide") is only 30 aa connected by a linker to a 60 kDa protein I am unsure if this would be visible in the Kratky plot. The linker is estimated as 7 residues. There is no oligomeriszation present (cur...
by Pernille
2015.06.16 15:24
Forum: Mixtures and Flexible Systems
Topic: EOM results
Replies: 6
Views: 3541

Re: EOM results

Hi Alex and thank you very much for your reply. The article was very helpful as well! (didn't realize there was a new publication on EOM:() I always run EOM on single concentration as there is a good chance that the flexibility will be concentration dependent. In this case I tries to run EOM on all ...
by Pernille
2015.06.10 08:58
Forum: Mixtures and Flexible Systems
Topic: EOM results
Replies: 6
Views: 3541

EOM results

Hi all I am running EOM (Atsas2.6) on a large protein linked to a small protein and having a small issue interpreting the results. The large protein can exist in two conformational states which results in a Dmax and Rg difference of 15Å and 2Å. As I am unsure which conformer is present in solution I...
by Pernille
2013.10.22 08:34
Forum: Mixtures and Flexible Systems
Topic: EOM with ligand
Replies: 4
Views: 2520

Re: EOM with ligand

Hi Alex
Yes I meant the trick for the carbohydrates and the results this morning looks a lot better.
I will have a look at your other suggestion later.
Thank you very much!
by Pernille
2013.10.21 19:15
Forum: Mixtures and Flexible Systems
Topic: EOM with ligand
Replies: 4
Views: 2520

Re: EOM with ligand

Hi Alex Thank you very much that seems to work! Actually the protein is an antibody consisting of 4 chains, why it might seem that parts are missing but they are not . I was earlier told by Giancarlo to evaluate is as 2 chains with p2 symmetry in order to get EOM to accept it. I have tried using oth...
by Pernille
2013.10.17 18:53
Forum: Mixtures and Flexible Systems
Topic: EOM with ligand
Replies: 4
Views: 2520

EOM with ligand

Hi I am using EOM to evaluate flexibility of a 3 domain protein and its running. The problem is when trying to run with the carbohydrates in the pdb file(18 of them), then EOM refuses to do sequence alignment. I have tried to compare the PDB sequence to the sequence in the "example" folder where Dom...