Search found 9 matches

by Nicholas
2017.05.10 12:49
Forum: Working with Models
Topic: Volumes used by crysol
Replies: 5
Views: 4652

Re: Volumes used by crysol

Tank you very much :D
by Nicholas
2017.04.27 14:22
Forum: Working with Models
Topic: Volumes used by crysol
Replies: 5
Views: 4652

Volumes used by crysol

When calculating a scattering profile using crysol a number of radii and volumes are used and reported. I'm trying to figure out what they are and how they are used in the calculation of the scattering profile. here I did a test with a random PDB file: C R Y S O L Version 2.8.3 -- 04/10/12 -- Progra...
by Nicholas
2014.09.19 10:28
Forum: Mixtures and Flexible Systems
Topic: EOM with distance constraints
Replies: 0
Views: 4789

EOM with distance constraints

Hi I'm trying to model a somewhat special case. I have a multi domain protein: A-link1-B-link2-C, where domains A, B and C are structured and described using crystallographic data. The two linkers are (presumably) flexible, however they might be linked via a disulfide bond. Is it possible to set a d...
by Nicholas
2014.03.27 21:03
Forum: Mixtures and Flexible Systems
Topic: Bunch with multiple chains
Replies: 6
Views: 2806

Re: Bunch with multiple chains

The protein has a fairly defined structure, with a closed kratky plot. I tried CORAL but it keeps moving some of the subunits, relative to each other, even when they are grouped. Even when I explicitly specify that they should be fixed. I also tried to fix all subunits, however I can see that the ar...
by Nicholas
2014.03.27 17:31
Forum: Mixtures and Flexible Systems
Topic: Bunch with multiple chains
Replies: 6
Views: 2806

Re: Bunch with multiple chains

Just to update, if anyone has a similar problem. After reading the CORAL manual I see that CORAL is much more fit for this task.
by Nicholas
2014.03.27 17:26
Forum: Mixtures and Flexible Systems
Topic: Bunch with multiple chains
Replies: 6
Views: 2806

Re: Bunch with multiple chains

Dear Alex,

Thank you for the reply, so I was trying the right thing. I will have to go back and check by sequence again. :-(
But as you say, CORAL might be a better tool.

Best regards
Nicholas
by Nicholas
2014.03.27 16:07
Forum: Mixtures and Flexible Systems
Topic: Bunch with multiple chains
Replies: 6
Views: 2806

Bunch with multiple chains

Hi, I'm wondering if it is possible to model a molecule containing two chains using bunch? I have a molecule consisting of chain A and chain B. Chain A together with a part of chain B (that I will call B1) form a domain with a structure defined in a pdb file. I'm not interested in the relation betwe...
by Nicholas
2011.11.07 23:46
Forum: Rigid Body Modelling
Topic: Anisometry in SASREF online
Replies: 1
Views: 2088

Anisometry in SASREF online

Hi How do you specify an expected anisometry in sasref online, it seems to be a parameter according to the log file: ... Disconnectivity penalty weight ......................... : 10.00 Expected particle anisometry ........................... : Unknown Shift penalty is normalized by ...................
by Nicholas
2010.04.06 16:16
Forum: Working with Models
Topic: .alm files in CRYSOL
Replies: 3
Views: 5512

SaxsMax wrote:
The ".alm" files produced from CRYSOL contain binary data. Is there a reader that reads these partial amplitudes?
You may try conv_alm.exe (available on ftp)
Is this still possible? Or is there another way of reading the partial amplitudes?

Nicholas