Search found 86 matches

by ckerr
2017.02.06 16:54
Forum: ATSAS Package in General
Topic: Illegal characters in file names - primus
Replies: 2
Views: 3383

Re: Illegal characters in file names - primus

This problem has been fixed in our development version - the next release of Primus should work with non-ASCII characters.
by ckerr
2017.01.13 15:36
Forum: Working with Models
Topic: Using Crysol for non-biological systems
Replies: 2
Views: 3451

Re: Using Crysol for non-biological systems

There is no way of specifying scattering length density of different dummy CA atoms in CRYSOL. However, you could always change the model so that the dummy atoms are not carbon but rather some other element with a different scattering length.
by ckerr
2017.01.12 18:55
Forum: Mixtures and Flexible Systems
Topic: Rg
Replies: 18
Views: 4662

Re: Rg

1) Enough that it is detectable in the SAXS data

2) If the flexible protein binds in more than one place then that would convey some rigidity. To be honest I'm just guessing here so don't take my word as gospel.
by ckerr
2017.01.12 15:39
Forum: Mixtures and Flexible Systems
Topic: Rg
Replies: 18
Views: 4662

Re: Rg

If you put the globular protein in the middle of the flexible protein without affecting the structure of the flexible protein then you would effectively have a core-shell structure with a dense core (the globular protein plus the inner part of the flexible protein) and a less dense shell (outer part...
by ckerr
2017.01.12 09:33
Forum: Mixtures and Flexible Systems
Topic: Rg
Replies: 18
Views: 4662

Re: Rg

The straight rod would have higher Rg
by ckerr
2016.12.08 12:27
Forum: SAXS & SANS Software
Topic: Image size
Replies: 1
Views: 3201

Re: Image size

The pixel size is not related to the beam size. If you have some way of accessing the image metadata (how to do this depends on the image format) then hopefully the pixel size will be saved there, otherwise it will at least have the detector make and model, which you can use to look up the pixel siz...
by ckerr
2016.12.02 16:00
Forum: Rigid Body Modelling
Topic: CORAL: problem achieving minimum no. of successful steps
Replies: 4
Views: 3724

Re: CORAL: problem achieving minimum no. of successful steps

As an input file I use dimeric xtal structure, but do not impose any symmetry in the search. If you do this, CORAL will consider the dimeric structure as one single chain with one 51 residue tail. I would recommend one of the following options: 1) Use EOM (if the tail is very flexible / disordered)...
by ckerr
2016.12.01 16:35
Forum: ATSAS Package in General
Topic: forbidden:you don't have the permission···
Replies: 2
Views: 3268

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

Try again - hopefully the problem has been fixed.
by ckerr
2016.11.24 17:52
Forum: Working with Models
Topic: Chi^2 missing in CRYSOL output
Replies: 8
Views: 5652

Re: Chi^2 missing in CRYSOL output

The latest version is 2.7.2 so I suggest that you upgrade. Then try running crysol and datcmp again and tell us if the problem still appears.

UPD: ATSAS 2.8.0 is out now.
by ckerr
2016.11.24 10:01
Forum: Working with Models
Topic: Chi^2 missing in CRYSOL output
Replies: 8
Views: 5652

Re: Chi^2 missing in CRYSOL output

What version of ATSAS are you using? A recent version should copy the sig(q) column into the .fit file so that it can be used to calculate the chi^2 - but your .fit file has no sigma column.
by ckerr
2016.11.23 11:36
Forum: Ab Initio Shape Determination
Topic: Strange outputs from MONSA
Replies: 2
Views: 3384

Re: Strange outputs from MONSA

MONSA should produce one .pdb file for each phase. If I remember correctly the -0.pdb file is the solvent phase i.e. it will look like a sphere with a void in the middle where your protein goes.
by ckerr
2016.11.02 10:00
Forum: ATSAS Package in General
Topic: sreflex normal modes
Replies: 8
Views: 5757

Re: sreflex normal modes

File "/home/miroslav/.pymol/startup/saspy.py", line 970, in sasref systemCommand(["crysol"] + ["-p"] + [fid] + [pdbtmpfn]) File "/home/miroslav/.pymol/startup/saspy.py", line 578, in systemCommand status = subprocess.call(command, **kwargs) File "/usr/lib/python2.7/subprocess.py", line 523, in call...
by ckerr
2016.10.14 08:19
Forum: Working with Models
Topic: Superposition of different envelopes
Replies: 2
Views: 3469

Re: Superposition of different envelopes

I don't think there's any way you can do that with envelopes that you have already calculated. However, you can calculate new pre-aligned dummy atom models using MONSA. For the deletion constructs, just tell the program that the deleted domain is "contrast-matched" out.
by ckerr
2016.09.28 12:03
Forum: Working with Models
Topic: protein peptide complex scattering profile
Replies: 3
Views: 3820

Re: protein peptide complex scattering profile

CRYSOL will by default use all ATOM and HETATM records in a PDB file which are not waters, explicit hydrogens, or rotamer alternatives of atoms which have already been read. So if the peptide is in the PDB file it will be included in the calculated scattering. Sorry, I was looking at the developmen...
by ckerr
2016.09.28 08:49
Forum: Working with Models
Topic: protein peptide complex scattering profile
Replies: 3
Views: 3820

Re: protein peptide complex scattering profile

You should aim to subtract what is left in the buffer after [some of] the peptide has bound to the protein. If the concentration ratio is 1:1 then there is no free peptide left after binding, so you should subtract the buffer without peptide. If you have a large excess of peptide then the concentrat...