Search found 642 matches

by AL
2018.06.19 10:54
Forum: Feedback
Topic: Education / Outreach sub
Replies: 5
Views: 2582

Re: Education / Outreach sub

Dear Peter C, feel free to ask your questions in this thread; we may create a subforum if there will be enough interest.
by AL
2018.06.18 11:21
Forum: Primary Data Processing
Topic: How can I decide Dmax correctly?
Replies: 5
Views: 2027

Validate your MW, try DARA, DATCLASS

Fig. 3 looks like your D max is about 265 A. Indeed your s min = 0.013 A -1 , so formally you cannot correctly estimate D max > 242 A. If D max = 265 A fits your expectations (for the MW computed from the sequence) make sure 'Rmax=0' is checked, save and give DAMMIN/DAMMIF a try. Before starting any...
by AL
2018.05.28 11:16
Forum: ATSAS Package in General
Topic: ATSAS release 2.8 is available
Replies: 6
Views: 4255

ATSAS release 2.8.4 is available

Download ATSAS 2.8.4 (academic users only) New platforms (beta): Debian 9 and Ubuntu 18.04. This is the last release for Debian 7. Due to incompatibilities of Qt4 with recent versions of MacOSX, there are no GUI programs (primus, chromixs etc.) in the MacOSX package of ATSAS 2.8.4. Changes in ATSAS...
by AL
2018.05.07 10:14
Forum: ATSAS Package in General
Topic: Removing yellow colour from file names and plot?
Replies: 2
Views: 1084

primusqt Line Style

Top right corner, right above the file names there is a drop-down menu "Data" - change it to "Line Style" - you'll be able to change the colour and line width of each data set.
by AL
2018.05.02 16:12
Forum: Ab Initio Shape Determination
Topic: Heterodimer 3D structure fitting on ab initio model
Replies: 1
Views: 897

supcomb

Try:

Code: Select all

supcomb template.pdb dammif.pdb --enantiomorphs=Y
SUPCOMB manual
SUPALM manual
by AL
2018.04.27 11:19
Forum: Mixtures and Flexible Systems
Topic: Help with RanCH
Replies: 5
Views: 1301

I-TASSER

Eh... I-TASSER?
by AL
2018.04.26 12:18
Forum: Mixtures and Flexible Systems
Topic: Help with RanCH
Replies: 5
Views: 1301

Re: Help with RanCH

Does RanCH take the sequence of the linker into consideration when generating pdb output files? No, it does not take te sequence into account. However you may choose which CA dihedral angle distribution will be used for all linkers ( compact-chain, native-like or random-coil ). For purpose of my re...
by AL
2018.04.26 12:03
Forum: Ab Initio Shape Determination
Topic: how to write the answer file for expert mode of dammin?
Replies: 2
Views: 947

Re: how to write the answer file for expert mode of dammin?

On linux please first run dammin with tee:

Code: Select all

tee answers.txt | dammin
then reuse answers.txt:

Code: Select all

dammin < answers.txt
by AL
2018.04.25 18:21
Forum: Mixtures and Flexible Systems
Topic: EOM on a homo-oligiomer
Replies: 8
Views: 1860

Re: The domains specified as fixed may be too far away

Tried it myself on my old heptamer project - indeed if both domains are fixed ranch says "The domains specified as fixed may be too far away" and hangs. I can generate models with fixed domains and flexible termini but flexible internal linkers seem to be impossible in EOM. I've opened a problem rep...
by AL
2018.04.20 12:58
Forum: Mixtures and Flexible Systems
Topic: Multiple NMR models for FFMAKER
Replies: 1
Views: 1078

crysol -nmr?

It's not clear what you want to achieve. If you run ffmaker with the --nmr option you get an ff.dat file with 20 curves. If you make one ff.dat file for one model - it will be useless for OLIGOMER . To get individual files with intensities from each model you may run CRYSOL like this: crysol 5n6r.pd...
by AL
2018.04.18 18:34
Forum: Mixtures and Flexible Systems
Topic: Help with RanCH
Replies: 5
Views: 1301

Re: The output files show A and B but not FL. Is this normal

jennthedukie wrote:The output files show A and B but not FL.
Do you mean the flexible linker is not present in the file if you open it in a text editor (should be only one CA for each residue) or the linker is not visible if you open it with your pdb viewer (pymol, rasmol...)?
by AL
2018.04.05 19:43
Forum: Ab Initio Shape Determination
Topic: question regarding GASBOR - model seems to be inside out
Replies: 2
Views: 993

Re: question regarding GASBOR - model seems to be inside out

Could there have been an update in the software between February and late March that would account for these discrepancies? For sure this is not the case - ATSAS 2.8.3 was released in December'2017, the next release is not available yet. You may check the version/revision in the log file, most prob...
by AL
2018.03.26 11:42
Forum: Working with Models
Topic: CRYSOL with multiple unit cells of PDB structure?
Replies: 1
Views: 1030

Please read the CRYSOL manual

... The monomer scattering intensity decays smoothly while the 4-unit-cell version is peaked. Does this make sense and indicate the beginnings of some Bragg peaks? You've computed the scattering up to 0.5 A -1 using just 51 points - that's why it looks bumpy. These default parameters are okay for a...
by AL
2018.03.21 14:13
Forum: Ab Initio Shape Determination
Topic: Negative χ2 value for ab initio modeling
Replies: 1
Views: 957

chi-squared cannot be computed without experimental errors

Do your data contain a column with experimental errors?
by AL
2018.03.05 15:47
Forum: Mixtures and Flexible Systems
Topic: EOM on a homo-oligiomer
Replies: 8
Views: 1860

Re: The domains specified as fixed may be too far away

rileydm wrote:Are there any requirements for the sequence file beyond plaintext, single letter residue code (as indicated in the manual?)
Hm, not really.

Does EOM run if you change to
  • Domain 1: [multimer][fixed]
    Domain 2: [monomer][free]?