Search found 651 matches

by AL
2018.04.26 12:18
Forum: Mixtures and Flexible Systems
Topic: Help with RanCH
Replies: 5
Views: 3289

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: 2568

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: 4189

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: 2700

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: 3289

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: 2557

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: 2739

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: 2485

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: 4189

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]?
by AL
2018.03.05 14:19
Forum: Announcements
Topic: EMBO practical course on solution scattering 2018
Replies: 0
Views: 6516

EMBO practical course on solution scattering 2018

https://www.embl-hamburg.de/biosaxs/courses/embo2018/img/embo-2018-hamburg.jpg EMBO practical course on solution scattering from biological macromolecules 19 - 26 November 2018 EMBL Hamburg The Course is aimed at young scientists working in the field of structural biology: biochemists, biophysicist...
by AL
2018.02.22 16:28
Forum: Mixtures and Flexible Systems
Topic: EOM on a homo-oligiomer
Replies: 8
Views: 4189

Re: EOM on a homo-oligiomer

Then try providing the domain with the oligomerization interface as a heptamer and the other domain as a monomer:
  • Overall symmetry: P7
    Sequence: [monomeric sequence]
    Number of domains: 2
    Domain 1: [multimer][fixed]
    Domain 2: [monomer][fixed]
by AL
2018.02.21 14:42
Forum: Mixtures and Flexible Systems
Topic: EOM on a homo-oligiomer
Replies: 8
Views: 4189

Re: EOM on a homo-oligiomer

Align your heptamer with ALPRAXIN . Open the aligned pdb file in a text editor, leave one monomer (any), remove the other six. Further split this monomer into two domains which should be connected by the internal flexible loop. Run EOM online : Overall symmetry: P7 Sequence: [monomeric sequence] Num...
by AL
2018.02.05 14:28
Forum: Rigid Body Modelling
Topic: Increase number of Harmonics in SASREF CV
Replies: 2
Views: 3487

Re: number of Harmonics in SASREF CV

Increasing the number of harmonics in SASREF is technically challenging. It is not planned to release a version of SASREF/CV/MX with more than 15 harmonics in the nearest future. You may try to shorten the fitting range to see if this improves the modelling. Use constant subtraction. You may do mult...
by AL
2017.12.13 13:33
Forum: Mixtures and Flexible Systems
Topic: Which program to use to model protein modified by DNA?
Replies: 2
Views: 3083

Re: Which program to use to model protein modified by DNA?

(It's not clear if your protein is partially unfolded. I'll assume it is well folded.) If you have a model of the protein - start with comparing fitting it to your "unmodified protein" SAXS data with CRYSOL . You may try to improve the fit with SREFLEX . If you have a model of the DNA you may model...
by AL
2017.12.07 14:17
Forum: Mixtures and Flexible Systems
Topic: EOM to model flexible C-terminus on dimeric protein
Replies: 1
Views: 2680

Re: EOM to model flexible C-terminus on dimeric protein

Number of residues per chain: 254 Alignment Problems: check the sequence and the domains Please run pdb2seq on your crystal structure - this will give you the sequence. Note that in case of a dimer you will get the same sequence twice. Please compare it in a text editor to the sequence provided to ...