Search found 21 matches

by mawhite
2018.10.10 23:26
Forum: ATSAS Package in General
Topic: EOM binary conflicts with Eye-of-Mate system binary in Mate (gnome2) Desktop
Replies: 0
Views: 127

EOM binary conflicts with Eye-of-Mate system binary in Mate (gnome2) Desktop

Hello, The binary for eom conflicts with the renamed 'Eye-of-Gnome' eom 'Eye-of-Mate' binary in the Mate re-branding of the Gnome2 desktop. Can this conflict be avoided in future releases of ATSAS? The Mate Desktop is popular because it continues the original user-friendly Gnome2 Desktop that was re...
by mawhite
2018.02.02 00:41
Forum: Mixtures and Flexible Systems
Topic: EOM homotetramer - alignment problems error
Replies: 1
Views: 389

Re: EOM homotetramer - alignment problems error

Catarina, You need to put the four D2 domains into separate files and then fix their position in EOM. The protein.seq file needs just one chain, and any linkers. Linkers should be at least 4 aa long.. echo "AAAA" > protein.seq pdb2seq D1_A.pdb >> protein.seq echo "AAAAAA" >> protein.seq pdb2seq D2_A...
by mawhite
2018.02.02 00:28
Forum: Mixtures and Flexible Systems
Topic: SREFLEX *Arrays Allocation Error* with large Complex
Replies: 1
Views: 366

SREFLEX *Arrays Allocation Error* with large Complex

Hello, I am trying to use SREFLEX to allow a large macromolecular complex of about 3,800 residues to deform to optimize the fit to our SAXS data. I have run SREFLEX on smaller molecules, but the molecular size seems to be limited by the programs ability to allocate arrays. This is machine independen...
by mawhite
2018.02.01 01:24
Forum: Rigid Body Modelling
Topic: CORAL/SASREF Dist Restraints Ambiguity with Symmetry
Replies: 0
Views: 781

CORAL/SASREF Dist Restraints Ambiguity with Symmetry

Hello, I am having a problem with the ambiguity of distance restraints when applied to symmetry related molecules. I am defining an interface on the symmetry axis with a distance restraint. With a single molecule and P2 symmetry this is unambiguous. If the interface is through residue 308 of the cha...
by mawhite
2018.01.31 23:55
Forum: SAS Experiment Design
Topic: replicate SAXS measurements
Replies: 1
Views: 960

Re: replicate SAXS measurements

Zach, In the simplest sense the standard dilution series is a replicate set, which demonstrates the reproducibility and concentration independence of your data. However, it does not account for sample preparation variation. Contaminants and buffer mismatch problems should vary between sample batches...
by mawhite
2018.01.25 20:18
Forum: Rigid Body Modelling
Topic: CORAL Domain grouping is not compatible with initial
Replies: 0
Views: 768

CORAL Domain grouping is not compatible with initial

Hello, CORAL is still giving errors when grouping certain domains. The simplest is a two domain heterodimer interacting through each CT domain ANT-ACT:BCt-BNt DImer.con ANT LINK 4 ACT CTER 6 BNt LINK 4 BCt CTER 6 coral << ... Dimer.con No No No No 2,4 0,0 #### produces the infamous " Domain 2: group...
by mawhite
2018.01.16 17:51
Forum: Mixtures and Flexible Systems
Topic: EOM with a putative dimer of IDP
Replies: 5
Views: 928

Re: EOM with a putative dimer of IDP

Frank, The distance will be the minimum distance for the closest residue pair, by symmetry, within each specified range. Too close and there will be clash issues, too far and you are no longer specifying an interface. Since this is going to be a crude IDP dimer model, 6-8 A should be a safe choice. ...
by mawhite
2018.01.11 23:39
Forum: Mixtures and Flexible Systems
Topic: EOM with a putative dimer of IDP
Replies: 5
Views: 928

Re: EOM with a putative dimer of IDP

Frank, When a symmetry interface is known, say in P2, then a distance restraint can be used in the Contacts file. In the case of IDP, you do not expect a symmetric dimer, so the Overall Symmetry should be set to [A]symmetry. So how best to model your interface. Do you have (1) a core beta sheet inte...
by mawhite
2018.01.11 21:01
Forum: Ab Initio Shape Determination
Topic: SASRES on prealigned Models? Turn off alignment?
Replies: 0
Views: 830

SASRES on prealigned Models? Turn off alignment?

Hello, SASRES aligns the selected Models, including enantiomorph inversion, before calculating the FSC. The alignment process is very time consuming. When SUPCOMB or SUPALM has already been run on a series of models it would seem to no longer be necessary. The enantiomorph search can be turned off w...
by mawhite
2016.08.20 17:59
Forum: Rigid Body Modelling
Topic: How to Model (Anomalous) Scattering from Metal Ions
Replies: 0
Views: 1382

How to Model (Anomalous) Scattering from Metal Ions

Hello, I am trying to model a two domain protein that binds CA 2+ in one of the domains. It seems clear that the calcium is affecting the scattering, and needs to be accounted for in the modeling. I have two questions: (1) How does CORAL or EOM recognize a calcium or account for its scattering? (2) ...
by mawhite
2016.07.06 22:14
Forum: Mixtures and Flexible Systems
Topic: EOM: FIxed PDB interfaces cause clashes
Replies: 0
Views: 1364

EOM: FIxed PDB interfaces cause clashes

Hello, I am seeing this problem whenever I fix two interacting domains/chains. The interfaces were determined crystallographically and do not contain clashes. However, EOM is producing the following warning: --------------------- ATTENTION! --------------------- - The domains specified as fixed show...
by mawhite
2016.05.27 19:59
Forum: Rigid Body Modelling
Topic: CORAL: Domain Fixation Order problem
Replies: 3
Views: 2544

CORAL: Domain Fixation Order problem

Hello, I am having a problem similar to the previous post "CORAL domain configutation issues". However, the problem is slightly different. The error "Domain *: fixation is not compatible with initial configuration" depends on the choice and order of the domains. The fixed domain, a heptameric pore f...
by mawhite
2016.05.20 18:52
Forum: Mixtures and Flexible Systems
Topic: GAJOE missing Rg and Dmax values for --POOL of PDBs
Replies: 4
Views: 1571

Re: GAJOE missing Rg and Dmax values for --POOL of PDBs

Yes, the problem caused me to write my own (Perl) utility to: (1) Create the crysol FIT files from a list of PDBs saxns_pdb4eom saxs.dat *.pdb NB. Crysol could be run in batch mode. (2) Read the FIT files and create the necessary files for Gajoe saxns_fit2eom *.fit (3) Now run gajoe on the files gaj...
by mawhite
2016.05.04 23:05
Forum: Mixtures and Flexible Systems
Topic: GAJOE missing Rg and Dmax values for --POOL of PDBs
Replies: 4
Views: 1571

GAJOE missing Rg and Dmax values for --POOL of PDBs

Hello, When running Gajoe on a pool of PDB files the R g and D MAX values are not calculated correctly in the Size_listXX.txt file. In fact the same values are used for every entry. GAJOE - version 2.1 - (r6669) atsas-2.7.1-1.x86_64 on CentOS6 gajoe --pool {enter input} Produces the following Size L...
by mawhite
2016.03.24 22:41
Forum: Mixtures and Flexible Systems
Topic: Modeling inner loop using EOM
Replies: 1
Views: 1381

Re: Modeling inner loop using EOM

Jun, I would suggest using CORAL, which is for rigid body modelling with flexible loops. EOM is for generating ensembles, which you may try after using CORAL. For internal loops in CORAL you will need to split the PDB model into two files in the in.con file. Note that if the LINKers or N-, C-TER are...