Search found 86 matches

by ckerr
2016.05.25 14:07
Forum: Working with Models
Topic: CRYSOL (2.8.3) from ATSAS 2.7.1-1 vs previous version
Replies: 1
Views: 3649

Re: CRYSOL (2.8.3) from ATSAS 2.7.1-1 vs previous version

The change in the Rg output was deliberate (don't ask me for the exact reasons though).

"Oxygen" is the correct spelling (Phosphorus and nickel were also corrected in 2.7)
by ckerr
2016.05.25 13:54
Forum: Mixtures and Flexible Systems
Topic: GAJOE missing Rg and Dmax values for --POOL of PDBs
Replies: 4
Views: 2137

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

A fix for this bug will be available in the 2.7.2 release.
by ckerr
2016.05.17 15:48
Forum: ATSAS Package in General
Topic: Unable to install ATSAS 2.7.1 on Centos 7.2
Replies: 1
Views: 3337

Re: Unable to install ATSAS 2.7.1 on Centos 7.2

We had already discovered this issue internally - it has been fixed in our development version and the fix will be included in the next release (hopefully within the next couple of weeks). If you need to install urgently and can't use an older version then I might be able to provide you with a 'prev...
by ckerr
2016.05.11 08:11
Forum: Primary Data Processing
Topic: Kratky and Porod +/- errors
Replies: 2
Views: 2384

Re: Kratky and Porod +/- errors

To get a Kratky plot you multiply the I(s) by s^2 - so (assuming you know s more-or-less exactly) you just multiply the errors by s^2 too. For a normalised Kratky plot you also have to account for possible errors in the I0 and Rg used in the normalisation. For the Porod plot you do the same but for ...
by ckerr
2016.05.09 08:17
Forum: Working with Models
Topic: error: unable to read input file: *.pdb
Replies: 3
Views: 2871

Re: error: unable to read input file: *.pdb

OS 10.10.5 and the command I'm using is $ "/Applications/ATSAS/bin/crysol *.pdb bd1971.dat -sm 0.3" I'm assuming you mean $ /Applications/ATSAS/bin/crysol *.pdb bd1971.dat -sm 0.3 (without the quotation marks) *.pdb means "all files with names ending in '.pdb' in the current directory". This so-cal...
by ckerr
2016.05.04 13:06
Forum: Working with Models
Topic: error: unable to read input file: *.pdb
Replies: 3
Views: 2871

Re: error: unable to read input file: *.pdb

Which OS are you using, and what exact command line are you typing?
by ckerr
2016.04.12 13:36
Forum: Working with Models
Topic: problem in CRYSON batch mode
Replies: 3
Views: 4336

Re: problem in CRYSON batch mode

Since ATSAS 2.7.0 it is now possible to specify negative values on the command line
by ckerr
2016.04.12 11:32
Forum: Primary Data Processing
Topic: Errors: Single shot SAXS vs SEC-SAXS.
Replies: 4
Views: 3758

Re: Errors: Single shot SAXS vs SEC-SAXS.

In theory, averaging to reduce the errors doesn't "reduce them to an unrealistic amount", rather the reduction is real and helpful. The whole point of doing an experiment is to distinguish between true and false hypotheses; lower errors increase the discriminating power. To get a better fit, it migh...
by ckerr
2016.04.04 09:07
Forum: Primary Data Processing
Topic: Scattering in absolute units
Replies: 1
Views: 1774

Re: Scattering in absolute units

I'm not sure if there is a way to do it in Primus but you can always use the command line tool DATOP http://www.embl-hamburg.de/biosaxs/manuals/datop.html. Alternatively, rather than adjusting the data, just multiply and divide the Guinier I0.
by ckerr
2016.04.01 14:00
Forum: Rigid Body Modelling
Topic: SASREF CV data input file format
Replies: 2
Views: 4407

Re: SASREF CV data input file format

This problem has now been fixed in libsaxsdocument, the fix will also be included in the next release of ATSAS. If you really want to, you can download the updated libsaxsdocument, compile it and use it to replace the libsaxsdocument(.so|.dll|.dylib) included in your current ATSAS installation. Usin...
by ckerr
2016.03.30 15:15
Forum: Rigid Body Modelling
Topic: SASREF CV data input file format
Replies: 2
Views: 4407

Re: SASREF CV data input file format

This is not a problem with SASREF itself but rather with libsaxsdocument ( https://github.com/emblsaxs/saxsview ), used by ATSAS to parse the data files. It seems that the reason is the line endings used in the file - the line endings only have the carriage-return character and not the newline chara...
by ckerr
2016.03.30 11:43
Forum: Ab Initio Shape Determination
Topic: Ab initio modelling with partially known structure
Replies: 5
Views: 7664

Re: Ab initio modelling with partially known structure

Since CREDO is outdated plus it doesn't seem to be able to do the coordinate conversion from all atom coordinates to a dummy Ca list, is there any other program that can generate Ca dummy atoms model from a known structure? On Linux (probably also Mac) running grep -e '^ATOM \+[0-9]\+ CA ' all-atom...
by ckerr
2016.03.30 11:33
Forum: Ab Initio Shape Determination
Topic: Transformation matrix
Replies: 1
Views: 3492

Re: Transformation matrix

The SUPALM/SUPCOMB module in the SASPy plugin for PyMOL has code to parse a transformation matrix from the SUPALM output and apply it to a model in PyMOL. Hopefully it should not be hard to adapt this to apply the transformation to a different model.

https://github.com/emblsaxs/saspy
by ckerr
2016.03.15 12:19
Forum: Mixtures and Flexible Systems
Topic: RANCH with P2: multichain PDB cannot be lined up
Replies: 2
Views: 1643

Re: RANCH with P2: multichain PDB cannot be lined up

The atoms in the final residue are in a different order between the two chains Chain A: ATOM 583 O PRO A 148 -32.210 0.487 5.221 1.00 68.42 O ATOM 584 N PRO A 148 -29.509 0.192 5.871 1.00 85.62 N ATOM 585 CA PRO A 148 -30.335 -0.979 5.548 1.00 83.47 C ATOM 586 CB PRO A 148 -30.007 -1.959 6.680 1.00 ...
by ckerr
2016.02.24 12:50
Forum: Ab Initio Shape Determination
Topic: Chi-Squared Values
Replies: 4
Views: 4724

Re: Chi-Squared Values

The chi-square test compares the discrepancies between your theoretical and experimental curves with the expected errors. The null hypothesis is that the discrepancies are entirely due to random experimental errors. A reduced chi-squared value much less than one means that the discrepancies are much...