Search found 46 matches

by sasha
2018.06.13 22:19
Forum: ATSAS Package in General
Topic: chromixs for MacOS 10.11.6
Replies: 2
Views: 2700

Re: chromixs for MacOS 10.11.6

Dear Adriana, thanks for reporting this issue. I cannot reproduce the problem, CHROMIXS 2.8.3 opens frames correctly through PRIMUS on MacOS 11.6 (El Capitan). From the system error message you attach I read: -a library has not been loaded properly (Library not loaded: /Applications/ATSAS/lib/libQtS...
by sasha
2018.02.05 19:55
Forum: Mixtures and Flexible Systems
Topic: SREFLEX *Arrays Allocation Error* with large Complex
Replies: 1
Views: 2732

Re: SREFLEX *Arrays Allocation Error* with large Complex

Dear Mark, thanks for reporting this problem. I see you are using ATSAS 2.8.0, this situation has been improved in the latest version (2.8.3). Please try again after installing the latest ATSAS . Alternatively, you can try adding the argument " -g resPerBlock=5 " to the SREFLEX command line call. Be...
by sasha
2018.01.24 16:23
Forum: Mixtures and Flexible Systems
Topic: Problem running Sreflex with the Primus graphical interface
Replies: 3
Views: 2968

Re: Problem running Sreflex with the Primus graphical interf

Dear Paola, From what you explain, the ATSAS binaries are not available on your system's PATH. In the latest ATSAS releases this is set automatically by the ATSAS installation script. What version of ATSAS and MacOS are you using? In any case, you should be able to fix this problem by setting the PA...
by sasha
2017.12.18 12:42
Forum: Rigid Body Modelling
Topic: SASREF problem in SASPy
Replies: 2
Views: 3056

Re: SASREF problem in SASPy

Dear Pernille, the issue was deeper in the Pyhon libraries that PyMOL 2.0 is using in Windows, now I found a workaround by calling SASREF with a different function. Please download the updated github version (for ATSAS 2.8.3), it should work properly: https://raw.githubusercontent.com/emblsaxs/saspy...
by sasha
2017.12.14 10:33
Forum: Mixtures and Flexible Systems
Topic: sreflex for neutrons. "ERROR log file does not exist"
Replies: 1
Views: 2647

Re: sreflex for neutrons. "ERROR log file does not exist"

Dear Anne, thanks for reporting this. I can't fully test it right now, but it looks like CRYSON is dying silently, probably related to RAM usage issues of the .bss segment in parallel threads. This seems particularly troublesome in Windows. Please try running SREFLEX again with the extra argument: "...
by sasha
2017.12.06 00:15
Forum: Rigid Body Modelling
Topic: SASREF problem in SASPy
Replies: 2
Views: 3056

Re: SASREF problem in SASPy

Dear Pernille,

Thanks for reporting this. Please install an updated SASpy for ATSAS 2.8.2 from (right-click, save as...):
https://raw.githubusercontent.com/embls ... r/saspy.py

the problem should be fixed in that version, if not, please let me know.

Best,

sasha
by sasha
2017.12.04 21:58
Forum: Mixtures and Flexible Systems
Topic: Sreflex DNS
Replies: 2
Views: 2761

Re: Sreflex DNS

Dear John,

this is a bug, the option should be there, but it's not.
This is fixed in ATSAS 2.8.3 (coming soon).

Best,

sasha
by sasha
2017.11.01 15:25
Forum: Mixtures and Flexible Systems
Topic: a question about the sreflex
Replies: 1
Views: 2642

Re: a question about the sreflex

Dear Frank, Thanks for your question. To input different parts of the structure in different PDBs, just type as stated in the manual: sreflex experimental.dat Dna.pdb,Protein.pdb This syntax overrides the partitioning of the structure, so DNA and Protein will be kept intact and only moved relatively...
by sasha
2017.10.17 15:26
Forum: SAXS & SANS Software
Topic: SASpy - a PyMOL plugin to work with SAXS hybrid models
Replies: 1
Views: 5390

Re: SASpy - a PyMOL plugin to work with SAXS hybrid models

The new PyMOL 2.0 has been released recently and it is available at: https://pymol.org/2/ This new PyMOL can work without a license and has more functionality than the educational version (render options, etc) There are installers available for Windows, Mac and Linux, which is particularly good for ...
by sasha
2017.08.30 17:41
Forum: Mixtures and Flexible Systems
Topic: How to use sreflex with protein_DNA complex?
Replies: 2
Views: 1532

Re: How to use sreflex with protein_DNA complex?

Dear Rosie, thanks for your post. There's currently no symmetry option in SREFLEX. Regarding the connectivity check, DNA.pdb and Proteinalone.pdb are far appart from each other in space, SREFLEX will not refine unconnected structures. You could get good results by separating DNA (chains C and D) and...
by sasha
2017.08.30 17:13
Forum: ATSAS Package in General
Topic: MacOS install problems
Replies: 2
Views: 3384

Re: MacOS install problems

Dear abeerasz, I just tried the installation package on Mavericks. It asked me to enter the password in the Terminal, for executing as sudo. Do you have permissions to run commands as sudo? Try the following: 1. Open the terminal app. 2. Go to where you have the downloaded ATSAS (probably cd ~/Downl...
by sasha
2017.07.22 08:51
Forum: Mixtures and Flexible Systems
Topic: Question regarding sreflex
Replies: 2
Views: 1610

Re: Question regarding sreflex

Dear Rosie, I guess the clashes are between BB.pdb (the complete model) and the rest of the pdb files (parts of it). Do not provide the complete model (BB.pdb) to SREFLEX, just the fractions of the model. If the protein is a dimer, I would recommend trying first with the two separated monomers (1.pd...
by sasha
2017.06.15 15:54
Forum: Working with Models
Topic: Force enantiomer creation
Replies: 6
Views: 9491

Re: Force enantiomer creation

One can create the enantiomorph of an ab-initio model with the ALPRAXIN program from the ATSAS package:
> alpraxin dammifModel.pdb --enantiomorph=Y
As of today the option is also available at the github SASpy PyMOL plugin.

Best,

sasha
by sasha
2017.06.01 17:15
Forum: ATSAS Package in General
Topic: Export Plots to Vector Format
Replies: 2
Views: 3343

Re: Export Plots to Vector Format

Dear sjc,

ATSAS currently does not provide a vector format output. I would recommend using R, gnuplot or matplotlib.
Find attached a matplotlib script as an example to plot .fir files directly into .pdf.

Best,

sasha
by sasha
2017.04.21 16:00
Forum: Working with Models
Topic: SUPCOMB error: unable to read pdb files
Replies: 3
Views: 3721

Re: SUPCOMB error: unable to read pdb files

Dear Anne, I assume that the files are indeed available in the directory where you are executing SUPCOMB (in case of doubt, please check with "ls" or "dir" commands). As an alternative, you can try the SUPALM program. If the problem persists, please let us know what version of ATSAS you are using (s...