Running CRYSOL

[Ying_Emma Zhu]

Hey there,

I am trying to use RAW to run CRYSOL as described in this tutorial. https://bioxtas-raw.readthedocs.io/en/latest/tutorial/s2_crysol.html

However, I don't see CRYSOL option under RAW-Tools-ATSAS when I had both RAW and ATSAS installed. Any step I missed to enable access to ATSAS via RAW?

Current RAW: 2.1.4. Haven't update it for a while in fear of losing saved Workspace.

ATSAS: Just downloaded 4.0.0.

PC system: windows 11

Any suggestion is appreciated! Thank you

Emma

[Jesse Hopkins]

Hi Emma,

The CRYSOL GUI was released in version 2.2.0. So you need to update RAW to have access to it. It shouldn't affect your saved workspaces.

All the best.

- Jesse

----

Jesse Hopkins, PhD

Deputy Director

BioCAT, Sector 18

Advanced Photon Source

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[Thomas Grant]

Hi Emma,

In the most recent RAW 2.3.0 release there is now a built in calculator similar to CRYSOL called PDB2SAS under the DENSS tools (i.e., no need to install separate software like ATSAS). 

Tom

To view this discussion on the web visit https://groups.google.com/d/msgid/bioxtas_raw/CAGRN2W0r%3Dob-gHyfAK4%3DOwDrZWO0M-3m0L-U3d3tqrjZQ3RVug%40mail.gmail.com.

[Thomas Grant]

Unfortunately I don’t have a windows machine to test this on. But if you are willing to send me the data (feel free to send to my personal email here) I can try on my Mac and Linux and see if the issue persists. 

Tom

On Thu, Jul 18, 2024 at 6:58 PM Ying (Emma) Zhu <ying....@gmail.com> wrote:

Ok thanks Thomas and I was excited to try it out. But I still got error messages:

An unexpected error has occurred, please report it to the developers.
System: Windows-10-10.0.22631-SP0
RAW version: 2.3.0
Prebuilt: True
ATSAS version: 4.0.0

Error:
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "bioxtasraw\DENSS.py", line 3056, in read_pdb
ValueError: invalid literal for int() with base 10: '    '

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "multiprocessing\pool.py", line 125, in worker
  File "bioxtasraw\RAWAPI.py", line 5620, in pdb2sas
  File "bioxtasraw\DENSS.py", line 5484, in run_pdb2mrc
  File "bioxtasraw\DENSS.py", line 2995, in __init__
  File "bioxtasraw\DENSS.py", line 3058, in read_pdb
ValueError: invalid literal for int() with base 36: '    '
"""


The above exception was the direct cause of the following exception:


Traceback (most recent call last):

  File "bioxtasraw\RAWAnalysis.py", line 13871, in _on_running_timer

  File "bioxtasraw\RAWAnalysis.py", line 13877, in _process_results

  File "bioxtasraw\RAWAnalysis.py", line 13978, in _process_pdb2sas_results

  File "bioxtasraw\RAWAnalysis.py", line 13978, in <listcomp>

  File "multiprocessing\pool.py", line 774, in get

ValueError: invalid literal for int() with base 36: '    '

I'm not sure what went wrong.

Thomas Grant <tome...@gmail.com> 于2024年7月18日周四 15:38写道：

[Jesse Hopkins]

Hi Emma,

My guess is that since both PDB2SAS and CRYSOL are having issues it’s a formatting issue with your input file. If you send me the .pdb/cif file that you’re using I can test it.

All the best.

- Jesse

----

Jesse Hopkins, PhD

Deputy Director

BioCAT, Sector 18

Advanced Photon Source

To view this discussion on the web visit https://groups.google.com/d/msgid/bioxtas_raw/CAJZJAnmeQtoOT4XiN-21SK9QVcwtg_1wg5mXb7C2U_iZNdCsNQ%40mail.gmail.com.

[Ying (Emma) Zhu]

Hi Emma,

[Ying (Emma) Zhu]

Thank you so much Jesse for the quick response. Yeah I downloaded RAW 2.3.0 and was able to follow the steps covered in the tutorial. But I got the below error message when running CRYSOL. Any ideas?

An unexpected error has occurred, please report it to the developers.
System: Windows-10-10.0.22631-SP0
RAW version: 2.3.0
Prebuilt: True
ATSAS version: 4.0.0

Error:

Traceback (most recent call last):

  File "bioxtasraw\RAWAnalysis.py", line 13871, in _on_running_timer

  File "bioxtasraw\RAWAnalysis.py", line 13875, in _process_results

ValueError: not enough values to unpack (expected 4, got 3)

Thanks,

Emma

Jesse Hopkins <jesse.b...@gmail.com> 于2024年7月18日周四 14:58写道：

[Ying (Emma) Zhu]

Thank you both for the advice, indeed there were some errors in the .pdb file. I managed to run PDB2SAS in RAW but the Chi^2 fitting was about 10. Since there are so many parameters to tune for the fitting, are there any tutorials for the process? Another question, how can we change the black background in the plot panel of RAW into white, as in the old version? I couldn't find the color setting in the documentation. 

Not sure you know this but, I am actually working with SAXS data for RNAs not proteins, is there any guideline for good fitting for RNA modeling?

Best,

Emma

Jesse Hopkins <jesse.b...@gmail.com> 于2024年7月18日周四 16:46写道：

[Thomas Grant]

Hi Emma,

Yes there is a tutorial on the RAW website: 

https://bioxtas-raw.readthedocs.io/en/latest/tutorial/s2_pdb2sas.html

Alternatively the paper itself (click “How to cite”) has more details on what the parameters mean. 

The simplest thing you could do is increase the Number of samples to 256, which may improve the fit. There is not much else that can be done to improve fitting, as it’s a largely deterministic process. If it doesn’t fit well, that typically means the model does not agree with the data. Be sure the PDB file contains only the atoms in the model you expect. For example, if you have a crystal structure with two monomers in the asymmetric unit, but your particle is only a monomer, be sure to extract just the monomer. 

The program works for both protein and RNA, so that shouldn’t be a problem. 

If your data are high signal, then a chi2 of 10 is not necessarily bad. I’d be happy to look at it myself if you are comfortable sending the PDB and the data. Also check for aggregation at the low q region, or interparticle interference (repulsion) which can often happen with nucleic acids. If the fit is only poor at the lowest q values, then maybe that’s an issue. 

All the best,

Tom

To view this discussion on the web visit https://groups.google.com/d/msgid/bioxtas_raw/CADzGFvTkGv2D8n9%2Bo0kLFGZD_U9cWsMRUv%3DquwHNREWm__%2BLdg%40mail.gmail.com.

[Jesse Hopkins]

Hi Emma,

As far as the dark plots go, RAW does its best to respect your system settings (on OSes where it can detect them). I’ve never seen this work on Windows, actually, which it seems like is what you’re on based on the error messages, but if you set your OS in light mode and start up RAW you should get the light plots. If you set it in dark mode and start up RAW you should get the dark plots. (Note that if you have RAW open you’ll have to restart RAW for this to take effect).

Here’s how you’d do that on Windows:

https://support.microsoft.com/en-us/windows/change-colors-in-windows-d26ef4d6-819a-581c-1581-493cfcc005fe

And Mac:

https://support.apple.com/guide/mac-help/use-a-light-or-dark-appearance-mchl52e1c2d2/mac

Tom’s provided a better answer about the PDB2SAS fit than I can, so I’ll leave it at that.

All the best.

- Jesse

----

Jesse Hopkins, PhD

Deputy Director

BioCAT, Sector 18

Advanced Photon Source

[Jesse Hopkins]

Actually, this is probably a better description for how to change windows light/dark modes:

 https://www.laptopmag.com/articles/enable-light-mode-windows-10

All the best.

- Jesse

----

Jesse Hopkins, PhD

Deputy Director

BioCAT, Sector 18

Advanced Photon Source