Search found 19 matches

by cjuark
2020.11.09 07:25
Forum: SAXS & SANS Software
Topic: Problems Getting MultiFOXS To Work With My Flexible System
Replies: 0
Views: 83

Problems Getting MultiFOXS To Work With My Flexible System

Hello, I am working on a three domain flexible protein, and would like to use multiFOXS to define the multiple states and conformations it has. After multiple failed attempts, I cannot get the calculations to get past RRT. Are my issues to do with pdb itself, the scattering profile I worked on, or a...
by cjuark
2020.09.15 21:41
Forum: Model evaluation and manipulation
Topic: Trouble Looping Missing Regions For Subsequent BilboMD
Replies: 1
Views: 388

Re: Trouble Looping Missing Regions For Subsequent BilboMD

On a whim, I googled "how to renumber a pdb file" and I found this website: https://swift.cmbi.umcn.nl/servers/html/renumb.html. I input the pdb I generated with EOM and magically, the output had my missing residues filled in. Highly recommend this method as it only took a few seconds.
by cjuark
2020.09.15 21:20
Forum: Model evaluation and manipulation
Topic: Trouble Looping Missing Regions For Subsequent BilboMD
Replies: 1
Views: 388

Trouble Looping Missing Regions For Subsequent BilboMD

Hello, I am trying to to loop in missing regions within a single chain multidomain protein which I have previously generated a model of using EOM at my local compute cluster. I have had recent success modelling in missing loop regions of a protein using the Modeller plug in within chimera, and then ...
by cjuark
2020.07.27 08:40
Forum: Rigid body modelling
Topic: Repeating BUNCH X Number of Times?
Replies: 1
Views: 872

Repeating BUNCH X Number of Times?

Saxier community, Is it possible for me to loop an ATSAS executable, in windows 10, multiple times from the command line? I would like to use a script similar to the example I will paste below. I will run some testing on the scripting, but was wanting some input on optimizing the script or if I'm do...
by cjuark
2020.07.27 07:58
Forum: ATSAS package in general
Topic: ATSAS 3.0.2 Installation Privileges
Replies: 2
Views: 1015

Re: ATSAS 3.0.2 Installation Privileges

I managed to get this to work. I was having trouble figuring out how to edit the PATH since it was my first time around. If anyone has the same trouble as me the next time, this website really helped me: https://www.architectryan.com/2018/03/1 ... indows-10/
by cjuark
2020.07.23 06:57
Forum: Mixtures and flexible systems
Topic: ATSAS 3.0.2 eom cannot read .seq file
Replies: 3
Views: 941

Re: ATSAS 3.0.2 eom cannot read .seq file

Thank you, AL, for your reply. I will work on getting this figured out with your generous reply! I'll take a look at the paths and what I am inputting, and then get back to you if I have any problems.

Thank you so much,

-Cody
by cjuark
2020.07.23 06:52
Forum: Rigid body modelling
Topic: SIGABRT problem with pre_bunch
Replies: 3
Views: 758

Re: SIGABRT problem with pre_bunch

Apologies for the late reply, AL. I've been working on getting a new computer and am pleased to working on it now. Through some trial and error after posting my original message, I found that the fasta file did not match entirely with the 4jgu pdb file that I have attached in this reply. After trunc...
by cjuark
2020.07.23 06:34
Forum: ATSAS package in general
Topic: ATSAS 3.0.2 Installation Privileges
Replies: 2
Views: 1015

ATSAS 3.0.2 Installation Privileges

Saxier members, I have recently begun using a new windows 10 laptop and planned on using ATSAS with it. On my old laptop, running ATSAS 3.0.1 and windows 10, I was able to call on the ATSAS programs anywhere in my computer and perform analysis in multiple directories. For example, I could open my te...
by cjuark
2020.07.10 12:07
Forum: Rigid body modelling
Topic: CORAL question for a beginner
Replies: 0
Views: 669

CORAL question for a beginner

Hello, I just learned of CORAL, and I just recently ran a three domain protein using CORAL via ATSAS online. After reading the manual, I am still a little confused as to what the options in the ATSAS online's version of CORAL represent. What do the options, to the left and right of my .pdb files, re...
by cjuark
2020.07.10 11:23
Forum: Rigid body modelling
Topic: SIGABRT problem with pre_bunch
Replies: 3
Views: 758

SIGABRT problem with pre_bunch

Hello, I have been working on modeling a three domain protein using BUNCH. Each of the three domains can be found in RCSB and are available as pdb's. When using pre_bunch, I specify my .fasta file as well as the three .pdb files for each domain using a wildcard. I get the following SIGABRT error mes...
by cjuark
2020.06.26 00:44
Forum: Mixtures and flexible systems
Topic: ATSAS 3.0.2 eom cannot read .seq file
Replies: 3
Views: 941

Re: ATSAS 3.0.2 eom cannot read .seq file

Not far below this post seems that someone else also had the same problems using EOM via ATSAS online: https://www.saxier.org/forum/viewtopic.php?f=10&t=5565 Since OP did not reply to AL's final comment, I am not sure if fixing the spaces worked for OP. The headers in my files did not have spaces, a...
by cjuark
2020.06.26 00:39
Forum: Mixtures and flexible systems
Topic: ATSAS 3.0.2 eom cannot read .seq file
Replies: 3
Views: 941

ATSAS 3.0.2 eom cannot read .seq file

Dear saxier members, I am attempting to run eom through the command line of my local machine (macOS 10.15.5), After indicating my preferred constrain model generation, I am prompted to input my .seq file for my specimen. This runs fine when adding the test lysozyme file in the ATSAS package, but not...
by cjuark
2020.06.26 00:36
Forum: SAXS & SANS Software
Topic: SCATTER IV: Guinier Approximation of Rg and Normalized Kratky Inquiry
Replies: 2
Views: 1522

Re: SCATTER IV: Guinier Approximation of Rg and Normalized Kratky Inquiry

Al,

apologies for not replying to this sooner, as I forgot to set my reply notifications on. Thank you for your input!
by cjuark
2020.04.29 17:18
Forum: SAXS & SANS Software
Topic: Finding Vc using SCATTER IV
Replies: 0
Views: 1013

Finding Vc using SCATTER IV

Dear SAXS Researchers, My PI and I found that determining the volume of correlation may be be helpful in our research involving scattering data of a few of our proteins. In SCATTER, I can derive a Vc Plot, and I was wondering how I can derive lc from this graph. From the instructions, I believe that...
by cjuark
2020.04.22 17:44
Forum: SAXS & SANS Software
Topic: SCATTER IV: Guinier Approximation of Rg and Normalized Kratky Inquiry
Replies: 2
Views: 1522

SCATTER IV: Guinier Approximation of Rg and Normalized Kratky Inquiry

To the SAXS community, This question involves the Guinier approximation of Rg in a protein, with the help of SCATTER IV. I am currently trying to assess changes in the dynamic flexibility in a sequentially bound three domain protein held by flexible linkers, as a function of calcium concentration. T...