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sebgg

RotaMol , Predicting the Collision Cross Section (CCS) Of Proteins based on PDB coordinates

9 posts in this topic

#1 ·  Posted (edited)

RotaMol is a user-friendly program that allows rapid analyses of protein size during viewing/editing in PyMOL.

Wrote this a while ago and have been coming up with slight improvements every now and then when I get free time, so the source isn’t really "finished", but it works well.

This script, named RotaMol, has to be used in conjunction with a protein modelling program called PyMol (not written by me). So if you dont have PyMol you wont be able to test this.

Once your protein is loaded into PyMol this script will essentially calculate the area of every face, for a user defined level of accuracy (pixelskip) and angle of rotation. It is then calibrated using the Zoom function in PyMol, and it spits out the average rotational area of the protein in Angstroms squared.
Included here is the source,
Also is a link to the Google code page where it is hosted for Full .EXE download, as well as all documentation - tutorials - back versions, and a more in depth description of how it works and various links,


Download here:
http://code.google.com/p/rotamol/downloads/list
latest version should be on top


Cheers,

Sebastian Eves-van den Akker
=====================================================================================================
Any questions about compatibility issues with older PyMOL versions or different language keyboards - don't hesitate to ask! (Preferably by email)

RotaMol v1.11 - APBS.au3

RotaMol v1.11 instructions.pdf

Edited by sebgg

GC - Program to rapidly manipulate DNA SequencesRotaMol - Program to measure Protein Size

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Updated with Version 1.05,

Changed GUI to make it much more user friendly, and tidied up the code a little, and improved the calibration function.

Cheers,

Seb


GC - Program to rapidly manipulate DNA SequencesRotaMol - Program to measure Protein Size

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#3 ·  Posted (edited)

v1.06 is now up,

minor changes but probably the last set of changes for a while, mostly GUI changes and to make program more usefriendly.

Seb.

(old)

Attached File(s)

RotaMol V1.06.zip (982.36K)

Number of downloads: 44 .

Edited by sebgg

GC - Program to rapidly manipulate DNA SequencesRotaMol - Program to measure Protein Size

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v1.08 is up,

Quite Alot of changes:

- No need to do manual measurements anymore! its totaly automated calibration functions.

- fixed a pause bug

-cleaned up the use of globals in script a bit.

apparently v1.06 had some issues starting on some computers, Have tested this version on multiple computers with different windows versions and no problems but let me know anyway.

Seb.


GC - Program to rapidly manipulate DNA SequencesRotaMol - Program to measure Protein Size

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Hi,

Wrote this a while ago and have been comming up with slight improvements every now and then when I get free time, so the source isnt really "finished", but it works grand and you never know someone else in the community might need it.

So what does it do?

This script, named RotaMol. has to be used in conjunction with a protein modeling program called PyMol (not written by me). so if you dont have PyMol you wont be able to test this.

Once your protein is loaded into PyMol this script will essentially calculate the area of every face, for a user definied level of accuracy (pixelskip) and angle of rotation. It is then callibrated using the Zoom function in PyMol, and it spits out the average rotational area of the protein in Angstroms squared.

included in the upload will be the source, the exe compiled (because it has a nice icon) and the instruction manual (pdf), incase any1 here is actually a mollecular biologist.

Cheers,

Sebastian Eves-van den Akker

Hi Sebastian,

I tried to predict the CCS for my protein using RotaMol files you provided. Even for the smallest protein (PDB ID = 1L2Y) it does not produce any number. Two messages appear in the external GUI (I can recall one of them: center, 10) and there is no outcome for the CCS.

After downloading the protein in PyMol, I get a message something like: " I'm pretty sure this is taking longer than usual, select OK to...." I tried hitting OK and not hitting OK but in either case did not get any calculated number for the CCS. Would you have any suggestions?

Thanks,

Negar

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#6 ·  Posted (edited)

Hi Sebastian,

I tried to predict the CCS for my protein using RotaMol files you provided. Even for the smallest protein (PDB ID = 1L2Y) it does not produce any number. Two messages appear in the external GUI (I can recall one of them: center, 10) and there is no outcome for the CCS.

After downloading the protein in PyMol, I get a message something like: " I'm pretty sure this is taking longer than usual, select OK to...." I tried hitting OK and not hitting OK but in either case did not get any calculated number for the CCS. Would you have any suggestions?

Thanks,

Negar

Thanks for the information,

I think the reason this has happened is PyMOL can be slow to load surfaces of some proteins.

v1.09 is now up that will fix this problem.

have added a separate load surface button which as far as I can see should solve this, simply click it first before starting the analysis (or load the relevant surface manually)

-also added a feature to measure electrostatics.

Thanks again,

Sebastian Eves-van den Akker

Edited by sebgg

GC - Program to rapidly manipulate DNA SequencesRotaMol - Program to measure Protein Size

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#7 ·  Posted (edited)

Recieved an Email from someone who had problems with compatability to an older veriosn of PyMOL.

(0.99)

If anyone else has compatability problems with older veriosns dont hesistate to let me know and Ill see what I can do.

The version of RotaMol available here is for PyMol 1.3.

Cheers,

Sebastian Eves-van den Akker.

Edited by sebgg

GC - Program to rapidly manipulate DNA SequencesRotaMol - Program to measure Protein Size

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#8 ·  Posted (edited)

Uploaded a Download link to Google code page for this project where there will be Full .EXE download, as well as all documentation - tutorials - back versions, and a more in depth description of how it works.

Changed electrostatics code to include percentage distributions - still need to add documentation on this though.

Here:

http://code.google.com/p/rotamol/

latest version should be on top

Compatibility with some keyboard settings is not good.

Currently working on French language keyboard compatibility - and while im at it to change the comments in the source/tutorial to French also. When finished will also upload this to the Google code page but probably not the source here.

Got afew more ideas in the pipeline - will post when changes.

Again any more suggestions of issues feel free to email me

Cheers,

Sebastian Eves-van den Akker.

Edited by sebgg

GC - Program to rapidly manipulate DNA SequencesRotaMol - Program to measure Protein Size

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#9 ·  Posted (edited)

Latest (and probably final) version added to top post and to the Google code page.

Now works as intended with APBS tools for measuring average external charge and size at the same time - documentation added as well.

http://code.google.com/p/rotamol/

Cheers,

Sebastian Eves-van den Akker.

 

--------------------------------------------------------------- old downloads ---------------------------------------------------------------------------

Attached File  RotaMol v1.09 - Lite.au3   25.54KB   101 downloads
Attached File  RotaMol v1.09 - Lite.exe   456.81KB   16 downloads
 

Edited by sebgg

GC - Program to rapidly manipulate DNA SequencesRotaMol - Program to measure Protein Size

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