Re: [PyMOL] align and RMSD calculation

[PC]

Hi Tsjerk and others,

Thank you, I did use PYMOL with cycles=0

Online tools I used were:

1) Superpose

 2) RMSDCalc from http://www.igs.cnrs-mrs.fr 

(not working now due to maintenance)

I also used biopython. PYMOL def differs from biopython value.

Thank you,

-----Original Message-----
From: tsje...@gmail.com
Sent: Fri, 3 Oct 2014 20:23:59 +0200
To: patrick.coss...@inbox.com
Subject: Re: [PyMOL] align and RMSD calculation

Hi Patrick,

What other tool do you compare to and how large is the difference? There are different ways to calculate the RMSD, and they may have some rounding errors.

Cheers,

Tsjerk

On Fri, Oct 3, 2014 at 8:17 PM, PC <patrick.coss...@inbox.com> wrote:

Hi,

Sorry its me again. Can someone tell me where I can find the code for the align command?

It seems the RMSD differs from other online tools I found.

Thank you 

-----Original Message-----
From: patrick.coss...@inbox.com
Sent: Fri, 3 Oct 2014 09:15:17 -0800
To: patrick.coss...@inbox.com, pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] align and RMSD calculation

Ignore this question, I found the answer it setting cycles=0.

Thank you 

-----Original Message-----
From: patrick.coss...@inbox.com
Sent: Fri, 3 Oct 2014 07:55:31 -0800
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] align and RMSD calculation

Hi everyone,

I was using align in PYMOL and wanted to calculate RMSD.

But, PYMOL gave the following result:

MatchAlign: aligning residues (696 vs 696)...

 ExecutiveAlign: 2177 atoms aligned.

 ExecutiveRMS: 73 atoms rejected during cycle 1 (RMS=0.38).

 ExecutiveRMS: 103 atoms rejected during cycle 2 (RMS=0.13).

 ExecutiveRMS: 105 atoms rejected during cycle 3 (RMS=0.08).

 ExecutiveRMS: 66 atoms rejected during cycle 4 (RMS=0.07).

 ExecutiveRMS: 32 atoms rejected during cycle 5 (RMS=0.07).

 Executive: RMS =    0.063 (1798 to 1798 atoms)

How can I calculate the RMS WITHOUT PYMOL throwing atoms away in attempt to improve the RMS?

I want the raw number.

Thank you

---

Free 3D Earth Screensaver
Watch the Earth right on your desktop! Check it out at www.inbox.com/earth

---

Publish your photos in seconds for FREE
Try IM ToolPack at www.imtoolpack.com

---

Free 3D Earth Screensaver
Watch the Earth right on your desktop! Check it out at www.inbox.com/earth

------------------------------------------------------------------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

--
Tsjerk A. Wassenaar, Ph.D.

---

Free 3D Earth Screensaver
Watch the Earth right on your desktop! Check it out at www.inbox.com/earth

------------------------------------------------------------------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net