Re: [PyMOL] align and RMSD calculation

2014-10-03 Thread Tsjerk Wassenaar
0 > *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. &g

Re: [PyMOL] align and RMSD calculation

2014-10-03 Thread PC
Fri, 3 Oct 2014 09:15:17 -0800To: patrick.coss...@inbox.com, pymol-users@lists.sourceforge.netSubject: 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.comSent: Fri, 3 Oct 2014 07

Re: [PyMOL] align and RMSD calculation

2014-10-03 Thread Matthew Baumgartner
Hi, You may want to check out the rms_cur command. http://www.pymolwiki.org/index.php/Rms_cur HTH, Matt Baumgartner On 10/03/2014 02:28 PM, Nat Echols wrote: On Fri, Oct 3, 2014 at 11:17 AM, PC > wrote: Sorry its me again. Can someone tell me where I can f

Re: [PyMOL] align and RMSD calculation

2014-10-03 Thread Nat Echols
On Fri, Oct 3, 2014 at 11:17 AM, PC wrote: > 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. > Are you running it with default arguments? If you do this: align object1, object2 it does an

Re: [PyMOL] align and RMSD calculation

2014-10-03 Thread Tsjerk Wassenaar
mol-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 -0

Re: [PyMOL] align and RMSD calculation

2014-10-03 Thread PC
-users@lists.sourceforge.netSubject: 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.comSent: Fri, 3 Oct 2014 07:55:31 -0800To: pymol-users@lists.sourceforge.netSubject: [PyMOL] align and

Re: [PyMOL] align and RMSD calculation

2014-10-03 Thread PC
Ignore this question, I found the answer it setting cycles=0.Thank you -Original Message-From: patrick.coss...@inbox.comSent: Fri, 3 Oct 2014 07:55:31 -0800To: pymol-users@lists.sourceforge.netSubject: [PyMOL] align and RMSD calculation Hi everyone,I was using align in PYMOL and

[PyMOL] align and RMSD calculation

2014-10-03 Thread PC
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 (