. The colorbyrmsd.py
> (http://pymolwiki.org/index.php/ColorByRMSD) script gives a nice illustration
> on how to approach this this.
>
> Carsten
>
> -Original Message-
> From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
> Sent: Friday, May 08, 2015 10:04 AM
&g
orge.net
Subject: Re: [PyMOL] RMS over a MD trajectory.
Thanks Thomas,
I was already printing k[i][3] (RMSD before refinement) instead of k[i][0]
(RMSD after refinement) but your "cycles=0" looks cleaner.
Cheers,
Albert
On 05/06/2015 05:14 PM, Thomas Holder wrote:
> Hi Albert,
>
>
Thanks Thomas,
I was already printing k[i][3] (RMSD before refinement) instead of
k[i][0] (RMSD after refinement) but your "cycles=0" looks cleaner.
Cheers,
Albert
On 05/06/2015 05:14 PM, Thomas Holder wrote:
> Hi Albert,
>
> Please pay attention to the difference between all-atom RMSD and RMSD
Hi Dmitry,
You have to load both molecules and then you could use the command
fit x-mol, dft-mol
You can find more examples and options on the PyMOL wiki,
http://www.pymolwiki.org/index.php/Fit
Cheers,
Osvaldo.
El may 7, 2015 6:00 a.m., "Dmitry B. Eremin" escribió:
> Hello everyone,
>
> I ha
Hi Albert,
Please pay attention to the difference between all-atom RMSD and RMSD after
outlier rejection.
http://pymolwiki.org/index.php/Align#RMSD
If your "trj" and "pdb1" have identical topology and matching atom identifiers,
then you can also use cmd.rms().
http://pymolwiki.org/index.php/Rms
Terribly useful Carsten!
I could easily do a loop and get the RMS along the trajectory:
k = []
for i in range(1,101): k.append(cmd.align("trj","pdb1",mobile_state=i))
for i in range(100): print k[i][0]
Cheers,
Albert
On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
> Hi Al,
>
> yo
Hi Al,
you would need to go through the Python API:
python
rms=cmd.align("mobCA","tarCA", quiet=0)
print rms
python end
rms contains a tuple with various parameters related to the superposition. The
first value in the tuple i.e. rms[0] should be the RMS value.
HTH
Carsten
--
DeLano; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] RMS
2009/8/29 David Hall
pymol.cmd.align("%s" % name_struct1, "%s" % name_struct2)
oh, thanks =)
should return a list, the first element of which is the rms, if I remember
correctly.
Warren can probably say
2009/8/29 David Hall
> pymol.cmd.align("%s" % name_struct1, "%s" % name_struct2)
>
oh, thanks =)
>
> should return a list, the first element of which is the rms, if I remember
> correctly.
> Warren can probably say what the rest of the elements are.
>
> On this note, maybe we could start documen
pymol.cmd.align("%s" % name_struct1, "%s" % name_struct2)
should return a list, the first element of which is the rms, if I remember
correctly.
Warren can probably say what the rest of the elements are.
On this note, maybe we could start documenting on the wiki what exactly all
these comman
2009/8/24 Warren DeLano
> Carlos,
>
> The complication is that align outputs RMS values for only those atomic
> pairs remaining following sequence matching following by a refined structure
> alignment (which omits atoms above a cutoff), whereas rms outputs the value
> for all atoms matched by ide
Carlos,
The complication is that align outputs RMS values for only those atomic pairs
remaining following sequence matching following by a refined structure
alignment (which omits atoms above a cutoff), whereas rms outputs the value for
all atoms matched by identifier (without any optimization)
Terena,
1) verify that your selection are valid by making sure the dots appear on
the screen
select selection1, ...
select selection2, ...
2) then check to be sure that PyMOL sees matched atoms between the two
selections:
indicate selection1 in selection2
indicate selection2 in selection1
If
Hi,
I could be wrong about this, but there are a couple of very picky
alignment/fitting commands in PyMOL, and I think this is one of them. If
it's one of the picky ones, it'll only work if everything about the two
selections looks the same. In this case, your residue ids don't match up.
Can you
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