Re: [PyMOL] RMS over a MD trajectory.

hon >>>> 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 va

Re: [PyMOL] RMS over a MD trajectory.

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, > >

Re: [PyMOL] RMS over a MD trajectory.

>>> 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.

Re: [PyMOL] RMS or RMSD for two structures

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

[PyMOL] RMS or RMSD for two structures

Hello everyone, I have a problem: I want to calculate RMS or RMSD for to structures one i’ve got from x-ray structure analysis and another from DFT calculations, but still can not understand how to perform it. hope You can help me. Sincerely, Eremin D., Section of structural studies, Laborator

Re: [PyMOL] RMS over a MD trajectory.

en >> >> -Original Message- >> From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] >> Sent: Wednesday, May 06, 2015 8:32 AM >> To: pymol-users@lists.sourceforge.net >> Subject: [PyMOL] RMS over a MD trajectory. >> >> Hi, >> I am trying

Re: [PyMOL] RMS over a MD trajectory.

The first value in the tuple i.e. rms[0] should be the RMS value. > > HTH > > Carsten > > -Original Message- > From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] > Sent: Wednesday, May 06, 2015 8:32 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] RMS ove

Re: [PyMOL] RMS over a MD trajectory.

TH Carsten -Original Message- From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] Sent: Wednesday, May 06, 2015 8:32 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] RMS over a MD trajectory. Hi, I am trying to compute the RMS between a PDB file and a Gromacs traject

[PyMOL] RMS over a MD trajectory.

Hi, I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I can see that "align" does things correctly when: align trj, pdb1, mobile_state=1 i. e., when I align the first snapshot of the trajectory with the PDB file. I also understand that PyMOL does compute the RMS along

Re: [PyMOL] RMS

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

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 what the rest of the elements are. > > On this note, maybe we could start documen

Re: [PyMOL] RMS

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

Re: [PyMOL] RMS

d in the output RMS > value. > > Cheers, > Warren > > > -Original Message- > > From: Carlos Ríos Vera [mailto:crosv...@gmail.com] > > Sent: Monday, August 24, 2009 1:44 PM > > To: pymol-users@lists.sourceforge.net > > Subject: [PyMOL] RMS >

Re: [PyMOL] RMS

; From: Carlos Ríos Vera [mailto:crosv...@gmail.com] > Sent: Monday, August 24, 2009 1:44 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] RMS > > Hello people, > > I'm trying to use pymol from a custom python scrypt. What I have done > is to align two struc

[PyMOL] RMS

Hello people, I'm trying to use pymol from a custom python scrypt. What I have done is to align two structures, but I need get the RMS value from that align but I have no idea how to do it. I tried to use the RMS command but the value differs from the value that I get from the align. Any Idea ho

[PyMOL] RMS values output to plugin?

I am trying to get the RMS values from pymol's align function to print into a plugin I've made. I have so far been unable to pipeline the info out and have not found a way to call back RMS values in pymol's cmd line. I have also not been able to figure out how to use the align function source c

[PyMOL] RMS of two small molecules

Hi, lets say I have a set of docked conformations and want to compare them with the conformation observed in a crystal structure (aka redocking). How can I get pymol to calculate RMS values for pairs of small molecules that probably don't have the same numbering? For now I tried to use the rms_c

[PyMOL] rms values for several states

Hi, I made Molecular Dynamics studies on a wildtype enzyme and its mutants. To compare the structures (in pymol 40 states for each enzyme) I have to find out which state of the one enzyme has the best rms to the other enzyme. Are there possibilities to solve this problem in pymol or maybe in p

RE: [PyMOL] rms

:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Teresa > Sent: Monday, January 10, 2005 1:58 PM > To: pymol-users@lists.sourceforge.net > Su

[PyMOL] rms- again :(

Hi to all Here I am again dealing with this rms command, see I want to do is to get the rms between two residues, one is in the subunit of the oxidized state of the protein while the other is in the same subunit but of the reduced state of the protein and I can't make it to work. At this point

[PyMOL] rms

Hi to all I'm trying to use the rms_cur command and I was successful when I did this: >select selection1, (object1 and i. 57 and (name c,o,n,ca)) >select selection2, (object2 and i. 57 and (name c,o,n,ca)) >rms_cur selection1, selection2 but when I try to specify the chain with the resid

[PyMOL] rms

Hi to all I'm trying to use the rms_cur command and I was successful when I did this: >select selection1, (object1 and i. 57 and (name c,o,n,ca)) >select selection2, (object2 and i. 57 and (name c,o,n,ca)) >rms_cur selection1, selection2 but when I try to specify the chain with the resid

[PyMOL] rms output

Hi, I'm using pymol to analyse a molecular dynamic simulation. I transformed my trajectory in an NMR style .pdb. It's really nice like that: I can see a movie of my simulation in pymol. Here come my question. I use intra_fit to align all my frames (states). And it's really fast to compute that. I

Re: [PyMOL] rms commands

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

[PyMOL] rms commands

Hey all, just the other day I discovered a nifty command in pymol. rms_cur selection1, selection2 determines the deviation between two (previously aligned) selections without doing a fit. Here's what I do: rms_cur (object1 and i. 20:29 and (name c,o,n,ca)), (object2 and i. 30:39 and (name c

[PyMOL] rms fitting and align

Dear folks, I have a couple of questions about the alignment and fitting functions of pymol. I've been using the 'align' and 'fit' functions of pymol apparently quite successfully, but I found it difficult to make the 'rms' or 'rms_cur' functions actually report anything. I can take a structure w