Re: [PyMOL] RMS over a MD trajectory.

) 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 To: Thomas Holder Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] RMS over a MD

Re: [PyMOL] RMS over a MD trajectory.

: [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, Please pay attention to the difference between

Re: [PyMOL] RMS over a MD trajectory.

-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 trajectory. I can see

[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,

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 e...@ioc.ac.ru escribió: Hello

[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 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 over a MD trajectory. Hi, I

Re: [PyMOL] RMS over a MD trajectory.

-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 trajectory. I can see that align

Re: [PyMOL] RMS over a MD trajectory.

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 trajectory. I can see that align does

Re: [PyMOL] RMS

-users@lists.sourceforge.net Subject: Re: [PyMOL] RMS 2009/8/29 David Hall dwash59_2...@yahoo.com 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

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 commands

Re: [PyMOL] RMS

2009/8/29 David Hall dwash59_2...@yahoo.com 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

[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

[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

[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

[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 residue

[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 residue

[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.

[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