[PyMOL] Rotation of Torsional Angle in peptide

Hi, I am trying to rotate the torsional angle in the peptide. However, instead of using PyMol I want to write a small script myself to understand better. I am trying to use the rotation matrix for axis-angle rotation but I am not able to do successfully. Can someone please help me in doing this.

Re: [PyMOL] Rotation of entire helix

Hi Alex, You have a couple options. First, use the rotate command: # rotate the selected atoms 4.5 degrees about the x axis. rotate x, 4.5, (sele) If you specifically know the axis of rotation, supply it as a vector. Next, PyMOL can also do rotations about an axis defined by two picked atoms.

[PyMOL] Rotation of entire helix

Hi All, So I have a structure that's fully modeled, but I have one alpha helix that is turned in a non-optimal way. Is there anyway to "rotate" the entire helix along its barrel while keeping everything else fixed? The objective is to turn it such that a critical side chain that was facing inward

Re: [PyMOL] Rotation of a Protein

Hi Kanika, you can do this with the "rotate" command, without any additional script (like Michael already suggested). Note: for a dimer the the center of mass does not yet define an axis, my example uses an arbitrary axis on the mirror plane between the monomers. # get some homodimer fetch 3p8

Re: [PyMOL] Rotation of a Protein

Create two new molecules from the originial. then import rotkit *rotateline Pos1=**atomcoordM1**, Pos2=atomcoordM2, degangle=60, molecule=dim1* 2011/10/9 kanika sharma > I need to rotate the second unit of the dimeric protein on the line joining > their center of masses. rotate it at a atep

Re: [PyMOL] Rotation of a Protein

I need to rotate the second unit of the dimeric protein on the line joining their center of masses. rotate it at a atep of 60 degrees till 240 degree.. 2011/10/8 Troels Emtekær Linnet > If you need rotations around an line, instead of axis, check out > > http://www.pymolwiki.org/index.php/Rotkit

Re: [PyMOL] Rotation of a Protein

If you need rotations around an line, instead of axis, check out http://www.pymolwiki.org/index.php/Rotkit Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/10/7 kanika sharma > Hello everyone, > I Have a prote

Re: [PyMOL] Rotation of a Protein

# get a molecule with 2 chains fetch 1t3r,async=0 # split it into two objects create new1, polymer and chain a create new2, polymer and chain b delete 1t3r # in the interface for new1, click: A -> movement -> deprotect # now you can rotate it individually rotate x,90,new1 On Fri, Oct 7, 2011 at 8:

[PyMOL] Rotation of a Protein

Hello everyone, I Have a protein with 2 chains. I have to rotate the second chain of the protein by 60,120,180,240 degrees each. Is there a script in PyMol that can do that? Best, Kanika -- All of the data generated in you

Re: [PyMOL] rotation of protein

Hi Chad, Kanika, Symexp is for generating symmetry mates, not for (re)constructing biological assemblies. If the BIOMT record gives an identity matrix, it means that there is no further information for building a biological unit. The biological unit is most likely contained in the PDB file. Note

Re: [PyMOL] rotation of protein

the symexp data may not always be consistent with the biomt transformations..although they turn out to be.. considering the case of 3hh7...the biological unit and asymm unit are same...to form a dimer of this protein...i cannot find a clue by biomt data REMARK 350 APPLY THE FOLLOWING TO CHAINS: A,

Re: [PyMOL] rotation of protein

I thought symexp() would accomplish this, no? From: http://pymol.sourceforge.net/newman/user/S0400xtal.html Something like: fetch 3hhz symexp mysymm, 3hhz, (3hhz), 2.75 (I came up with 2.75 by trail-and-error as 2.5 generates no symmetry mates and 3.0 generated too many) In the case of 3m2m, th

Re: [PyMOL] rotation of protein

my protein is 3m2m..iv downloaded the biological assembly 1 for this.. http://www.rcsb.org/pdb/explore/explore.do?structureId=3M2M to generate dimer for this the BIOMT data is like this from the pdb filei dont know how will this work if its an identity matrix.. REMARK 350 BIOMOLECULE: 1 REM

Re: [PyMOL] rotation of protein

Hi Kanika, In 3HHZ.pdb, I find: REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 22-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, K, L, M, N, REMARK 350AND CHAINS: O, R REMARK 350 BIOMT1 1 1.00 0.00 0.000.0

Re: [PyMOL] rotation of protein

I have a dimeric protein 3HHZ.to generate the dimer foll transformations have to be madethe problem is that this is an identity matrix,so will not change anything...can anyone help with this?? how can i get the asymmetric unit to generate dimer?? REMARK 350 APPLY THE FOLLOWING TO CHAINS:

Re: [PyMOL] rotation of protein

Hi, Kanika, are you looking for biological units of proteins when you say stable dimer? If this is the case, I recommend the page: http://pdbwiki.org/index.php/Biological_unit at the bottom of the page you can find four very useful servers for the determination of biological units of proteins (

[PyMOL] rotation of protein

Hi, i am working to generate a dimer of my protein..I have made a duplicate of my proteinCan any one tell me how to rotate my molecule to get maximum stability..??? Regards.. Kanika -- Free Software Download: Index, S

Re: [PyMOL] Rotation/Translation

On 5/29/2010 8:21 AM, J. Fleming wrote: > Hello, > > I've been using 'super' to align the C-alphas within one domain of two > different models of the same protein while leaving the second domain > to move freely. I can do this using: > > super (A and resid 1-100 and name ca), (B and resid 1-100

Re: [PyMOL] Rotation/Translation

Quoting "J. Fleming" : Hello Jon & ML, > print cmd.get_object_matrix("A") > > How do I go from the matrix to an angle and distance? according to http://www.pymolwiki.org/index.php/Get_object_matrix you should recieve a 4x4 matrix which contains the inital and target translation as lower and

[PyMOL] Rotation/Translation

Hello, I've been using 'super' to align the C-alphas within one domain of two different models of the same protein while leaving the second domain to move freely. I can do this using: super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca) What I would like to do is determine the

[PyMOL] rotation axis representation with arrows and shaft

Hi all I am working with a multidomain protein. which is present in closed and open conforamtion because of the motion in the domains of the protein. I would like to describe the roation angle of the different domains of the protein and the direction of the domain motion of my structure as a picto

Re: [PyMOL] rotation

Dave, origin molA rotate y,90,molA origin molB rotate y,90,molB origin all Cheers, Warren > -Original Message- > From: David Garboczi [mailto:dgarbo...@niaid.nih.gov] > Sent: Wednesday, March 04, 2009 10:05 AM > To: pymol-users@lists.sourceforge.net > Subject: [

[PyMOL] rotation

I have a homodimer. I place it at an arbitrary place on the screen, where it looks nice. Now move the monomers apart from each other in x. translate [10, 0, 0], object molA translate [-10, 0, 0], object molB Then I want to rotate each monomer 90 deg so that each monomer's contribution to

Re: [PyMOL] rotation origin

On Monday 08 November 2004 11:19, Kostas Tripsianes wrote: > Because the new object is of interest I need to set the rotation > origin. The optimal would be the centre of that object. Can't you just zoom in on your new object? You can use the action menu in the GUI, or the command "zoom object" w

[PyMOL] rotation origin

Hallo fellows I come back with a problem that its solution is of great importance to me. In my last thread I mention that I have a PDB that contains a linker and I think I am now able to discard it by creating a new object. Because the new object is of interest I need to set the rotation or

RE: [PyMOL] Rotation of maps when aligning

an alignment.) > > > >-- > >mailto:war...@delanoscientific.com > >Warren L. DeLano, Ph.D. > >Principal Scientist > >DeLano Scientific LLC > >Voice (650)-346-1154 > >Fax (650)-593-4020 > > > > > > > > > >>-----Original Message- > >>

Re: [PyMOL] Rotation of maps when aligning

(Esben Peter Friis) Sent: Tuesday, May 11, 2004 12:16 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Rotation of maps when aligning Hi PyMOLers I have a bunch of structures, for which I have calculated electrostatic potential maps (using Gromacs and MEAD). I can easily load the structur

RE: [PyMOL] Rotation of maps when aligning

-Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > EPF (Esben Peter Friis) > Sent: Tuesday, May 11, 2004 12:16 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Rotation of ma

[PyMOL] Rotation of maps when aligning

Hi PyMOLers I have a bunch of structures, for which I have calculated electrostatic potential maps (using Gromacs and MEAD). I can easily load the structures and corresponding maps into PyMOL and display a color coded surface. But when I try to align the structures, only the atomic coordinates

Re: [PyMOL] rotation about an arbitrary vector?

Dear Will, You wrote: The camera movement I would like to do is a little more than simple rotations or spirals, so it would be very helpful to me to be able to rotate about an arbitrary vector, rather than just the principle axes, in mdo commands. Is there a way to do this? There is. The mov

[PyMOL] rotation about an arbitrary vector?

PyMOL folks, I've been putting together movies of molecular trajectories on and off all summer, and have found pymol to be great for this purpose. I now need to put together something sexy for an end of the summer, and am trying to make a movie with alot of camera panning. The camera movement I wo