Re: [PyMOL] Merge PDB files
Josh, The trick is that each otherwise identical structure in a PDB file must have its own segment identifier in order to avoid ambiguity. In recent version of PyMOL, there is a "segi=1" option to symexp which will automatically assign such an identifier to each copy. load $TUT/1hpv.pdb symexp sym, 1hpv, 1hpv, 5.0, segi=1 create merged, all save merged.pdb, merged dele all load merged.pdb Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Joshua Adelman Sent: Thursday, January 11, 2007 12:15 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Merge PDB files I was wondering if there was a simple way to merge pdb files generated by Pymol's 'generate symmetry mates' command? I have a dimer in the available pdb file and want to make the full hexamer that is formed via a trimer of dimers. Any suggestions would be most appreciated. Josh -- Joshua L. Adelman Biophysics Graduate Group Lab: 510.643.2159 218 Wellman HallFax: 510.642.7428 University of California, Berkeley http://nature.berkeley.edu/ ~jadelman Berkeley, CA 94720 USA jadel...@berkeley.edu -- - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Merge PDB files
I was wondering if there was a simple way to merge pdb files generated by Pymol's 'generate symmetry mates' command? I have a dimer in the available pdb file and want to make the full hexamer that is formed via a trimer of dimers. Any suggestions would be most appreciated. Josh -- Joshua L. Adelman Biophysics Graduate Group Lab: 510.643.2159 218 Wellman HallFax: 510.642.7428 University of California, Berkeley http://nature.berkeley.edu/ ~jadelman Berkeley, CA 94720 USA jadel...@berkeley.edu --
Re: [PyMOL] Sequence view size
Aaron, Unfortunately, there is no good way to do this at present. A very ugly hack would be to save the current image and then measure its dimensions. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of aaron bryden Sent: Thursday, January 11, 2007 11:03 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Sequence view size Is their any way to get the size in pixels of the sequence view like their is of the internal gui, or the size in pixels of the space actually used for drawing? I know that glGetDouble(GL_VIEWPORT) but this doesn't take into account the internal gui or the sequence view. I can find a way to get the size of the internal gui but not the sequence view. thanks, Aaron - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] CE Align v0,1
Howdy, I've just finished implementing the CE alignment algorithm in Python/C as a PyMol plugin. The CE algorithm, is a fast/accurate structure-based alignment program. (At this point, I have left out a few optimization steps; those will come later.) Before I release the code to the public, I'd like to make it more reliable by asking for help from a couple testers. I need about a half a dozen people with various computing environments. I especially need Mac and Windows users, since I work solely on Linux. If you'd like to help test the code, please let me know and I'll package it up and send it over. It installs very easily and should work on all platforms that have access to a C-compiler and a working Python distribution with distutils and Numpy installed. If you'd like to help, or have comments/questions, please contact me through email (see attached address). Cheers, -- J -- Jason Vertrees http://vertrees.org/ http://pymolwiki.org/ http://best.utmb.edu/
[PyMOL] Sequence view size
Is their any way to get the size in pixels of the sequence view like their is of the internal gui, or the size in pixels of the space actually used for drawing? I know that glGetDouble(GL_VIEWPORT) but this doesn't take into account the internal gui or the sequence view. I can find a way to get the size of the internal gui but not the sequence view. thanks, Aaron
Re: [PyMOL] distance atom-protein surface
I needed to have a measurement of the "actual" physical long dimension of a protein model to compare with x-ray scattering data. I activated the surface mesh feature and at the extreme ends of the longest axis, right at the surface boundary, created a carbon atom at each position, then simply used the distance measurement wizard to measure the distance between the too points. praedor On Wednesday 10 January 2007 11:29, Andreas Henschel wrote: > Hi Giacomo, > > you can either create an atom at that position > (see eg. http://www.rubor.de/bioinf/tips_python.html#chempy) and than > use the distance command (or wizard). [...] > Giacomo Bastianelli wrote: > >Dear Pymol users, > > > >I would like to measure the distance between an atom and > >a specific point (not another atom) in the surface of the protein. > >Is it possible with pymol? > >do I need additional scripts? > > > >Thanks in advance, -- Reichstag fire is to Hitler as 9/11 is to Bush
Re: [PyMOL] Pymol cone shape?
Hi William, Maybe the attached python script will be of some use. It contains a function (and some helper functions) to draw a CGO arrow in PyMOL. It contains code for drawing a cone for the head of the arrow. Hope it helps, Tsjerk On 1/10/07, William Scott wrote: Let's ask on the pymol mailing list... On Jan 10, 2007, at 11:02 AM, Martin.Laurberg wrote: > Damn, I can convert my 1969 CNS base pair restraints into what they > call > CGO drawn lines, and thereby display enforced hydrogen bonds, but I > wish > to draw cones for the base pair ladder as ribbons can do it. Oh > well, .. > > > > On Wed, 10 Jan 2007, William Scott wrote: > >> >> I think it is possible, but I don't know how. >> >> >> >> On Jan 10, 2007, at 9:24 AM, Martin.Laurberg wrote: >> >>> Hi Bill, is it possible to draw a cone-shape in pymol? >>> >> - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 from pymol import cmd from pymol.cgo import * from math import * # # Some functions to allow drawing arrows (vectors) in Pymol # In need of proper documentation... # # Please don't distribute (parts of) this file, without credits # # (c)2006 Tsjerk A. Wassenaar, PhD, University of Utrecht # # t s j e r k w .at. g m a i l .dot. c o m # http://nmr.chem.uu.nl/~tsjerk/ # def t( X ): if not X: return X Y = [] for i in range( len( X[0] ) ): Y.append( [] ) for j in X: Y[i].append( j[i] ) return Y def v_add( a, b ): return ( a[0]+b[0], a[1]+b[1], a[2]+b[2] ) def v_sub( a, b ): return ( a[0]-b[0], a[1]-b[1], a[2]-b[2] ) def vecprod( a, b ): return ( a[1]*b[2]-a[2]*b[1], a[2]*b[0]-a[0]*b[2], a[0]*b[1]-a[1]*b[0] ) def inprod( a, b=None ): if b: return a[0]*b[0] + a[1]*b[1] + a[2]*b[2] else: return a[0]*a[0] + a[1]*a[1] + a[2]*a[2] def svmult( s, a ): return ( s*a[0], s*a[1], s*a[2] ) def norm( a ): return svmult( 1/sqrt(inprod( a )), a ) def mvmult( R, x ): y = [] for i in R: y.append( inprod( i, x ) ) return tuple(y) def mv_add( X, a ): Y = [] for i in X: Y.append( v_add( i, a ) ) return Y def mmmult( R, X ): Y = [] for i in X: Y.append( mvmult( R, i ) ) return Y def smatrix( v ): return [[ v[0], 0, 0 ], [ 0, v[1], 0 ], [ 0, 0, v[2] ]] def rmatrix( v ): cosx, sinx = cos( v[0] ), sin( v[0] ) cosy, siny = cos( v[1] ), sin( v[1] ) cosz, sinz = cos( v[2] ), sin( v[2] ) return mmmult( mmmult( [[1,0,0],[0,cosx,-sinx],[0,sinx,cosx]], [[cosy,0,-siny],[0,1,0],[siny,0,cosy]] ), [[cosz,-sinz,0],[sinz,cosz,0],[0,0,1]] ) def block( i, dphi ): ddphi = 0.25*dphi phi0 = i*dphi phi1 = phi0+ddphi phi2 = phi1+ddphi phi3 = phi2+ddphi phi4 = phi3+ddphi sqrt2 = sqrt(2) return [ (-0.5*sqrt2,-0.5*sqrt2*cos(phi2),0.5*sqrt2*sin(phi2)), (1,0,0), (0,cos(phi0),-sin(phi0)), (0,cos(phi1),-sin(phi1)), (0,cos(phi2),-sin(phi2)), (0,cos(phi3),-sin(phi3)), (0,cos(phi4),-sin(phi4)) ] def cgo_triangle_fan( X ): Y = [] while ( X ): i = X.pop(0) Y.extend( [ NORMAL, i[0], i[1], i[2], ] ) for i in range( 6 ): i = X.pop(0) Y.extend( [ VERTEX, i[0], i[1], i[2], ] ) return Y def cgo_arrow1( S, E, r=0.2, hr=0.4, hl=1.0 ): P0 = S D = v_sub( E, S ) DL = inprod( D, D ) P1 = v_add( S, svmult( (DL-hl)/DL, D ) ) P2 = E # Define a vector orthogonal to P1-P0 V = v_sub( P1, P0 ) V = norm( V ) if V[2] != 0: A = ( 1, 1, -(V[0]+V[1])/V[2] ) elif V[1] != 0: A = ( 1, -V[0]/V[1], 0 ) else: A = ( 0, -V[0], 0 ) A = norm( A ) B = vecprod( V, A ) print (inprod(V), inprod(B), inprod(A)) R = t([ svmult( hl,V ), svmult( hr,A ), svmult( hr,B ) ]) # Define the transformation matrix (scale and rotation) #C = v_sub( P2, P1 ) #scale = ( hl, hr, hr ) #rotate = ( 0, acos( C[0]/sqrt(C[0]**2+C[2]**2) ), acos( C[0]/sqrt(C[0]**2+C[1]**2) ) ) #R = mmmult( smatrix( scale ), rmatrix( rotate ) ) obj = [ CYLINDER, S[0], S[1], S[2], P1[0], P1[1], P1[2], r, 1, 1, 1, 1, 1, 1, COLOR, 1, 0, 0, BEGIN, TRIANGLE_FAN ] N = 10 dphi = 2*pi/N crds = [] for i in range(N+1):
Re: [PyMOL] change the sphere size of a chosen atom ?
Ni Hao Feng, First of all, please do not include an complete daily digest in a question (or reply) on this or any user list. If required, cut out only that part which connects to your question or reply. Then, in addition to Bobs comments, you can also use the terminal or a script, using the command: set sphere_scale, 0.3 (or another value) This will do what it says and scale your atoms sphere radius with the factor given. Another possibility is to assign a different atomic radius to your atom: alter e. s, vdw=newradius_float_argument maybe like: alter e. s, vdw=vdw*0.9 Note that you may have to "rebuild" your scene, if you were already using a sphere representation. Best, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
