Re: [PyMOL] ribbon view of c-alpha only coordinates
On Monday 01 November 2004 18:05, Cathy Lawson wrote: Some PDB files (notably models fitted into EM density) contain only C-alpha coordinates. When read into Pymol, Ive found that the coordinates appear as a constellation of individual atoms, and selecting a ribbon view doesn't connect them with lines. Try set ribbon_trace,1. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] transformation matrix
On Friday 22 October 2004 02:07, Milton H. Werner, Ph.D. wrote: I assume there is a way in pymol to read a DALI rotation/transformation matrix so that two dissimilar molecules can be intelligently aligned. Can someone tell me how it is done? I have a simple Python script that extracts the transformation matrices from the Dali report file. If someone has a way to use this matrix in PyMol, we'd be set: #!/usr/bin/env python # Script to extract 3x4 transformation matrices from Dali report files # Lieven Buts, 22-Oct-2004 import re,sys dali = open(sys.argv[1],r) pattern = re.compile(r'^## MATRICES') # Find section with matrices line = dali.readline() while not pattern.match(line): line = dali.readline() dummy = dali.readline() pattern = re.compile(r'^ *$') line = dali.readline() while not pattern.match(line): # Read matrices until first empty line one = line.split() two = dali.readline().split() three = dali.readline().split() code = one[2] matrix = [ one[4],one[5],one[6],one[7], two[4],two[5],two[6],two[7], three[4],three[5],three[6],three[7] ] matrix = tuple(map(float,matrix)) print code print (%8.3f %8.3f %8.3f %8.3f\n * 3) % matrix print line = dali.readline() Cheers, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] unit cell
On Monday 16 August 2004 02:44, Jianghai Zhu wrote: In pymol, how do you draw a unit cell? The cell constants are in the pdb file and the manual says pymol can display unit cell. I just could not figure out how to do it. load molecule.pdb show cell,molecule You may then have to zoom out and/or change the clipping planes to show all of the unit cell. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] Cavity display?
On Friday 23 July 2004 13:41, Dirk Kostrewa wrote: I wanted to have a program that can easily calculate cavities in proteins to be displayed with pymol (see e-mails below for details). Thanks to Gareth and Lari I've got two pointers to such programs: I've tried PASS, recommended by Lari and got a surface picture of my cavities within literally a few minutes, as Lari already wrote. The rTools (http://www.rubor.de/bioinf/pymol_rubor.html) also contain a fucntion to interface PASS with PyMOL. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations
On Thursday 15 July 2004 13:30, Daniel Rigden wrote:
-- begin configuring for MALOC linkage
checking for FETK_INCLUDE... yes
checking for FETK_LIBRARY... yes
checking maloc/maloc.h usability... yes
checking maloc/maloc.h presence... yes
checking for maloc/maloc.h... yes
checking for maloc_link in -lmaloc... no
configure: error: MALOC libraries or headers missing: exiting on error!
I saw some messages about libraries during compilation of maloc. I
don't known if they have anything to do with the apbs compilation
problem but I added /usr/local/lib/i686-pc-linux to /etc/ld.so.conf and
did a /sbin/ldconfig and it didn't help.
I went through the following steps:
# unpack maloc tarball
cd maloc
./configure --prefix=/usr/local
make
make install
#This produces some error messages which
# I still have to look into
cd ..
# unpack apbs tarball
cd apbs-0.3.1
export LDFLAGS=-L/usr/local/lib/i686-pc-linux
export FETK_INCLUDE=/usr/local/include
export FETK_LIBRARY=/usr/local/lib
./configure --prefix=/usr/local
make
make install
make install steps were done as root. My LDFLAGS were empty before I
started. If they are not, you may have to use
export LDFLAGS=${LDFLAGS} -L/usr/local/lib/i686-pc-linux
instead.
Hope this helps,
--
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
Re: [PyMOL] Question about surface calculation
On Sunday 14 March 2004 06:27, Fred Berkovitch wrote: When I type show surface, how is that surface calculated? Is it a true solvent-accessible surface? Does PyMol take into account heteroatoms (e.g., a metal or an Fe-S cluster) in the calculation? As for the latter question, this is determined by the surface_mode setting. After set surface_mode,0 (the default) heteroatoms are ignored and the surface is generated only for the protein atoms, leaving water molecules and ligands alone. After set surface_mode,1, all atoms are included for surface generation. You can also create separate objects to generate exactly the surfaces you want. Cheers, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] restoring default surface coloring
On Tuesday 02 March 2004 07:56, Matt Franklin wrote: [...snip...] I then realized that I had absolutely no idea how to restore the default surface coloring! (Except by quitting and restarting...) set surface_color, default didn't work, nor did set surface_color, atom_color. All I could get was solid colors. I'm guessing there's some special color name I should be using, but what is it? You can use something like color white,object to set an object to a fixed color, or the utility command util.cbag(object) (note the parentheses and quotes) to color the object by atom type and set the carbon atoms to green. There's cbag for color by atom type, carbons green, cbaw for white carbons, cbay for yellow carbons and so on. Alternatively, you can use the color menu in the internal GUI. Hope this helps, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] Select Atom Change View
On Wednesday 14 January 2004 15:54, Douglas Kojetin wrote: Is it possible to do the following through the command line ... -- select an atom (say the CA of residue 25) and bring the view of the molecule within PyMOL so that 25.CA is 'up front' (or closest to the viewer's point of view)? Yes, zoom (resi 25 and name CA) should do the trick. You can specify an additional buffer space around the selection (zoom (resi 25 and CA),2 for example). If you have multiple chains and molecules, you will have to make your selection more specific (zoom (protein and chain A and resi 25 and name CA) for example). There are many abbreviations for long selections. Type help selections for more information. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] make cartoon from carbon atom trace?
On Monday 05 January 2004 23:18, Ann Mullin wrote: I have some PDF files which only contain the backbone carbon atoms, and I would like to use PyMOL to show a cartoon representation of the backbone. Any suggestions? There is a setting called cartoon_trace. By default it is set to zero and PyMOL will not connect Calpha atoms when the other atoms are absent. You can change the setting in the corresponding menu, or with the command set cartoon_trace,1 PyMOL should now draw cartoons through the Calpha positions, although it might get confused if there are multiple chains in the PDB file and connect the last atom of one chain to the first of antoher. In that case it will be necessary to create separate objects for the different chains. There is an analogous setting ribbon_trace for the ribbon representation. In this case, separate chains do not appear to get connected. Best wishes to all for 2004, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] H-bonds
On Tuesday 06 January 2004 20:06, Sanishvili, Ruslan wrote: Is there a way to calculate and display H-bonds within a selected model without going through the distance wizard? Selecting the pairs of atoms manually via the distance wizard seems very inefficient and even dangerous (too subjective for H-bond assignment). 1) The dist command will draw distance lines between all atoms of two different selections that are within a a specified cutoff distance from each other. A very rough approach for identifying potential hydrogen bonds would be something like dist (protein and elem n,o) , (ligand and elem n,o), 3.5 This will connect all nitrogen and oxygen atoms in objects protein and ligand that are within 3.5 A from each other. 2) A more thorough approach would be to use a program designed to identify hydrogen bonds using more complete criteria. The rTools for PyMOL (available at http://www.rubor.de/bioinf/pymol_rubor.html ) provide an interface to the HBExplore program at http://www.imb-jena.de/www_bioc/hbx/hbx.html. See the rTools documentation for more details. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] Selecting a lot of residues
On Wednesday 03 December 2003 22:25, Gwendowlyn S. Knapp wrote: Maybe I didn't word my question right. I have several proteins (like 15-20) that i need to do this for and i also have these lists. i was wanting to see if there was anyway to have pymol read in that list automatically so i didn't have to type in all the residues (ie, about 60 on each protein). OK , here's a third possiblity. This little Python script -- from sys import stdin,stdout stdout.write(select group,(protein and chain A and resi ) first = 1 for line in stdin.readlines(): if not first: stdout.write(,) stdout.write( line[:-1] ) first = 0 stdout.write()\n) -- when used as python make_select.py list list.pml will transform a list of residues like 5 10 50 51 52 100 into a single-line PyMol command select group,(protein and chain A and resi 5,10,50,51,52,100) which can be copied/pasted into PyMol, or read from the file with @list.pml. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] Selecting a lot of residues
On Wednesday 03 December 2003 22:25, Gwendowlyn S. Knapp wrote: Maybe I didn't word my question right. I have several proteins (like 15-20) that i need to do this for and i also have these lists. i was wanting to see if there was anyway to have pymol read in that list automatically so i didn't have to type in all the residues (ie, about 60 on each protein). I see two possibilities: 1) write a PyMol function to read the residue list and make the appropriate selections. I do not have enough experience to do this yet. 2) use an editor or script to transform the residue list into a PyMol select command that can be sourced. If the residue list looks like this: 5 10 50 51 52 100 in a file list then a command like sed -e s/^/(protein and resi / -e s/$/) or \\\/ list list.pml will create a file list.pml like this: (protein and resi 5) or \ (protein and resi 10) or \ (protein and resi 50) or \ (protein and resi 51) or \ (protein and resi 52) or \ (protein and resi 100) or \ The ^ in the sed command means beginning of the line, the $ means end of the line. The backslash at the end of each line indicates that the command continues on the next line. There should be no characters after the backslash (other than the newline). Two manual edits transform this into select group,((protein and resi 5) or \ (protein and resi 10) or \ (protein and resi 50) or \ (protein and resi 51) or \ (protein and resi 52) or \ (protein and resi 100) ) Note the additional parentheses around the complete expression. This can be executed in PyMol by typing @list.pml and should select the indicated residues in the molecule protein. Hope this helps, -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel
Re: [PyMOL] you know what would be cool?
On Monday 17 November 2003 14:06, Laurence Pearl wrote: I should add that I don't actually know how to program in python and have no idea how its 'tuples' work, so this is a very FORTRAN-like routine - feel free to improve it. I have attached a Pythonized version of the code. It uses docstrings for the functions, try...except blocks to check some of the parameters, and things like (%8.3f * 17) to save some repetition of format specifiers. Python is cool! I have also changed the script to add two commands to PyMol using cmd.extend: camtrav first,nframes,selection,zoom,buffer and seqfly object,firstres,lastres. Usage examples: #- load protein.pdb run camera_travel.py mset 1 x150 zoom all camtrav 1,100,(resi 50),1,4 mplay # This will zoom in from the complete molecule to residue 50. #- #- load protein.pdb run camera_travel.py mset 1 x150 seqfly protein,1,8 mplay # This will visit the sequence from residue 1 to 8 #- Finally, I ran into some trouble in a lysozyme structure (PDB 103L). At residue 139, cosom becomes slightly larger than 1 (1.0008 or so) and acos(cosom) fails. Also, omega and sinom become zero in this case, so the divisions by sinom fail. I added some checks to normalize this situation and stop the code from crashing, but we should look into what's causing this. -- Lieven Buts Department of Ultrastructure Vrije Universiteit Brussel# camera_travel - Laurence Pearl, November 2003 # Pythonized by Lieven Buts, November 2003 import cmd from math import sqrt,acos,sin def quaternion(view): Returns a quaternion representation of a view matrix. nxt = [1,2,0] q = [0.0,0.0,0.0,1.0] tr = view[0]+view[4]+view[8] if tr 0.0 : s = sqrt(tr + 1.0) qw1 = s / 2.0 s = 0.5 / s return ( (view[5] - view[7]) * s, (view[6] - view[2]) * s, (view[1] - view[3]) * s, qw1 ) else : i = 0 if (view[4] view[0]): i = 1 if (view[8] view[i+3*i]): i = 2 j = nxt[i] k = nxt[j] s = sqrt ((view[i+i*3] - (view[j+j*3] + view[k+k*3])) + 1.0) q[i] = s * 0.5 if (s != 0.0): s = 0.5 / s q[3] = (view[k+3*j] - view[j+3*k]) * s q[j] = (view[j+3*i] + view[i+3*j]) * s q[k] = (view[k+3*i] + view[i+3*k]) * s return q def camera_travel(first,nframes=30,sel='(all)',zflag=0,zlevel=2): Generate progressive view matrices to move the camera smoothly from the current view to a view defined by a PyMol selection. first - start frame nframes - duration sel - atom selection that defines the orientation at the end of the sequence zflag - flag to indicate whether the final view should be 'zoomed' or not zlevel - buffer space for zooming final view (as in cmd.zoom) try: first=int(first) except: print camera_travel: first frame must be an integer return -1 try: nframes=int(nframes) except: print camera_travel: number of frames ff=float(1.0/nframes) old_view = cmd.get_view(2) # print ( view : ( + %8.3f, *17 + %8.3f) ) % (old_view) # print oldtran : %8.3f %8.3f %8.3f % (old_view[12], old_view[13], old_view[14]) # do orient operation on selection cmd.orient(sel,0) # if zoom to selection is required add this into view matrix if zflag: cmd.zoom(sel,zlevel,0,1) # get new view new_view = cmd.get_view() # capture new zoom/clip parameters ozc1 = new_view[11] ozc2 = new_view[15] ozc3 = new_view[16] # calculate shift in zoom/clip parameters dzc1 = (ozc1 - old_view[11]) * ff dzc2 = (ozc2 - old_view[15]) * ff dzc3 = (ozc3 - old_view[16]) * ff ozc1 = old_view[11] ozc2 = old_view[15] ozc3 = old_view[16] # capture new translation vector component ox = new_view[12] oy = new_view[13] oz = new_view[14] # calculate shift vector dx = ox - old_view[12] dy = oy - old_view[13] dz = oz - old_view[14] dx = dx*ff dy = dy*ff dz = dz*ff ox = old_view[12] oy = old_view[13] oz = old_view[14] # capture old and new rotation matrix components in quaternion form # m[0][0] = v[0] m[0][1] = v[1] m[0][2] = v[2] # m[1][0] = v[3] m[1][1] = v[4] m[1][2] = v[5] # m[2][0
Re: [PyMOL] color choices
Jianghai Zhu wrote: When I use color command, how many choices do I have for colors? Can I use direct rgb value? The color command uses color names. You can define your own colors with RGB values using the set_color command: set_color whatever = [ 1.0, 0.3, 0.7 ] After that you can use color whatever, ... -- Lieven Buts Department of Ultrastructure
Re: [PyMOL] Help! Color by atom/H-bond display/mouse on OSX
Luca Jovine wrote: 1) Is there any typed command one can use to color a selection by atom type (rather than manually doing so by using the internal GUI pop-up menus)? The util module contains a number of functions that color the atoms according to type, with different colors for the C atoms. For instance, util.cbay three in a .pml script will color object three by atom type, with the carbon atoms in yellow (color by atom yellow). Other functions from ../modules/pymol/util.py are cbag, cbac, cbas, cbap, cbak, cbaw and cbab (grey (carbon), cyan, salmon, purple, pink, white (hydrogen) and slate). -- Lieven Buts Brussels Free University
Re: [PyMOL] molecular sculpting
DeLano, Warren wrote: Right now I'm not sure the sculpting feature is more than entertainment, but my expectation is that it will become part of PyMOL's crystallographic model building system in the future. I agree. I think it has great potential there, as it allows for a more physical or intuitive way of manipulating the model than moving individual atoms or turning torsion angles. -- Lieven Buts Brussels Free University
Re: [PyMOL] molecular sculpting
patricia.a.elk...@gsk.com wrote: I would like to understand the molecular sculpting possibilities of pymol but haven't been able to figure it out yet. When using the wizard, the first request is to click and atom but how to proceed from there? I have used the bit of script provided on the web page and deformed the benzene ring but have not been clever enough to see the possibilities from that. Could anyone provide just enough of a step-by-step push-this, click-that lead into the molecular sculpting to get me started? I don't know about the script or the wizard (yet), but I did try the sculpting demo in the Demo menu. You can then just drag atoms by left-clicking them while holding down the control key. The dragged atom moves, everything it is connected to is dragged along, and the structure tries to minimize its energy. Great fun! -- Lieven Buts Department of Ultrastructure Brussels Free University
Re: [PyMOL] Babel and File Format Conversion
Bob Havlin wrote: You probably know about this already, but incorporating the file format converter named babel http://www.eyesopen.com/babel.html would make PyMol universal for nearly all file formats. The development of Babel is being continued in the OpenBabel project at http://openbabel.sourceforge.net/. -- Lieven Buts Brussels Free University
[PyMOL] Creating separate objects from a starting structure
Hello all, I am working with a PDB file that contains a protein molecule (chain id A) and three different ligands in its binding site (as chains B, C and D). This file was made by combining three superimposed complex structures to illustrate the relationsips between the modes of binding of the different ligands. I used PyMol and the following script to create an overview figure: [ PyMol script ]- # Load the PDB file containing all the elements load combination.pdb # Separate structure into different objects # chain A is the protein create lectin,(A//) # chains B,C and D contain three different ligands create one,(B//) create two,(C//) create three,(D//) # delete the original structure delete combination # Set view hide lines,all zoom one,3 # set orientation,... # Color atoms according to functon color white,lectin # site 1 color green,(/lectin///85,86,106,132,138,220/) # site 2 color bluegreen,(/lectin///104,45/) # Generate van der Waals surface show surface,lectin # Ligands in different colors set stick_radius,0.05 color magenta,one show sticks,one color yellow,two show sticks,two color red,three show sticks,three This works very well. Maybe a wizard could be created to automatically split a structure into separate objects for the different chains? -- Lieven Buts Vrije Universiteit Brussel
