[PyMOL] (almost) using APBS within PyMOL
Okay, I think I'm getting real close to having this working (Mac G4 AlBook, OSX 10.3.5, Apple X11, X11PyMOL 0.97) Here's my simple-minded approach so far, to get electrostatics in PyMOL instead of the Honig Lab's online GRASS setup (which is also good). 1) maloc and apbs have been successfully compiled from source and installed in /usr/local 2) M. Lerner's APBS Tools plugin 'About' tab says to load a structure; the 'Visualization' tab says to load a molecule and a map So, I just loaded a pdb file like I usually do, and displayed as cartoon 3) set the correct location of the apbs binary (/usr/local/bin/apbs), clicked 'Set grid', then clicked 'run APBS' 4) those pink anchor handles in pymol started flashing around my protein cartoon, then a pause, then the cartoon disappeared and the pink anchors flashed around some more, then all went black. Nothing happens when I click 'Update' under the Visualization tab. 5) PyMOL output: _ coarsedim is [155.64339675903321, 159.7681230545044, 272.30599403381348] finedim is [111.55493927001953, 113.98124885559082, 180.17999649047852] center is [128.19829940795898, 61.232932090759277, 21.427999496459961] finegridpoints is [225, 257, 385] radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr WARNING: 48 atoms did not have formal charges assigned WARNING: 96 atoms did not have properties assigned ObjectMapLoadDXFile-Error: Unable to open file! _ supposing the WARNINGs are harmless, I'm not sure what to try next. Maybe I need the electron density map after all? --Michael
[PyMOL] color individual residues on a surface?
Hi PyMOL'ers I'm trying to figure out how to do something that looks like the following figure: http://www.uvm.edu/~mbovee/structures/surface.png It seems any individual residues I color always map onto the cartoon ribbon representation rather than onto the surface representation. Is this currently possible in PyMOL to do what is pictured in the link above? Thanks, --Michael Bovee, Ph.D. Dept. of Biochemistry University of Vermont
[PyMOL] problem with dist
Hi,I'm running MacPyMOL 0.95 on a G3 Lombard/BronzeKeyboard Powerbook, OSX 10.2.8. The ref manual says to measure distances you can ctrl-shift left, and then right click to select the positions to measure. I can ctrl-shift left click to select the first atom, but ctrl-shift right click doesnt do anything. My workaround is to ctrl-shift left click twice, which displays the path to the atom in the command history window. I can then copy paste them in behind a dist command. Can anyone else confirm this behaviour? Thanks, --Michael
Re: [PyMOL] question on differential coloring of protein chains
On Tuesday, February 17, 2004, at 02:57 PM, ALEX DAJKOVIC wrote: hello- i am new to pymol and am trying to figure out how to differentially color different chains (i.e. different proteins) in the structure i am viewing. the structure i am working with is actually a structure of two proteins that were co-crystalized and i would like assign different colors to them. thanks for your help. alex dajkovic Hello Alex, I think what you want is to use the 'select' function in combination with the 'resi' function. This is documented in the reference manual. Following is a helpful summary that was sent to me by Robert L. Campbell, Ph.D. Let's say I wanted to create a single residue selection for Lysine 465 (and I choose to call the selection 'K465'), so that I could color and display it the way I wanted: (insert your particular atom coordinates file name where you see square brackets below) ___ select K465, ([filename] and chain A and resi 465) or you could shorten the selection string: select ak465, (abc c. a and r. 465) or use the shorthand notation: select ak465, /abc//a/465 ___ ˜ Now to create multiple residue selections, just separate the start and end residue numbers by a colon, I think, following the word 'resi' Once you create your unique selections they show up in the right panel list and you can further manipulate their display properties as you see fit. Regards, --Michael
[PyMOL] cannot print most of user manual pdf
Hi there, Trying to make myself a desk copy of the user manual is proving to be a pain. I can print the text of the table of contents, but anything with screen shot graphics never prints from our new HP2300 (48MB of memory). The refman pdf printed fine, but this userman pdf file seems corrupted in some way. It is only 1.4 MB, but I cannot even print a selection of 4 pages onto a one sheet page layout. Is this a known problem, or just MY problem? :0) Thanks, --Michael
[PyMOL] assign secondary structure?
Hi, I have a 'raw' pdb file of atom coordinates only, and I'm hoping to use the dss command in pymol to get helix and strand designations that I can paste back into the header space of the pdb so that I can model fancy helices and strands and so forth to get a nice picture in pymol. Then I can superpose features with homologous proteins for which this header info is available. I just didnt want to modify or create this header info 'by hand' if I didn't have to... But, I can't get dss to work in pymol (even the refman warns that this algorithm has not been rigorously validated). The refman says USAGE is dss selection, state Does this mean I need to first make a selection that encompasses some part (or whole) of the molecule, or should this work on the entire pdb? I don't know what 'states' are so I just opted for '0' which is supposed to mean 'all states'. Thanks, --Michael Bovee
[PyMOL] cannot 'fit' a particular pdb file
Hi, I have loaded 3 pdb files of homologous forms of an enzyme. The 'fit' command works for superimposing/aligning two of them, but the third file always gives a No Atoms Selected error. Is there something in the pdb file I can fix? As a general rule now, I Hide Everything at first and then Show Lines as I begin with a new PyMOL session. I can see all three molecules, just can't align the third one (EcHRSade) with the first two (TtHisRS and SaHRS). PyMOLfit TtHisRS, SaHRS Executive: RMS =4.222 (718 to 718 atoms) PyMOLfit TtHisRS, EcHRSade ExecutiveRMS-Error: No atoms selected. PyMOLfit EcHRSade, TtHisRS ExecutiveRMS-Error: No atoms selected. PyMOLfit EcHRSade, SaHRS ExecutiveRMS-Error: No atoms selected. Thanks, --Michael
[PyMOL] aa residues disconnected from 'fancy helices'?
Hi all, I'm just starting to try out PyMOL (fink package 0.90-2, running through Apple's X11beta2, on a Lombard G3PB, MacOS 10.2.4). Its much easier to learn that I thought it would be! Well done Warren, and codevelopers! One puzzling thing I've noticed: when I build a model of my protein of interest using 'set cartoon_fancy_helices,1' and then show sidechains for several key catalytic residues, I find that the amino acids that reside along beta sheet or alpha helix regions appear properly connected to the alpha carbon backbone representation, but sidechains of amino acids that reside on 'strand' regions appear to float in midair and do not connect to the strand backbone. Anyone else seen this behaviour? Thanks! --Michael Bovee University of Vermont
Re: [PyMOL] aa residues disconnected from 'fancy helices'?
Friday, November 7, 2003, 8:50:13 AM, you wrote: MB ...I built a model of my protein of interest using 'set cartoon_fancy_helices,1'...but sidechains of MBamino acids that reside on 'strand' regions appear to float in midair and do not connect to the strand MBbackbone... On Friday, November 7, 2003, at 12:37 PM, Jacob Corn wrote: snip turn off Smooth Loops under the Cartoon menu... Jacob Ayup, that did the trick. Thanks! --Michael
