Re: [PyMOL] coordination bonds
On Sun, May 23, 2010 at 6:33 PM, Maia Cherney wrote: > Thank you for your help. However, I have 4 Mg ions in the au, so all Mg > ions (and all coordinated ligands) got connected. I need only coordination > for one Mg. > Then you need to qualify the selection with the residue number, and repeat up to 4 times. Same principle still applies, though: dist (elem mg and resid 341), (all within 2.2 of (elem mg and resid 341)) this particular example may be unnecessarily verbose if the residue number is unique. -Nat -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] coordination bonds
On Sun, May 23, 2010 at 3:55 PM, Maia Cherney wrote: > I would like to show coordination bonds between Mg ion and its ligands > (oxygens) as broken lines, the distance of Mg-O bond is between 1.9-2.2 A. > dist elem mg, (all within 2.2 of elem mg) Might need to try a slightly longer length to catch everything. -Nat -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] for evaluation only
On Thu, Apr 29, 2010 at 3:03 PM, victor kenyon wrote: > i am an academic using pymol and the new build places a "for > evaluation only" graphic on top of the rendered structure. not very > helpful for presentations, publications and the like. how do i > circumvent this without using chimera to generate my images for pubs. > Use the open-source version, I would be very surprised if that overlays anything. Or download one of the builds of version 0.99, which is missing some nifty features but still more than adequate for publication graphics as long as you don't need to show anisotropic Bs. http://www.pymol.org/rel/099/ -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Continously check the file of a molecule, and do action when it gets modified
On Fri, Mar 26, 2010 at 5:14 PM, Werner Schroedinger <
werner.schroedin...@googlemail.com> wrote:
> For making this procedure faster and more automaticm I wonder if somehow
> can I tell pymol to pay atention to some external file, or for the
> ligand being visualized now, to its copy on the hard disk, and
> continuosly monitor it, so when it detects a change (for instance,
> beacuse the quantum program did something) reload the molecule and
> display it.
>
There may already be a built-in function to do this in PyMOL, but I'm not
aware of it. It's easy to script in Python, however. The code below
definitely works on Mac. Depending on how fast your calculation is, you may
want to increase or decrease the interval, but 2s is a reasonable place to
start.
-Nat
from pymol import cmd
import threading
import os.path
import time
class monitor_file (object) :
def __init__ (self, file_name, object_name, interval=2, verbose=True) :
self.file_name = file_name
self.object_name = object_name
self.interval = interval
self.abort = False
self.last_mtime = 0
if os.path.isfile(file_name) :
self.reload_file()
self.last_mtime = os.path.getmtime(file_name)
def reload_file (self) :
if self.verbose :
print "Reloading %s as '%s'" % (self.file_name, self.object_name)
cmd.load(self.file_name, self.object_name, state=1)
def start (self) :
if self.verbose :
print "starting thread"
t = threading.Thread(target=self.run)
t.start()
def run (self) :
while not self.abort :
if os.path.isfile(self.file_name) :
if self.verbose :
print "checking file mtime. . ."
current_mtime = os.path.getmtime(self.file_name)
if current_mtime > self.last_mtime :
self.reload_file()
self.last_mtime = current_mtime
time.sleep(self.interval)
return True
def stop (self) :
self.abort = True
# Usage
m = monitor_file("/var/tmp/caffeine.pdb", "caffeine")
m.start()
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[PyMOL] recentering and zooming on xyz coordinates
Is there a way to do this in such a way that the rest of the view matrix changes appropriately, including clipping planes, etc.? There is a handy pair of functions in Coot that do this: set_rotation_centre(x, y, z) set_zoom(30) which has the advantage of adjusting the perspective and focusing on exactly the residue/molecule of interest. I tried to emulate the first part in PyMOL: def recenter_and_zoom (self, x, y, z) : view = list(cmd.get_view()) view[12] = x view[13] = y view[14] = z cmd.set_view(view) which sets the center of rotation, but the perspective is screwy because the rest of the view matrix is unchanged. I can figure out the equivalent 'zoom' command for the residue of interest if I really need to, but I already have the coordinates computed, so I'd rather try to figure out how to adjust the zoom level through the matrix instead. (Sorry if this is a little incoherent - I still don't understand matrix arithmetic in OpenGL.) thanks, Nat -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] getting Residue environment distances and residue-residue distances programatically
On Tue, Mar 23, 2010 at 12:48 PM, hari jayaram wrote: > Hi > I want to write a python/pymol script that will give me residue -residue > distances within a pdb file programmatically > > I know that within pymol I can get a distance object using > > select r55 , chain A and resi 55 > select r 22 , chain A and resi 22 > > distance (r55) ,(r22) > > This creates the dist01 object . If I wanted to do this using a python > script and get a pretty print of all the distances in the distance object , > how do I do that? > Also pointers to other python toolkits that can allow me to make such > measurements outside pymol will be greatly appreciated. > CCTBX will do this for sure - it supports a selection syntax very similar to PyMOL's. It isn't particularly intuitive, however; if you're interested in using it, contact me offline and I can send you some examples. There is also BioPython, which is written for bioinformatics rather than crystallography and appears to have a much simpler API (but will definitely read PDB files). -Nat -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 5
On Sun, Feb 14, 2010 at 4:39 PM, David Hall wrote: > I don't think DynoPlot can't do this. Are there even callbacks to > watch for things like changing state in the Pymol GUI? Maybe that > should be a feature request as it would allow for a lot more powerful > plugins. Callbacks that we can bind to through TKinter to watch for > modifications in the OpenGL window of Pymol like changing state, > moving atoms, etc, then we can easily build boxes that reflect these > changes. If this is somehow already possible, I would love someone to > point me to an example. Check out pymol.importing.load_callback - is that what you were thinking of? (I think I've tried this before, but I can't remember exactly what the behavior was.) -Nat -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] color by element
On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera wrote:
> How can I use the color by element (HNOS) function present in the GUI,
> in a script?
>
I don't think there's a single command that does this; I've always done
something like this:
color grey80, elem c
color white, elem h
color red, elem o
color blue, elem n
color orange, elem s
and so on (in python, these become 'cmd.color("grey80", "elem c")', etc.).
I just discovered that there is also a separate color name for each
element, e.g. "color carbon, elem c" will work, but the default coloring
scheme seems a bit wacky sometimes (carbon is green, etc.). If there was a
convenient way to switch between available color sets (e.g. all of the
options available in the menus), that would be awesome. Currently the
atom-name colors are hardcoded in C, unfortunately.
Nat
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Re: [PyMOL] New Feature Ideas
On Thu, Jan 21, 2010 at 6:10 AM, Schubert, Carsten [PRDUS] < cschu...@its.jnj.com> wrote: > 4) A better density wizard, let's just copy coot and be done with it. > Ability to dynamically bind density levels or some other properties to > the scroll-wheel for that matter. > +1 > 6) Integration/bundling of wxPython as an alternative to TCL/Tk?? > Also +1. Warren mentioned this last year as a possibility for integrating PyMOL with the Phenix GUI, and in theory support for embedding a PyMOL view in wxPython is already present. However, that code appears to be very old and not maintained - I couldn't get it to work even after updating it to use the newer wx modules. I suspect there is not much work to do in order to resurrect it, but I don't know enough about PyMOL internals, or have time to learn. Note that this feature (if it were open-source) would allow anyone to make a native Mac PyMOL GUI and distribute that, so it isn't something I'd ask Schrodinger to subsidize. (If anyone else is interested in helping figure this out, however, let me know.) 7) Internal FFT routines to be able to read map-coefficients > +2. I believe the CCP4 libraries for this are open-source, so those are one option. CCTBX is another (I have tried this and it works), but this will be a lot more overhead. -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Preserving sec. structure in states for animation
On Tue, Jan 12, 2010 at 11:13 AM, Schubert, Carsten [PRDUS] < cschu...@its.jnj.com> wrote: > I am trying to make a movie form a set of morphed pdb files. Currently > the individual files are loaded into the same object with increasing states, > all pdb files contain the SHEET and HELIX record created by dssp. The > object is then displayed as a cartoon. When I loop over the states I > noticed that Pymol only seems to take secondary structure information from > the first pdb file into account. For instance I have a helix which is split > into 2 during the morph, but only displayed as one helix during the > animation, albeit a bit stretched. Loading the individual files produces the > right sec. structure. Any idea how I can convince Pymol to update the > cartoon representation with each frame? > I don't think there's any way to do this that doesn't involve some scripting. My experience may be out of date, since I last tried this around 2002, but I don't think the movie API has changed much since then. I ultimately rendered each frame separately (i.e. different object for each PDB file) using the same view matrix. However, depending on how finely you want to show the changes in secondary structure, something like the following should work: load frame1.pdb, morph . . . load frame20.pdb, morph mset 1 -10 mpng movie, first=1 alter morph and resi 100:120, ss='H' mset 11 -20 mpng movie, first=11 This is just off the top of my head - I can't guarantee that it will work exactly as written, but it's pretty close to what you need. In theory, it will produce 20 frames, movie0001.png through movie0020.png, which should appear continuous. -Nat -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Electron density grid
On Thu, Dec 17, 2009 at 10:54 AM, Jason C Porta wrote: > I have been trying to modify the grid spacing on 2Fo-Fc map that was loaded > into PyMol directly from phenix.refine. The mesh object is generated from > the isomesh command. Basically, I would like there to be fewer grid points > so that the density isn't so thick. If anyone has any advice, it would be > greatly appreciated. The grid spacing is built in to XPLOR maps. The only workaround I can suggest is to start from the map coefficients in MTZ format, and run CCP4 FFT to output a CCP4 format map with the grid spacing you prefer. (0.33*resolution is the default in most programs, but phenix.refine uses 0.25*resolution.) I'll add a program to the Phenix GUI to do this at some point. For now, I'll see if I can make it easier to change the resolution factor from the GUI. -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Alignment Objects
On Fri, Sep 11, 2009 at 1:59 PM, Maia Cherney wrote: > Is it posible in pymol to select all residues of a certain type > automatically, like all arginines or all lysines + arginines in a chain? select resnam arg select chain A and (resnam lys or resnam arg) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] about secondary structure assignement: help
On Tue, Jul 21, 2009 at 12:23 PM, Paola Beassoni wrote: > Dear Pymol Users, > i am working with some pdb files with no secondary structures assignments > embedded on it. Then when i try to see my molecules on cartoon diagrams, i > see the secondary structure different to another programs, VMD for example. > I used the command alter (for example alter 10-34/, ss='S'), and i am > capable of assign the secondary structure that i want but this is just > temporary. If i save the molecule, when i oppen it again it has the original > secondary structure and no the altered one. > Can anyone help me about this??? I really prefer pymol instead other > programs for visualization! The most compatible solution is probably to generate the HELIX and SHEET records for your PDB file, which PyMOL will read (not sure about VMD). There is an open-source program called KSDSSP that will do this: http://www.cgl.ucsf.edu/Overview/software.html#ksdssp I haven't used it very much, but it's supposedly a re-implementation of the original DSSP algorithm, so theoretically very robust. If you're continually generating new PDB files (e.g. refining the structure, etc.) you'll probably need to keep these records in a separate file and paste them into every new PDB file, since most programs won't retain that information when writing files. If you don't like the results, it's fairly simple to modify the records to suit your taste. Alternately, you can save a PyMOL script containing the alter commands and just invoke that every time you load your structure. -Nat -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Homology Modeling in Pymol
On Tue, Jun 30, 2009 at 2:24 PM, Buz Barstow wrote: > I have a very large library (almost 1000) of similar genetic > sequences, for which I would like to generate homology models. Does > anyone know of a way to automate requests to a homology modeling > server, such as SWISS-Model through pymol, or alternatively through > python? I believe Modeller uses Python - never tried it myself, though. There is a server for Modeller but academic users can download the program itself. There is in fact an API for using SWISS-Model from a Perl script (which could probably be converted to Python, or wrapped by a Python script), which I used years ago for a similar project. As far as I know this is unpublished, probably because they don't want people to trash their server, but they were happy to supply it when I contacted the site maintainer. They asked that I limit the frequency of my requests, however. I would recommend emailing them. (I have no idea how Modeller compares to SWISS-Model, but I suspect it's more rigorous, especially when sequence homology is remote.) There are other ways to go about this - bioinformaticists have been abusing online databases and servers like this for years - but it's considered bad etiquette to do this without permission (and some groups explicitly forbid this use). -Nat -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Newbie attempting to python script: ImportError: No module named _cmd
On Fri, May 1, 2009 at 3:57 AM, Luke Goodsell wrote: > I'm trying to set up my machine to be able to run python scripts using > the PyMol API, but whenever I try to import the pymol module, I get the > following output: > . . . > I am running Mac OS X 10.5.6. I downloaded MacPyMol 1.1r1 from > http://delsci.com/macpymol/ (the educational edition, as I am a student). > My PYMOL_PATH: /Applications/PyMOLX11Hybrid.app/pymol > My PYMOL_EXE: /Applications/PyMOLX11Hybrid.app/Contents/MacOS/MacPyMOL > . . . > I copied the contents of /Applications/PyMOLX11Hybrid.app/pymol/modules > to /System/Library/Frameworks/Python.framework/Versions/2.5/lib/pymol, > as per my understanding of the top of __init__.py > It's not entirely clear to me what you're trying to do, but I'm pretty certain it's guaranteed not to work. You can't just take compiled objects from inside app bundles and move them around - especially on Mac. You definitely shouldn't be installing PyMOL modules that way. If you need them available for importing by /usr/bin/python, download the open-source version from SourceForge and install it using python distutils (i.e. "python setup.py build" and so on). I just tried this and it seems to work fine - only takes about 10 minutes. -Nat -- Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Roving detail and Roving density
On Wed, Apr 22, 2009 at 6:37 PM, Craig Smith wrote:
> I was looking at the demos in pymol (wizard --> demo) and saw
> interesting features called roving detail and roving density. I
> looked in the manual on how to do this feature but couldn't find it.
> Could anyone point me in the right direction or show me how to
> interactively display electron density as I move through my structure.
>
This is what I do (sorry, it's in Python, but easily converted to PyMOL
commands). It assumes that you have two maps loaded, named "2fofc" and
"fofc".(Some of it is cribbed from the C code for the roving density
demo.)
cmd.set("roving_detail", 20)
cmd.set("roving_isomesh", 20)
cmd.set("roving_origin", 1)
cmd.set("roving_sticks", 0)
cmd.set("roving_ribbon", 0)
cmd.set("roving_lines", 0)
cmd.set("roving_spheres", 0)
cmd.set("roving_nb_spheres", 0)
cmd.set("roving_polar_contacts", 0)
cmd.set("roving_polar_cutoff", 0)
cmd.set("roving_map1_name", "2fofc")
cmd.set("roving_map1_level", 1)
cmd.set("roving_map2_name", "fofc")
cmd.set("roving_map3_name", "fofc")
cmd.set("roving_map2_level", 3)
cmd.set("roving_map3_level", -3)
cmd.isomesh("rov_m1", "2fofc", 1.0, "center", 20)
cmd.isomesh("rov_m2", "fofc", 3.0, "center", 20)
cmd.isomesh("rov_m3", "fofc", -3.0, "center", 20)
cmd.color("skyblue", "rov_m1")
cmd.color("green", "rov_m2")
cmd.color("red", "rov_m3")
This might not be ideal - some of those 'set' commands may be unnecessary or
incorrect. However, the end result works more or less like Coot, which is
what I was aiming for.
-Nat
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[PyMOL] Roving density
Hi-- Can the roving mesh be used without changing the model appearance? I'd prefer to just show the entire structure as lines only, but it looks like the roving_detail setting controls both model and mesh. thanks, Nat
Re: [PyMOL] Ray Tracing A Protein Gallery
On Mon, Dec 15, 2008 at 11:41 AM, Buz Barstow wrote: > I'm making a gallery of protein molecules for my PhD thesis. I'd like > to find an automatic way to ensure that all of the ray traced images > have the same scale. Is there an easy way to do this? > Translate every model so that the center is at the origin, then use the set_view command to apply the same viewing matrix for each model. (You can still rotate the models, just don't zoom.) I'm not sure if there's already a simple way to do the translation from within PyMOL, but it should be quite straightforward using cctbx or CNS or something similar. -Nat
Re: [PyMOL] remove cartesian coordinate from w/in transparent metal ions
On Wed, Oct 29, 2008 at 11:39 AM, Thomas S. Leyh, Ph. D. wrote: > Every once in a while, I try to show a metal ion as a tranparent > sphere and inevetiably get stuck trying to make the tiny cartesian > coordinate system that appears at the center of the sphere disappear so it > doesn't "show through". Suggestions? > I think you want "hide nonbonded". I have a related question: is there a way (or could there be) to control the default appearance of molecules upon loading? Personally, when I use PyMOL I almost always want to look at cartoons, without nonbonded atoms. Something as simple as a few new settings that I could throw in ~/.pymolrc would be fine.
Re: [PyMOL] displaying anisotropy ellipsoids in PyMOL v0.99rc6 running on Windows XP
Tim Fenn wrote something to do this a few years ago, but I don't think you can ray-trace them: http://www.stanford.edu/~fenn/pdb_aniso.py On Mon, Sep 22, 2008 at 2:48 PM, "Javier M. González" wrote: > Hi all, could someone advise me on the simplest way to display anisotropy > ellipsoids in PyMOL v0.99rc6 running on Windows XP? > Is there any script to do this? > I haven't moved to the latest versions of PyMOL yet. > > Any help would be appreciated. Thanks in advance. > > Javier. > > -- > Lic. Javier M. González > Instituto de Biología Molecular y Celular de Rosario, IBR-CONICET > Universidad Nacional Rosario, Facultad de Ciencias Bioquímicas y > Farmacéuticas, Area Biofísica > Suipacha 531 CP S2002LRK > Tel: +54 341 4350661 / 4350596 / 4351235 Ext.109 > FAX: +54 341 4390465 > Rosario, Santa Fe, ARGENTINA > gonza...@ibr.gov.ar > > > - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > >
Re: [PyMOL] export 2 molecules to one pdb file?
Just use the (PyMOL) command line: "save complex.pdb" will save all objects. You'll need to figure out what directory you're in first - by default, this is probably /Applications, but "cd ~" will get you home. (Hey Warren, could this be changed so "cd" alone works, like in a Unix shell?) (Or if you have more than just those two molecules: "save complex.pdb, object1 or object2") On Wed, Aug 13, 2008 at 12:01 PM, Paul Shannon wrote: > Thanks to Warren for setting me straight on independent positioning of > molecules. > > Now I wish to write out the two molecules, together, to one pdb file, > as required by RosettaDock. I must be blind. They say: > >...from the main menu, File→Export Molecule can be used to write > a PDB file containing >the starting structure with both docking partners. > > The closest menu option I can find (using MacPyMol) is File->Save > Molecule... > The resulting dialog apparently only allows one object to be written. > > Any advice? Thanks! > > - Paul > - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] Mac OS X install, general PyMOL function - badly need overview
> I have downloaded the version (0.79.dmg.gz) of the PyMol package > suggested by Luca Jovine, but don't know how to get a working version of > Python installed. The only links I can find are to Python .exe files > for versions 2.1 and 1.5.2, and I have no idea which of the other > downloads (xx-contrib, ext) are needed. For that matter, is the v. 0.79 It's been a while since I played with the Mac version (0.79), but I recall it not needing any additional installations. Python is pretty tightly integrated into PyMOL in the "default" setup, from what I can tell. Anyway, the installed application should run with a simple double-click, though I ended up invoking it from a shell. I imagine the non-native version would be considerably more complicated to set up, but I haven't tried it. > tutorials back in May - did anything come of that? A basic intro to > PyMOL is what I, a confirmed nonprogrammer (and damned proud of it) > need, no doubt like many others. Maybe some academics have already put I've found the manual does an adequate job of introduction, even if it's very outdated. My only real complaint is that it barely touches on the subject of programming with/for PyMOL (I'm a programmer, not a crystallographer). There's also this: http://pymol.sourceforge.net/tutorial/index.html It's geared towards Windows users, but this shouldn't make too much of a difference. -Nat
Re: [PyMOL] Secondary structure assignments
> The best way to avoid "derivative work" concern is to code in a "clean room" > fashion, without reference to someone else's code. In principle, this could > be done working from the original paper(s) that describe an algorithm. I assume this is what authors of other packages have done in the past. If there's enough interest, and no one is working on this already, I'd be willing to take a stab at it. > Not that I'm volunteering ;-) Just that I would hate to see someone who was > willing and interested in implementing secondary structure code for PyMol to > be frightened off the job if, indeed, it could be done in a way that respects > others' rights. The other thing I'd find useful is some molecular mechanics tools, particularly energy minimization. Blending PyMOL with MMTK seems like a good way to do this, since MMTK's license looks fairly liberal. Personally, I'd have to spend two weeks looking at the code for both packages before I could even start thinking about how this would need to be done. I'm certainly not capable of implementing anything like that from scratch- I slept through math class in college. -Nat Echols
[PyMOL] clipping planes
I don't understand how these work at all. Is there any straightforward way, given a structure's position and dimensions and the desired camera position, to calculate the ideal position for the plane? How does PyMOL decide where to put the planes? Right now I'm missing by a small amount and atoms disappear randomly. thanks, Nat
Re: [PyMOL] Secondary structure assignments
> Ideally util.ss could become a shell that would know (from the environment?) > if dssp or similar was installed, then either run dssp and parse the output > to assign the ss, or else run the ss asignment code in the current util.ss if > no other options were available. I've basically done this, though right now it uses STRIDE because the output is easier to parse- it just uses popen2() to read the output from the STRIDE executable (Does anyone actually know what the difference is between these two programs?). But since I already wrote a dssp parser in Perl, it shouldn't take long to modify. My feeling is that it would be better to have a robust secondary structure algorithm built in, since I've already hit limitations in the method I'm using. Though to be honest, I've been getting away with using util.ss for some time now. > The ability to write a pdb with the newly generated ss information would be > useful as well (or perhaps pymol already can do this if it knows the > protein's ss?). I've done this too, though I think it breaks with more than one chain right now. If I get around to cleaning this up I'd be more than happy to pass it on. -Nat
Re: [PyMOL] Secondary structure assignments
> Yes, please. There are some structures that have to be generated by using > symmetry operations defined in the "REMARK 350" lines in the pdb file > (example: > 1jjy.pdb). The only way (I know of, if you know a better one, please tell me) > to > do this is going to http://pqs.ebi.ac.uk where the complete structure is > generated for you. However, the caveat is: This service removes the secondary > structure information, and up to now I have manually copy-pasted it into the > new > pdb file (Annoying work, really). Unfortunately, the script I came up with won't deal with that; it basically uses a third-party program to rescan the input file and uses the alter command to correctly set the structure (or combines this with file loading as a single command). If anyone would like this, I'm happy to email it to them, but it's not really a good general solution. How hard would it be to incorporate the DSSP algorithm? I was looking at the source for RasMol, which has a complete implementation. My feeling is that this could be ported without too much misery. However, RasMol's license terms are different, and I suspect even a complete translation into Python with the ChemPy API would still be considered a "derivative work", meaning it wouldn't be able to be part of the main distribution, and meaning someone would still have to code DSSP from scratch. (I have utterly no idea how it works, but RasMol's code seems clear enough despite lack of comments) -Nat
Re: [PyMOL] Secondary structure assignments
> programs. So I am in search of a solution. Can one manually create a > secondary structure assignment matrix to insert into the PDB file? I must > admit that as a novice I do not understand the formatting of the secondary > structure matrices that I have seen embedded in some PDB files. Is there a > resource somewhere that explains the formatting of such a matrix? I've been fiddling with this for my own work; I wrote a parser in Perl to embed structural annotation in a PDB file based on output from DSSP, STRIDE, or RasMol. Unfortunately it doesn't handle multiple chains yet, but I'm working on making it more general. I suppose since I only use this for loading files into PyMOL, I could just write it in Python as a PyMOL module. . . would that be useful to anyone else? The complete PDB specification for SS annotation is here: http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_42.html http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_44.html http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_45.html However, PyMOL's built-in commands end up being much easier to use... I wish I'd realized that before I wrote my parser. > Alternatively, is there a manual series of Pymol commands to directly assign > secondary structure for a protein for insertion into the .pml script file? alter atom_selection, ss='L' (or 'H' or 'S', I think) > Even better, is there a separate program that can assign secondary structure > and then allow you to save the revised PDB file with the secondary structure > assignments inserted into the PDB output. I would be willing to accept any If there is, I'd like to know too! -Nat Echols Gerstein Lab Yale University
Re: [PyMOL] Suppress some output
> Is there a way to keep my program 'quiet', > or I can customize the output message myself? Depending on your OS and shell, something like this may work: denethor:~ > /usr/local/pymol/pymol.com >/dev/null 2>/dev/null This works under Bash in any modern Linux distribution, from what I've seen. I suspect it would work on Irix too (still using Bash). I've had the exact same problem- mainly with util.rainbow(). -Nat
Re: [PyMOL] pymol without GL
> pymol.com -c scriptname > But you have to get your view first somehow. I can't do this until I compile it; if I try running a pre-existing build I get errors because one of the GL libraries isn't found. I've ended up just installing GL on my system, but the crack technical wizards at SuSE have decided I need Qt and KDE as well. . . on web server. *sigh* It's not really important that I be able to do this, and there's plenty of disk space to spare, but I prefer limited installs on a server. By the way, has anyone else experimented with hardware antialiasing on NVidia cards under Linux? I've had mixed results so far, and I'm not sure what I'm doing wrong (this is with a GeForce 4 Ti 4600). -Nat
[PyMOL] pymol without GL
quick question: I'm trying to do batch jobs on a server. Obviously, there's no X or OpenGL installed. Is there any way to build PyMOL without any graphical frontend, and just use it as a raytracer? I don't want to go through the trouble of adding in these libraries... thanks, Nat
[PyMOL] view area
Hi-- I'm trying to render a large number of images of a trajectory automatically. I have two problems: 1. There doesn't seem to be any way to manually speciify the view area. Thus, if I want all images to be in the same frame of reference, I need to load them all as different states of the same object, e.g. "load frame01.pdb, mov" many times over. This works fine, but even with 4GB of memory PyMOL crashes when I load everything in. I've found a way around this, but it would be much simpler if I could specifiy exactly what angle and window to use for rendering. I'm pretty sure this doesn't exist right now, but will it in the future? 2. Using pretty much any method, PyMOL frequently lops off part of the molecule. This has become a large problem; I'm using PyMOL quite a bit to make animations (replacing Molscript entirely), and frequently an interesting part of the structure will be out of frame. How can I avoid this? This is all being done on the command line (usually invoked by some CGI script), so I have no way of adjusting the zoom. 'zoom' hasn't been too much help. Any advice would be much appreciated. I'm trying to do stuff that would be messy in pretty much any environment (e.g. I can't even load all the structures with less than 1GB of memory), but the viewport problems apply to pretty much anything. thanks, Nat
