Re: [PyMOL] align and RMSD calculation

On Fri, Oct 3, 2014 at 11:17 AM, PC wrote: > Sorry its me again. Can someone tell me where I can find the code for > the align command? > It seems the RMSD differs from other online tools I found. > Are you running it with default arguments? If you do this: align object1, object2 it does an

Re: [PyMOL] pymol svn

I'm getting the same error for a completely unrelated SourceForge repository (but strangely, another works fine). I suspect they're having server problems - it wouldn't be the first time. -Nat On Wed, Apr 30, 2014 at 1:39 PM, Andreas Förster wrote: > Dear all, > > trying to update PyMOL with t

Re: [PyMOL] Roving maps from scripting level?

On Fri, Jan 24, 2014 at 11:55 AM, Schubert, Carsten [JRDUS] < cschu...@its.jnj.com> wrote: > I am trying to get the roving density features to work from a scripting > level w/o invoking the Density Wizard. Setting up the following script > loads fine, but does not enable roving. Is there anything

Re: [PyMOL] ccp4 map sigma setting

On Wed, Feb 20, 2013 at 2:21 PM, Yarrow Madrona wrote: > When I display ccp4 maps in pymol they look a bit larger than I am used to > seeing in coot for a given sigma setting. Is it common for users to > increase the sigma setting when displaying maps in pymol? Have you tried: set normalize_ccp4

Re: [PyMOL] default settings

On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg wrote: > You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol > does try to read it when it starts up. > > However, it errors every time. > > If I put just this one command in the file and start up PyMol, it comes back >

Re: [PyMOL] default settings

On Wed, Jan 30, 2013 at 10:43 AM, H. Adam Steinberg wrote: > This is great, but looks like it's only for Windows? Where would one put this > pymolrc.pym file on a Mac? > > Quoting the wiki: "On a linux-type system, this file will be located in /path/

Re: [PyMOL] default settings

On Wed, Jan 30, 2013 at 8:33 AM, H. Adam Steinberg wrote: > Is there anyway to change the default settings in PyMol so that when I open > the program, it is using my specified defaults? or perhaps there is a way a > script can automatically be run at startup? Or automatically run when I > fetch in

Re: [PyMOL] Shrinking the sidebar

On Mon, Dec 10, 2012 at 12:02 PM, Alex Truong wrote: > I was just wondering if it was possible to shrink the sidebar width so I > have more viewing space? I regularly work with multiple windows open, > usually splitscreen (vertically split). Since I do most of my work on a > laptop with a 14-inch

Re: [PyMOL] Pymol in command mode - no output

On Mon, Nov 26, 2012 at 8:28 AM, Per Larsson wrote: > I'm running a pml-script file to render some images on a remote server, using > pymol 1.4, but I do not get any output at all. And no error message, so it is > hard to troubleshoot, unfortunately. > > To reduce the complexity of my script, I

Re: [PyMOL] cctbx and pymol version 1.41

On Fri, Oct 26, 2012 at 10:37 AM, joseph Lyons wrote: > I currently source cctbx from /usr/local/xtal/cctbx/cctbx_build/setpath.sh > with pymol in /usr/local/xtal/pymol_1.41/pymol > > I have tried the getting pymol to recognise the cctbx.python however I have > run into difficulties. > > I tried m

Re: [PyMOL] Is there or should there be a pymol annotation server?

On Fri, Jul 13, 2012 at 2:12 PM, Jason Vertrees wrote: > It would be nice if publishers required a common CSV format for > specifying contacts and annotations. Then we could easily pull the > data from reliable resources. But, alas, this doesn't exist. One possible (albeit incomplete) way to do t

Re: [PyMOL] Messed up structures in movie

On Wed, May 23, 2012 at 10:20 AM, Rituparna Sengupta wrote: > Sorry about the lack of description in the previous post. > The chemicals show incorrect bond connections. Some of the rings go missing. > In all, the structure changes and just by looking at it, its possible to tell > that the struct

[PyMOL] where does PyMOL install to on Windows?

I'm trying to figure out how to launch PyMOL automatically from a script on Windows. I'm stuck with the 0.99 build for now, where the .exe is C:\Program Files\DeLano Scientifc\PyMOL\PyMOL.exe Is this now C:\Program Files\Schrodinger\PyMOL\PyMOL.exe in the newer versions, or somewhere else? th

Re: [PyMOL] To build protein structure model?

On Mon, Jan 30, 2012 at 6:05 AM, Hong ZHAN wrote: > I am a new guy in this area.. And I just want to know how to build a > structure model of my protein from homologues crystal structure and protein > seq.??? You probably want to try using a homology modeling server for this rather than PyMOL:

[PyMOL] single pymol installation, multiple OSes

I have a weird problem: we have a cluster of Linux computers (managed by Sun Grid Engine) running at least three different distributions of Fedora. I compiled PyMOL on the head node (Fedora 8) and I want to invoke it on the command line to generate images as part of some other computations. I'm u

Re: [PyMOL] pipe structure to pymol

On Mon, Jan 23, 2012 at 12:42 PM, Simon Becker wrote: > I would like to visualize the intermediate structures my program > produces during the computation cycle. Every iteration it generates a > new structure. Is there a way to display this structure in pymol, using > e.g. a pipe? Does anyone have

Re: [PyMOL] pipe structure to pymol

On Mon, Jan 23, 2012 at 12:42 PM, Simon Becker wrote: > I would like to visualize the intermediate structures my program > produces during the computation cycle. Every iteration it generates a > new structure. Is there a way to display this structure in pymol, using > e.g. a pipe? Does anyone have

Re: [PyMOL] util.cba* for deeppurple...

On Tue, Jan 3, 2012 at 11:08 AM, Francis E Reyes wrote: > Seems like the pymolwiki doesn't show you can use util.cba in that way  . In > fact help util.cba is ambiguous. > > Anyway to specify an object or selection with that?  util.cba("deeppurple", > (selectionhere))  doesn't seem to work. Did

Re: [PyMOL] util.cba* for deeppurple...

On Tue, Jan 3, 2012 at 10:43 AM, Francis E Reyes wrote: > Is there anyway to change the carboncolor for coloring by atom type to deep > purple? > > http://www.pymolwiki.org/index.php/Advanced_Coloring#Coloring_by_atom_type > shows that i only have a limited set of util.cba* commands. util.cba("

Re: [PyMOL] PyMOL 1.5 release

On Mon, Nov 21, 2011 at 8:55 PM, Donnie Berkholz wrote: > I always wonder, are there actually people who feel they gain some sort > of competitive advantage by having access to PyMOL features first? > Doesn't seem to make sense because anyone else can pay for the same > level of access. Plus it's

Re: [PyMOL] compare crystal packing of two different Space Groups

I've never found a clean way to do this - what I do is to save a PDB file with the original model and the relevant symmetry mates, which I then use for the alignments. There may be a way to do is with object groups, however. (FYI, you'll probably also need to rename the chain IDs for the symmetry

Re: [PyMOL] insertion code

On Tue, Feb 15, 2011 at 2:07 PM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Interesting question. PyMOL's wildcards can help here: > > select allButInsertionsA, not (i. *A) > > This will look for all residue NUMBERS that end in "A" and select > everything but that. > Thanks, that

[PyMOL] insertion code

Is there a way to select specific insertion codes - or rather, their absence? I'm automatically building up selections like "chain A and ((resi 1:5) or (resi 10) or (resi 13))", and I want to ignore insertions, which tend to duplicate residue numbers. "help selection" didn't turn up anything, and

Re: [PyMOL] Wiki down?

On Thu, Jan 27, 2011 at 9:54 AM, Schubert, Carsten [PRDUS] < cschu...@its.jnj.com> wrote: > I am just getting a blank page when I try to access the Pymol Wiki. Do > other people see the same problem? > Working fine for me (using Safari on a Mac). -Nat

Re: [PyMOL] use PyMOL code in outer tkinter application

On Tue, Dec 21, 2010 at 2:42 PM, Jason Ferrara wrote: > I've been using the pymol2 interface to run pymol inside Qt widgets. There > doesn't seem to be any documentation for it, but once you figure it out it > seems to work well. Do you think you could put a quick summary of how to do this on t

Re: [PyMOL] Possible bug in set cartoon_cylindrical_helices

On Thu, Jun 17, 2010 at 3:41 PM, hari jayaram wrote: > In my tests obj01 is the object created from a selection and then the > property set for that object. But it seems that this does not just > create a cylindrical helix for just that object. > > For some reason the cartoon_cylindrical_helices

[PyMOL] what version did the "group" command appear in?

Sort of an obscure question, but I've run into problems with a plugin I wrote - based on what I've seen so far, I'm pretty sure it isn't in 0.99, but it would be helpful to know what the minimum required version is. thanks, Nat --

Re: [PyMOL] (no subject)

On Fri, May 28, 2010 at 10:49 AM, Thomas Juettemann wrote: > Hi Chris, > > the emails are only sent to you because you subscribed to the pymol-users > list. > If you don't want them anymore you need to unsubscribe. > > Click on "Show details" at the top of this email. Click then on: > unsubscribe

Re: [PyMOL] morphing between complexes

unfortunately I've already tried that server and I've seen that also in that case, the ligand is stripped out.I obtain movies with only the protein movements. I don't know if i have problems with my pdbs: I have 245 residues + 1 ligand (246). it has the ATOM and not the HETATM indication, could be

[PyMOL] double-click

This is a new pet peeve of mine: it's too easy to select a residue instead of bringing up the menu of actions. I still haven't figured out what the difference is, but I keep selecting by mistake. Is there any way to either control the sensitivity of the clicking, or turn off mouse selections

[PyMOL] mixing ray_shadows states

I'm trying to make a high-quality figure showing ligand binding in a cleft, incorporating sticks, electron density, and some combination of cartoon/surface/lines for the protein. Ray-traced shadows make the perspective much clearer but also add visual "noise" - for instance, the electron densi

Re: [PyMOL] Another Nvidia question (7676 driver)!

Any body know how to fix this. Have people tested this driver? Should I load an earlier driver? When dealing with NVidia cards, I've found this is always the first thing to try whenever a problem arises. Their Linux drivers are updated to support new hardware and fix old bugs, but they often

[PyMOL] scenes and movies

Apologies if this has been asked/answered already. My rotation student just showed me how PyMOL animates the transition between scenes, which makes for some beautiful zooming effects. Is it possible to capture these in a movie? thanks, Nat

[PyMOL] applying matrices to objects

Is there a simple tool for taking a rotation and translation matrix - in this case, the BIOMT records from a PDB file - and applying it to an object? Doesn't necessarily have to be in PyMOL; a simple script/program would do. thanks, Nat

Re: [PyMOL] align/fit

you can set the number of cycles of refinement on the command line. change this: > align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca to this: > align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca, 0, 0 I forget what the first 0 means; the second means "don't refine." It'll use all matching

Re: [PyMOL] fit command

> Fit only works with objects that are identical in terms of atom number, > chainID, atom name and what not. This is not the case for a protein on > one side and a protein plus ligand on the other. I've gotten away with some differences between chains. Sometimes you need to force it to fit using

Re: [PyMOL] keynote

> On a second note (and sorry to open up this debate again), What is the > consensus for displaying a pymol movie in a presentation package such as > powerpoint? i've tried avi and mpeg but i find that there is a loss in > the quailty when compared to the sharpness of a animated gif. I'm pretty su

Re: [PyMOL] sticks with different radii

> You can't just do: > set stick_radius, .5, name n+ca+c+o > set stick_radius, .2, ! name n+ca+c+o > because both selections belong to the same object and the whole object > is affected by the setting change. On the other hand, you CAN do this: show lines show sticks, name n+ca+c+o set stick_radi

Re: [PyMOL] Getting Closer to Wiki Time!

> Please revise, extend, and embellish. - structure alignment (pretty simple, but a lot of people don't know how to use the various commands) - as part of movies, a large section on available 3rd-party apps and codecs would be very useful (as well as workarounds for PowerPoint madness) -Nat

Re: [PyMOL] Desparate call for help

> I don't have red hat support yet. The problem appears to be that the > nvidia installer (nvidia...6629pkg2.run) is getting confused as to which > kernel is running. Just a couple of quick thoughts -- 1) Does /usr/src/linux point to the original installed kernel soruces or the updated kernel sou

Re: [PyMOL] animation format

> There is a well documented bug in Powerpoint 2004 for mac regarding > movie playback performance which seems to be the problem. There are > hundreds of posts on Microsoft's support forums. Actually when you > build the slide in PPT 2004 in edit mode the preview of the movie plays > fine but not

Re: [PyMOL] animation format

> Thanks to the poewrful software I was able to create some protein > animations using Python. As a mac user I have the option to save > directly the animation for quick time player. From the options I have > upom save, I tried 'movie' and 'animation' and both formats show a > reduced performance w

[PyMOL] display problems with 0.98b

I just downloaded the beta the other day and this is the first time I've tried it out. When I'm typing commands in the graphics window or using the menus on the internal interface, the display frequently breaks apart - a large rectangular portion literally gets clipped off from the rest of the vie

[PyMOL] pymol and cctbx

I'm trying to use Robert Campbell's draw_axes script with PyMOL 0.97 on Linux. Is there a simple way to get stock PyMOL to recognize stock CCTBX? I'm not having any success here. (If I have to I'll use the special distribution on the lab's Mac, but I'd rather just get it going on my computer.) t

Re: [PyMOL] blinking pictures on sgi4DIRIX646

> Hi, I have pymol 0.97 installed on a sgi workstation. However it keeps > the old picture when I move the molecule, which seems like a long time > delay. I wonder if people have similar experience. What kind of SGI? Anything less powerful than an Octane is going to be pretty useless for PyMOL.

Re: [PyMOL] animation using pymol

> areas of the protein that undergo movement and show general trends. There is > also a server at Yale (http://www.molmovdb.org/molmovdb/ ) that will perform > simulated annealing while morphing between two structures, thereby producing > intermediate structures that violate fewer protein restrain

Re: [PyMOL] having problems with batch rendering

> I have commented out most all the "quality" settings until I can figure > this thing out. well, if you comment out the setting for 'ray_trace_frames', it'll be using OpenGL for rendering. but you've launched on the command line, so there is no OpenGL. uncomment that line, and see if it works.

[PyMOL] extra bonds

I know this has come up before and I can't remember what the solution was. PyMOL is drawing bonds between the protein I'm interested in, the ATP analog, and the bound metal ions, presumably because the metals are close enough to the protein and analog for bonds to be autodetected. Is there a way t

Re: [PyMOL] Powermate dial with Pymol on OS X

I'm very curious about this dial all of a sudden - I just started doing refinements, and I'd love to use my laptop as much as possible instead of our slow old SGIs. Has anyone used it on Linux? How's it work with O? Could it theoretically be programmed to, say, flip through rotamer libraries or t

Re: [PyMOL] embeding pymol in a web page

> The downloaded script is then executed by Pymol, which can uses Python's > socket abilities to download PDB files and run Pymol commands on them. H, I like this idea. Can PyMOL open files directly over the web? It would be nice to simply type PyMOL> load http://server/1cll.pdb, calmodulin

Re: [PyMOL] Is exporting CGOs vertices possible?

PyMOL will already dump POVRAY format files; you should be able to feed these to Blender somehow. This looks like it might be useful: http://jmsoler.free.fr/util/blenderfile/povanim.htm No idea if it will work well. . . but probably worth a try before writing something yourself. On Wed, 10 Mar

Re: [PyMOL] Zoom in a movie

Hmmm, I've been wanting to do the exact same thing, and I'd reached the conclusion that the only way to do it would be to write a Python script. I'd be happy to share it when (if) it gets written (perhaps this week, since I'm stuck without real work for now). Ideally, it'd be nice to have even mor

Re: [PyMOL] PyMOL and programming languages other than Python

> I am not suggesting at all that users should now start coding for PyMOL > in BASIC - naturally, the best way to extend PyMOL remains to write > additional program modules in Python. Nevertheless, for people who > already write code in languages other than Python, the above strategy > might repres

Re: [PyMOL] Release in progress...

What's been added? I didn't see a changelog. . . (the 'dss' command, by the way, looks unbelievably awesome.) On Sat, 25 Oct 2003, Warren L. DeLano wrote: > (in a whisper) > > I'm still in the process of building binaries, but pioneers are welcome > to start downloading 0.92, if your platform i

Re: [PyMOL] pymol 0.90 on redhat 9.0 - no Tk window

Tkinter is a separate Python module that's an interface to the Tcl Tk library. It's probably just not installed on your system, but it is included in the RH 9 distribution (tkinter-2.2.2-26.i386.rpm) so it should be easy to find and install. On Wed, 22 Oct 2003 fr...@mit.edu wrote: > Hi PyMOLers

Re: [PyMOL] Segment Identifiers

if 'foo' is the segid of your kinase, PyMOL> select kinase, segi foo PyMOL> color green, segi foo it doesn't seem to care about any leading or lagging spaces, as far as I can tell. On Thu, 16 Oct 2003, Jonathan Ostrem wrote: > How are segment identifiers used. I have a PDB file with a kinase

RE: [PyMOL] Pymol script screenplay

> By the way, you can also use extra RAM to speed up ray-tracing > by 2-3 fold if you set hash_max to 150-200. Wait, I'm curious - what does this command do, and what are the limits? For a machine with 2GB of memory, what can I get away with? Will I have problems if I run multiple invocatio

[PyMOL] bug in rpm?

I just got a shiny new Gateway laptop - essentially a ripoff of the 15" Apple (but cheaper), with NVidia chipset. I installed RedHat 9.0, NVidia drivers, and the PyMOL rpm for rh9, but I get segfaults when I try to run 'pymol'. The tar.gz file works perfectly, so it's not a problem for me, but I

[PyMOL] Standalone Mac version

I'm stuck using some OS X computers that do not allow installation of software. Does anyone have (or can quickly build) PyMOL 0.9 as a single directory that I can launch pymol.com from without having to make any changes to the system? Given the circumstances, I probably need to work out of /tm

[PyMOL] weird artifact with cylindrical helices

I'm trying to make some figures for a review, and I'm seeing weird little partial spheres show up when I try to ray-trace a polymerase structure: http://bioinfo.mbb.yale.edu/people/nat/weird.png They're in the bottom third of the picture, and seem to show up in the same location in the structure

Re: [PyMOL] PyMOL v0.90 Released

This looks terrific. However, I'm having problems building on both Linux and Irix (using the Intel cc and SGI cc, respectively). It compiles fine, but './pymol.com -c' fails with "Fatal error: can't initalize module sglite". It's still right where it should be in contrib/sglite - any idea why th

Re: [PyMOL] membrane object?

> Has anyone been succesful in depicting a membrane surface in pymol? The > archives showed a similar question from John Maynes but no answer. > I would like to render my protein above a membrane surface as cover art for a > soon-to-be published paper. I'm not entirely sure I understand the quest

Re: [PyMOL] pymol crashes with large pdb files

> Now there is a twist to the story. We also run linux (redhat with 2.4.18 > kernel) on a 2 CPU 930MHz (1GB RAM, Nvidia GeForce2 GTS) PIII. Working > speed is much slower but no crashes when ray-tracing from the exact same > pml script. > Can it be that linux makes better use of its physical memory

Re: [PyMOL] pymol crashes with large pdb files

> Is there a limitation to the number of atoms or subunits pymol can handle? > I reset max_triangles from 10^6 to 10^7. Didn't change a thing. Exactly how much memory does your computer have? And what OS are you running? I've definitely crashed PyMOL before on a Linux system when I tried to do t

Re: [PyMOL] Clipping planes and slab thickness for different objects?

> I have one object showing the surface of a protein and another object showing > a ligand inside the protein. > Is it possible to use the clip command to define different clipping planes > for the 2 objects. > I want so "cut" the proteinsurface using clip, but the Ligand inside the > protein sh

Re: [PyMOL] ligand rendering

> I'm new with Pymol and I would like your help in the following problem: > I have a receptor image that I want to emphasize the ligand in its interior. I'm a big fan of transparent surfaces for this, e.g.: http://bioinfo.mbb.yale.edu/people/nat/mbp.mpg > Its a nonpeptidic ligand that I would lik

RE: [PyMOL] Will a faster graphics card speed up ray tracing?

> Not at all. The only way to increase ray tracing speed is to > upgrade your CPU. I think a 100-150 Ghz Pentium 8 is just about > optimal. On this note, our collaborators in CS have a test Itanium2 box that I have an account on - I've been planning to try out a bunch of comp. bio. softwar

Re: [PyMOL] April PyMOL News: Kick-off, OpenGL Cards, Unix

> Pymol at least *compiles* under a vast amount of processor > architectures, if only under Linux: > http://buildd.debian.org/build.php?arch=&pkg=pymol > Nothing wrong with testing your code on as much platforms as possible of > course :) It's harder than you think. I have a *really* old SGI, whi

Re: [PyMOL] Comparison SGI <-> PC?

> workstation (O2, Octane, Fuel, Onyx)? I've got an old Pentium III PC with 450 > MHz and a (non-stereo) Nvidia GeForce2 MX440 graphics card side-by-side with > an SGI O2 with a R12000 processor: a simple pymol (0.86) movie of a protein > sketch at 800x800 resolution and maximum display quality req

Re: [PyMOL] PDB SS Question

> They are different, especially at the ends of the helixes ... the web SS > seems to have longer helixes than the pdb HELIX info. Is one more > 'correct' than the other? If in doubt, obtain DSSP (it might be installed locally already) and go with whatever it tells you: http://www.cmbi.kun.nl/gv/

[PyMOL] parallel em code

Hi-- This sounds a bit offtopic, but it's related to a project that would probably be built off of PyMOL. Does anyone have any experience with protein dynamics software that runs on clusters and performs energy minimization? I've seen all sorts of pure MD packages that run on clusters (GROMACS,

Re: [PyMOL] x-windows pymol, fink and os x

> 0. Upgrade to 10.2.3 if you have not already done so. On a side note, did they fix NIS compatability again after breaking it in 10.2? I dropped OS X as soon as I discovered that, since that made it nearly useless for the environment I work in. If they got it working again, that and the new X

Re: [PyMOL] movie maker for linux?

SAMPEG: http://rachmaninoff.informatik.uni-mannheim.de/sampeg/ Works beautifully- very high quality movies most of the time. I've fully automated animations with PyMOL this way. Images need to be converted into Targa format first, but this is pretty standard. --

[PyMOL] colors

I just discovered that I can't set colors with more than one decimal point of precision. Is there any way around this? I'm trying to get a background that blends in with part of a web page. Nathaniel Echols

[PyMOL] b-factors?

Can PyMOL do coloring by B-factors? I didn't see anything about this in the manual. If not, I'll go ahead and write a new function, unless someone else is working on this. thanks, Nat Echols

[PyMOL] pymol-on-linux questions

I'm planning on yanking the Quadro 2 from a machine we bought as a server. Would I see any actual performance gain? Which chip is actually faster, at least for what I'd be using it for? thanks, Nat Echols Gerstein Lab Yale University

[PyMOL] ss coloring

Is there any way to color by secondary structure? I know of other programs that do this (Molmol, for example- though its colors are hideous); I'd be happy using a scripted solution if that's easiest. I'm guessing there's some easy way to loop through residues or atoms and determine what their str