[PyMOL] rendering missing segments

Hi Thomas et al, There was a recent question on the board about missing residues and the possibility of reading SEQRES headers and PyMOL being able to show the missing bits in the sequence view, perhaps with the amino acid letters grayed out to distinguish the gap. I know the reply was "PyMOL does

[PyMOL] APBS plug in (2.1) with PyMOL v1.7

Hi all, I was trying to use the APBS plug in with PyMOL version 1.7 and I'm getting this error with pymol generated files not being found in the tmp directory: Could not find /var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated.dx so searching for /var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0

Re: [PyMOL] Faster way to find polymer chains?

do?" I had forgotten about those get_ commands. Much appreciated! -Seth On Sun, Jan 23, 2011 at 5:58 AM, Thomas Holder < spel...@users.sourceforge.net> wrote: > Hi Seth, > > I think this one-liner will do the job for you: > > print cmd.get_chains('polymer') > >

[PyMOL] Faster way to find polymer chains?

Hi All, I am script-plowing through PDB files and extracting unique chain identifiers only for "polymers" using PyMOL's polymer selection. Right now my code is a kind of brute force thing like this: cmd.create ("justpolys","polymer") polymer_chains=[] for a in cmd.index("justpolys"):

Re: [PyMOL] small molecule geometry gets whacked in creating multi-state object

send me a few PDB examples? > > Cheers, > > -- Jason > > On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris wrote: > > Hi all, > > I feel I should know this one. I have a program looping through structures > > and bringing each small molecule into a single multi-sta

[PyMOL] small molecule geometry gets whacked in creating multi-state object. rebuild?

Hi all, I feel I should know this one. I have a program looping through structures and bringing each small molecule into a single multi-state object so I can tab through the states. I do: create all_lig, this_ligand, 1, 1 then go on to the next one: create all_lig, next_ligand, 1, 2 and so on

Re: [PyMOL] Rendering in parts

, endrow, startcolumn and endcolumn to the > ray command. That might be handy when using pymol for raytracing > scriptwise on a cluster. But you'll be disappointed if you expect it > will keep your scene from crashing Pymol (but then there's the > hash_setting...). > > I

Re: [PyMOL] PyMOL-users Digest, Vol 41, Issue 8

Tsjerk, I think you are missing the point of Tom's post, which was a suggestion to aid someone who's computer could NOT deliver the image in "as high a rsolution as you want', so Tom was proposing a way to break the image down into bite-size chunks that the computer COULD then handle. So the sugges

Re: [PyMOL] y axis rock and mplay frame rate

Seth, > > set sweep_speed, 3.5 > > set movie_fps, 3 > > Cheers, > Warren > > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:supp...@delsci.com > -- > *From:* Seth Harris [mailto:set...@gmail.com] > *Sent:*

[PyMOL] y axis rock and mplay frame rate

Is there a way to modulate the speed and amplitude of the y-axis rocking that is enabled through the "rock" command and button? I am capable of scripting my own rocking movie, of course, but in the current usage the frames are already dedicated to visiting electron density map peaks and I don't wan

[PyMOL] place atom at coordinates/screen center?

I feel like I should already know this one, but is there a command line way to add an atom at specified coordinates? or at screen center? I thought there was a new-ish pseudoatom functionality but I can't seem to find or recall details. Can one specificy atom type as well? I was looking to annotat

[PyMOL] setting for 2 button mouse view mode

Hi all, we have a user with a 2 button mouse who would like pymol to start up that way (i.e. without having to go to the mouse menu and select 2 button viewing mode every time he starts). I had a look around for a setting we could put into his pymolrc file, but the only things with promising name

[PyMOL] RE: povray image mapping and default pigments

thanks for listening! -Seth -- Forwarded message ------ From: Seth Harris Date: Apr 18, 2006 2:18 PM Subject: povray image mapping and default pigments To: pymol-users@lists.sourceforge.net This is for the povray gurus out there... Occasionally I muck around with the time-consumin

[PyMOL] povray image mapping and default pigments

This is for the povray gurus out there... Occasionally I muck around with the time-consuming practice of trying to map pictures onto molecular surfaces with povray. I had this working to some extent, but something has changed (I think with the povray file format produced by pymol & make_pov where

[PyMOL] RE: filter for edit settings window

Hi Michelle, In case no one's mentioned it yet, Zac Panepucci has contributed a grepset.py script which, after being run, allows you to type "grepset x" to see all settings (and their values) associated with whatever x is. It's not directly integrated into the pymol distribution but pretty

[PyMOL] RE:Ray-tracing inner surface backside

Paul (& Bob), Have you tried set two_sided_lighting, 1 Cheers, seth

[PyMOL] RE: labels not displaying

Marilyn, We saw this between unix and PC and one user figured out that label_font_id's were different. Thus older versions didn't recognize as many fonts as newer ones. I'm thinking this matches your description if the binaries on the two machines are in fact different versions. Try: set label_fo

[PyMOL] documentation vs features

Just to pipe up for the other side, while I would by no means defend the lack of documentation as a good thing, given limited resources I actually prefer new features at the expense of documentation. I realize there is a large range of computer expertise in the pymol user community, and obviously t

[PyMOL] RE: Angstrom-squared values for solvent/protein contact surface per residue

Just to throw my 2 cents in following Warren's invitation, I think Mark Gerstein's programs work well for this (calcsurf.exe or something...they're on his web site) ccp4's areaimol does something similar, though I can't recall whether its output was atom by atom. In either case, you may have to add

[PyMOL] RE: making a movie from saved scenes

Hi Sun, Warren (and others?) has posted some text before about this. A simple template for it is as follows with the key being that mview interpolate command at the end. This works, but I haven't been through it recently to remind myself of the nuances of the animate=0 options and the view=0 optio

[PyMOL] label positions, centered, left, or right

Hi all, Minor thing, but thought I'd ask... Labels now appear to be centered on whatever atom they are labeling. Previously, the left-hand side of the label was on the atom (left-anchored). Is there a way to choose whether the label is left-anchored, centered, or right-anchored? I find that it's

[PyMOL] Re: PyMOL-users digest, Vol 1 #1103 - 3 msgs

Some options were posted along these lines but you have to know what to look for since they are under titles like EM-izing your structure. You can try: set surface_quality, -3 (I think that's as low as you can go, more negative doesn't get any blobbier). And a bit less simple but I think you'll p

[PyMOL] Re: New spectral color pallette

This is more half an answer than the real deal, but when I had the same issue I opted for the quick work around of setting the range from -100 to 100 for the blue-white-red palette which effectively made 0-100 correspond to white to red only since there were no negative B factors/conservation score

Re: [PyMOL] label alternate conformations

up. On 12/7/05, Robert Immormino wrote: > > This series of commands seems to do the job although a little sloppy. > > label alt a+"", "A%s-%s" % (resn, resi) > label alt b+"", "B%s-%s" % (resn, resi) > hide labels, alt "" > &g

[PyMOL] label alternate conformations

Hi, I'm writing a small script to visit alternate conformations, stepping through each as a frame in a movie with the cursor keys. I'd like to label them to distinguish the alternates so I can see which I'd like to keep or not, but: label alternates, name only displays the atom name without the

[PyMOL] small molecule bond valences, revisited

Hi all (again!), Warren, I know I half brought this up at the user's meeting but I can't remember if there was a clear answer...so maybe it means not yet, but didn't recall that either. Question: is there a way to preserve small molecule bond valence information? Background: I know pymol has som

[PyMOL] cursor arrows for rotamers vs movies

Hi Warren et al., Thanks very much, Warren, for the rotamer libraries and mutagenesis wizard. I am very attached to cycling through rotamers using the cursor arrow keys. However if I have a movie set up, it takes precedence of the cursor key bindings, and right arrow steps through movie frames le

[PyMOL] re: Movie (one more)

Hi, I get these as a digest so sorry if someone's already spoken to this. Laurence Pearl wrote some code to interpolate between scenes as you describe. Kristian Rother wrote a very nice set of framework commands (and more) to make movies. I wrote an extension of Laurence's commands so that

[PyMOL] low res surfaces, CRYST headers, rotamers

Hi PyMOLarians (sorry, I've been reading Bush quotes and his tragic knack for inventive names for nationalities..) Hope it's not terrible form to bundle questions: Is there a way to have PyMOL save header information? It would help, for instance, if the CRYST card were preserved after editin

[PyMOL] linux and multi-button mouse

Yo, I just wrote a really long email to the list. So long that my web mail secretly logged me out during the time that I was writing it. The upshot of this is that 1) I am angry and 2) you are all spared the rambling version and hopefully get the more succinct version summarized here: I ha

[PyMOL] RE: wire mesh spheres?

Continuing on the transparency aspects of the original question... When I ray trace Warren's recent example of transparent CGO's, it seems that of the objects behind a given transparent one, only those that are fully opaque show through the front one. That is, the spheres in the back get bloc

[PyMOL] stereo projection with PyMOL

I was curious if anyone has successfully done stereo over a projector with PyMOL. That is to say not the cross-eyed stuff but the shutter-glasses type stereo. I was recently trying to do this for a company presentation from an SGI. On the same machine Insight can do stereo (although they tell

[PyMOL] hbond criteria in distance mode=2?

Hello PyMOLers, I am displaying hydrogen bonds using: distance hbond, protein, ligand, mode=2 which makes some nice dashed lines for hydrogen bonds but doesn't always display all the hbonds one might expect. For instance, in some cases there are is an N on the ligand molecule and a backbone

[PyMOL] smoothed path through protein?

trajectory hugging along one edge of a helix. upgraded script version available shortly as I now have it working from the command line rather than just from scripts. Thanks for any ideas, seth -- Seth Harris, Ph.D. Agard Laboratory Suite S416 Box 2240 UCSF/HHMI 600 16th Street San Francisco, CA

[PyMOL] addendum ribbon rider script typo

pts at code should come with a blanket warning concerning the perils with which they are fraught. Ciao, Seth -- Seth Harris, Ph.D. Agard Laboratory Suite S416 Box 2240 UCSF/HHMI 600 16th Street San Francisco, CA 94143-2240 (Shipping Zip 94158) 415.502.2930

[PyMOL] RE: Zoom in a movie...Ribbon Rider!

that again. I have tried to make sure that the history of it is properly annotated, and assume this respect will be continued down the line. p.p.s I don't believe I have broken anything in the final last-minute editing clean up pass (still rough, though!), but let me know if it doesn&#x

[PyMOL] how to get minimum distances in script?

Hello all, I am trying to write a script that will go through each residue in a dimer interface and determine for each one how close it is to the partner monomer. I can interactively plot all the distances within a certain cutoff using the handy: distance chosen, residue_selected_on_first_ch

[PyMOL] color by grasp phi map potential?

Well, this question is probably directed straight to Warren unless someone's found it in the code or I've missed an obvious button. Main question: I wrote out a GRASP potential map and read it in to PyMOL with no complaints. How do I then go about applying it to a surface (i.e. coloring the

[PyMOL] aforementioned NCS snapshot script

lag, and this too is simply copied over from the first view. ### This script has been hacked out (and I do mean hacked) by Seth Harris. ### shar...@msg.ucsf.edu for any suggestions/feedback/gratitude ### Thanks to Warren DeLano for PyMOL! from pymol import cmd from Numeric import * from LinearAlg

[PyMOL] orthoscopic vs. not in ray tracing

Quick question, I hope: It seems that "ray" always renders the image in the orthoscopic view regardless of whether I set orthoscopic, 0 or set orthoscopic, 1 although these settings do influence the non-ray traced standard view. Is this true or am I missing something? I'm trying to ray trace

[PyMOL] script for snapshots of your NCS-related copies

Hi, I wrote a rudimentary Python script to be run from PyMOL that makes png snapshots of identical views of your NCS-related molecules. I find it helpful for comparing map features and different conformations between NCS copies, particularly since I have 8 NCS copies in my current project's