Re: [PyMOL] One-Button Mice on Macs

Warren, what's up with this? Pymol and one-button mouse?? What's next? Pymol on abacus? Wouldn't it rather be time to remind Apple to provide ergonomic equipment? Andreas ps. I would be interested in hearing if anyone has found an ingenious use for the dozens of shiny slick white

Re: [PyMOL] Problems with rendering and saving

Hey Florian, I'd say it's a limitation of your graphics card. Others should correct me if I'm wrong. In any case, on my computer, I can write a 6400x4800 pixel2 file. PyMOLpng test ScenePNG: wrote 6400x4800 pixel image to file test.png. A different question is why I or you would want to

Re: [PyMOL] PyMOL-users Digest, Vol 5, Issue 22

Oh, works like a charm. (If you're a bit more descriptive about your problem, we can help you better.) Andreas surendra negi wrote: Is there any 32 bit version of pymol? I am unable to install it in XP - Original Message

Re: [PyMOL] differential helix transparency

Hey Satinder, transparency can only be set for objects, not for selections. Thus, you have to create different objects corresponding to your helices. Like so: create helix1, i. 23:30 # wherever your first helix is create helix2and3, i. 40:45 or i. 70:83 # the other two helices show

Re: [PyMOL] Show residues and sticks

The other day I got annoyed always having to type and not (name c,n,ca) when I want to see sidechains without the mainchain. The attached script takes care of this. run sidechain.py sidechain resi 34 (instead of show sticks, resi 34 and not (name c,n,ca)) Andreas Andrea Spitaleri wrote:

Re: [PyMOL] Show residues and sticks

) [ and not:] [ show sticks, resi 34 and not (name c,n,ca) ] Chris also pointed out that this feature exists somewhere in the pymol GUI (For whatever selection, under the show menu, at the bottom there is sidechain - lines, sticks, spheres). Thanks. Andreas Andreas Forster wrote: The other day

Re: [PyMOL] Showing the surface

Hi Michael, try to set a low resolution in addition to the increased VdW radii. Play around with the following set of commands: set gaussian_resolution, 9.0 # or whatever looks best map_new mapName, gaussian, 3.0, object # number is separation between grid lines, 1 is way too detailed for low

Re: [PyMOL] image metadata plugin

I was actually thinking about a related approach. Could one include a feature in PyMOL allowing the user to save notes with a session? I've really come to like saving sessions but going back to them later I often wonder what the objects are exactly, what the views were meant to represent, which

Re: [PyMOL] protein cartoon/floating sidechains/ligands

Hey Gary, in order to have sidechains be attached to your cartoon representation, the cartoons must not be smoothened. set cartoon_flat_sheets, off will do that. Be warned that your sheets will look like the ocean beyond the reef of Tunnels beach. To get just a sidechain, type show sticks,

Re: [PyMOL] between views

Tassos, Dirk, sorry for the very late reply, but I've just now finished going through a few hundred list mails that had accumulated. For converting scenes to movies, Joel Bard's slerpy is really shweet. Check it out at http://www.pymolwiki.org/index.php/Slerpy. What I do is the following -

[PyMOL] transparency cross-fading

Hey all, I've run into the following problem while making some movies with MacPyMOL 0.99rc6. I have a protein in surface representation that I start with transparency = 0 and a cavity (voidoo-created map) as surface with transparency = 1. In other words, the protein surface is visible, the

Re: [PyMOL] pymol in the background

Hey Gordon, I don't quite understand your problem. Pymol can be run in the background (or even remotely) by calling it as pymol -qc script.py When you want to use it interactively, the shell it was started from is used for all sorts of output. Why do you need this shell? Just open

Re: [PyMOL] viewport report?

Hey Thomas, try this: width,height = cmd.get_session()['main'][0:2] print width, height or print (cmd.get_session()['main'][0:2]) Andreas Thomas Stout wrote: Hi All -- I have a rather old session file that I would like to replicate in a new session file. Essentially, I want to carry

[PyMOL] exploding proteins

Dear all, I just checked out PyMOL 1.1r0 revision 3367 via subversion. When I open any old pdb file (eg. fetch 1ubq), the protein is displayed as if irradiated with a free-electron laser ( https://fileexchange.imperial.ac.uk/files/5b706c5efa/lines.png). The cartoon

Re: [PyMOL] exploding proteins

Hey Warren, unfortunately, none of your suggestions fixes the problem (which isn't really one anyway as I never use the lines representation). If I set both ati_bugs and nvidia_bugs, the display is completely messed up. https://fileexchange.imperial.ac.uk/files/dfc7e41276/ati_nvidia.png I'll

Re: [PyMOL] pymol does not open from a terminal

Maia, you have to install libpng and/or libpng-devel. Andreas On Fri, Sep 11, 2009 at 3:04 AM, Maia Cherney ch...@ualberta.ca wrote: Hi, Could you please help me with a pymol problem. I have ubuntu linux and I have pymol in the /usr/bin (comes with ubuntu installation) and also one in the

Re: [PyMOL] how to get RMSD from align command

Hey Thomas, if you want to use align anyway, make sure to use the quite=0 option. The quiet option (if present) is set to zero by default for parsed PyMOL commands, but is not set for Python API calls. align is nearly equal to cmd.align(quiet=0) Thus, if you want to get rmsd output, include

Re: [PyMOL] superimpose option

Hey Saeid, use the 'super' command. Type super protein1, protein2 For more information, check teh wiki. Andreas On Tue, Dec 8, 2009 at 7:07 AM, saeid mirzaei smirzae...@yahoo.com wrote: Hi everyone, could some one tell me I can use Pymol for superimposing two protein or not if so

Re: [PyMOL] APBS problem

Hi Albert, I apologize that I take your email for a grumpy old man's rant, but I feel this mailing list is getting washed out with poorly formulated questions. What happened to specifying what OS you use, what version of PyMOL, what version of the apbs plugin. Also, to give answers, it would

Re: [PyMOL] on PDB

http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures Andreas On Thu, Nov 26, 2015 at 2:24 AM, Smith Liu wrote: > Dear Shane, > > get_view is a nice command. Is any way to change the original PDB based on > what we get by set_view to get the new pdb? > >

Re: [PyMOL] on using pymol scripts

Dear Smith, right click on https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/centroid.py, select Save Link As. This is a good skill to have because it allows you to download all sorts of things from the internet. You can use Google Chrome, Mozilla Firefox and Microsoft Edge for

Re: [PyMOL] PyMOL for iPad issues

Dear João, type set grid_mode, on to see your models side by side. You might have to align them first. Use the command super model1, model2 for that. All best. Andreas On Tue, Feb 28, 2017 at 5:27 PM, João Oliveira Jr. wrote: > Hi > > Please, when using PyMOL

Re: [PyMOL] Coordinates of an atom

Dear Mohsen, when I Google "pymol coordinates atom", the top hit is this: https://pymolwiki.org/index.php/Get_Coordinates_I Worth a try. All best. Andreas On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi all, > > > > Can anyone please help me