Re: [PyMOL] Label charge sites, termini, check contrast

Hi Jared, Thank you for teaching me that special feature on pymol; on my pymol version set label_position worked (instead of set label_offset). Neena On Sun, 31 Jan 2021 at 20:17, Jared Sampson wrote: > Hi Neena - > > There is also a `label_offset` setting, which can be given an x,y,z vector

Re: [PyMOL] Label charge sites, termini, check contrast

Or you can use "3 button edit mode" with a combination of Control (on a Mac) and the left mouse button. It allows you to move the label in first 2Ds, release, rotate and do it again to position exactly where you want it, e.g. in front, behind etc. BW Jon On Mon, 1 Feb 2021 at 21:23, Jared

Re: [PyMOL] Label charge sites, termini, check contrast

Sorry, I replied from my phone earlier...the correct setting is `label_position`. https://pymolwiki.org/index.php/Label_position Best, Jared On Sun, Jan 31, 2021 at 8:17 PM Jared Sampson wrote: > Hi Neena - > > There is also a `label_offset` setting, which can be given an x,y,z vector > in

Re: [PyMOL] Label charge sites, termini, check contrast

Hi Neena - There is also a `label_offset` setting, which can be given an x,y,z vector in viewport coordinates. So if you want all labels to be in the foreground compared to their respective atom(s), you might set it via: set label_offset, [0,0,5] I believe this can also be done in an

Re: [PyMOL] Label charge sites, termini, check contrast

Hi Ali, Thank you for the brief and thorough explanation! All those commands gave exactly what I was looking for! Many thanks, Neena On Fri, 29 Jan 2021 at 18:36, Ali Saad Kusay wrote: > Hi Neena, > > A simple way to label in PyMOL is to simply select the atom you want and > enter the

[PyMOL] Label charge sites, termini, check contrast

Hello PyMOL users, Is there a way to label charge sites and termini on PyMOL as I have shown in the below figure instead of using Paint? In addition, is there a way to check color contrast for this peptide structure for making it more accessible to the readers? [image: image.png] Many thanks,

[PyMOL] label color

Hello PyMOLers, In version 2.2.3 under Win upon ray-tracing label color changes. Is there a way to prevent that from happening? Thank you. Regards, Vaheh Oganesyan, Ph.D. Scientist, Biologic Therapeutics AstraZeneca R |

Re: [PyMOL] Label volume

Hi Thomas, Cool, I did something like that, copied the selection "%obj and index 1" then labeled it. So I got an independent label. Multi-line labels was somewhat hackish: cmd.label( label_obj_name, '"' + "\\n".join([ f'ID {i}', f'Class {ensemble.klass}', f'S

Re: [PyMOL] Label volume

Hi Pedro, it's only possible to label atoms. If you need an independent label, create a pseudo atom: pseudoatom label="Hello World" You can move the atom (or the label) in 3-Button Editing mouse mode while holding CTRL and dragging with the left mouse button. Cheers, Thomas > On Aug 12,

Re: [PyMOL] Label volume

And how to place a single arbitrary label on the object or segment? Em seg, 12 de ago de 2019 às 13:55, Pedro Lacerda escreveu: > Hi PyMOL list, > > Is possible toshow a label independent of the associated object be > enabled? > > Or is possible to label a volume or map? > -- > Pedro Sousa

[PyMOL] Label volume

Hi PyMOL list, Is possible toshow a label independent of the associated object be enabled? Or is possible to label a volume or map? -- Pedro Sousa Lacerda *Laboratório de Bioinformática e Modelagem Molecular* *Faculdade de Farmácia / UFBA* *@pslacerda* *+55 71 9 9981-1856*

Re: [PyMOL] label

Hi Albert, Incentive PyMOL can do that, simply type: label all, stereo This feature is provided by a proprietary library and thus not available in Open-Source PyMOL. Cheers, Thomas On 16 Sep 2015, at 03:15, Albert wrote: > Hello: > > Does anybody have any idea

[PyMOL] label

Hello: Does anybody have any idea whether pymol could label the absolute configuration (R/S) for a chiarity atom? Thank you very much. Albert -- Monitor Your Dynamic Infrastructure at Any Scale With Datadog! Get

[PyMOL] Label problems (PyMOL ver. 1.6)

Dear Pymol Users, I have installed PyMOL 1.6 built from source code on Ubuntu and Windows on June 23, 2013. I've noticed that the label of distance (or angle) is not shown properly. I describe the steps to reproduce: 1. load a PDB file. 2. select two atoms by clicking the middle button on the

Re: [PyMOL] Label by selection identifier

Hi Jordan, use the first operator: PyMOL label first foo, foo or for the first CA atom in foo: PyMOL label first (foo and guide), foo Cheers, Thomas Jordan Willis wrote, On 05/21/13 11:07: Yes thank you! I meant to post that as my solution considering it works pretty good

[PyMOL] Label on top of molecules?

Hello PyMOL users, When I print atom names with label all, name the labels are often behind the spheres (I use balls and sticks representation). I tried moving labels around, but my system is very dence -- and labels generally get under one or another sphere. Is there a way I can print labels

Re: [PyMOL] Label on top of molecules?

Hi Boris, set float_labels, on will do the job. But it doesn't seem to affect ray-traced images. Then you might want to manually adjust label_position. See http://www.pymolwiki.org/index.php/Label_position For example, set label_position, (0, 0, 20) will bring labels 20 angstroms in front of

Re: [PyMOL] Label on top of molecules?

Hi Boris, Takanori had some good ideas to try. I just wanted to let you know that you uncovered some bugs that we've taken note of and will fix in both on-screen rendering and in ray traced mode. Cheers, -- Jason On Wed, Oct 17, 2012 at 7:47 AM, Boris Kheyfets kheyfbo...@gmail.com wrote:

Re: [PyMOL] Label entire movie

An: Rasbach, Anke Cc: pymol-users@lists.sourceforge.net Betreff: Re: [PyMOL] Label entire movie Hi Anke, you can use the message wizard to place a text box to the upper left corner of the viewport. PyMOL wizard message, Some free text Cheers, Thomas Rasbach, Anke wrote, On 09/21/12 13:35

Re: [PyMOL] Label entire movie

Hi Anke, Rasbach, Anke wrote, On 09/24/12 13:08: [...] Is it also possible to change font and box color? no, that's not possible. The colors are hard-coded. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen

Re: [PyMOL] Label entire movie

Hi Thomas, On Mon, Sep 24, 2012 at 11:11 AM, Thomas Holder spel...@users.sourceforge.net wrote: [...] Is it also possible to change font and box color? no, that's not possible. The colors are hard-coded. That's not quite right. You can change the text color with some trickery. The syntax to

[PyMOL] Label entire movie

Hi everyone, we have generated a quite complex pymol movie and would like to include a label that is always located in the lower right corner throughout the entire movie. We have already labeled a pseudoatom positioned at the lower right corner but due to camera motions the text is flying

Re: [PyMOL] Label entire movie

Hi Anke, you can use the message wizard to place a text box to the upper left corner of the viewport. PyMOL wizard message, Some free text Cheers, Thomas Rasbach, Anke wrote, On 09/21/12 13:35: Hi everyone, we have generated a quite complex pymol movie and would like to include a

Re: [PyMOL] Label using API

Hi Ritu, when using the API, you need to quote the text label twice: cmd.label(chain d and name C1, 'whatever') It's a string in a string :) Cheers, Thomas Rituparna Sengupta wrote, On 05/30/12 22:42: Hi, Can anyone tell me how to label something using the API. I'm having trouble with

[PyMOL] Label using API

Hi, Can anyone tell me how to label something using the API. I'm having trouble with it and the API usage is not listed in PyMol wiki. I use label chain d, whatever from the command line and it works fine. But I want to use it in a script. I tried using cmd.label(chain d, whatever) but

[PyMOL] label position

Dear all, I want label a few distances independently with my own labels. I set a label in the form label /wt//A/THR`254/CA, 10.0+ u\u00c5.encode('utf-8') which I can move independently using the set label positio command. If I incorporate a second label and try to change the position with the

Re: [PyMOL] label position

Christian, I want label a few distances independently with my own labels. I set a label in the form label  /wt//A/THR`254/CA, 10.0+ u\u00c5.encode('utf-8') which I can move independently using the set label positio command. If I incorporate a second label and try to change the position with

Re: [PyMOL] Label N-Glycosilation with Pymol

On Jul 19, 2010, at 12:29 PM, José Ignacio Sánchez Gallego wrote: Hi everybody, I have to make a 3D structure of my protein, I mutated some aminoacids in order to add some N-linked glycans, does anyone know is it possible to show the glycosilation on the surface of the 3D structure?? It

Re: [PyMOL] label bond type and molecule name

Sebastian, Here's some help on labeling: # label all atoms with the object name (file name minus extension) label *, model # label by residue name label *, resn Your command, label C10, resn was a good guess, but that asks PyMOL to label the atoms in the object called 'C10' by their residue

[PyMOL] label bond type and molecule name

dear all, i am quite new to pymol and even if i looked up the documentation i still have two -probably *very* stupid- questions: i can't find a way to label the bond type (single, double, triple, aromatic) in a multimol2, i didn't even find a way to select bonds at all... also i don't manage

Re: [PyMOL] label

Gauri, Are you looking for a script that will locate contiguous stretches of a alpha-helical residues and then label one of the atoms in that helix with the helix's ordinal number? If so, nothing like this exists yet, but it would be a cool little script to write. Cheers, -- Jason On Thu, May

[PyMOL] label

Dear All, Is there an option to label the alpha helices in a sequential manner, domain wise in a pdb file using pymol? Thanks Cheers Gauri -- ___ PyMOL-users mailing list

Re: [PyMOL] Label size in different scenes

scene? Thank you. Vitaly - Original Message - From: Jason Vertrees jason.vertr...@schrodinger.com Date: Tuesday, April 13, 2010 4:47 pm Subject: Re: [PyMOL] Label size in different scenes To: Vitaly Vostrikov vvos...@uark.edu Cc: pymol-users@lists.sourceforge.net Vitaly, Great

Re: [PyMOL] Label size in different scenes

Vertrees jason.vertr...@schrodinger.com Date: Tuesday, April 20, 2010 9:57 am Subject: Re: [PyMOL] Label size in different scenes To: Vitaly Vostrikov vvos...@uark.edu Cc: pymol-users@lists.sourceforge.net Vitaly, What you want is the mdo command. Check it out: http://www.pymolwiki.org

Re: [PyMOL] Label size in different scenes

jason.vertr...@schrodinger.com Date: Tuesday, April 20, 2010 9:57 am Subject: Re: [PyMOL] Label size in different scenes To: Vitaly Vostrikov vvos...@uark.edu Cc: pymol-users@lists.sourceforge.net Vitaly, What you want is the mdo command. Check it out: http://www.pymolwiki.org/index.php/Mdo. We

Re: [PyMOL] Label size in different scenes

settings in a Pymol scene? Thank you. Vitaly - Original Message - From: Jason Vertrees jason.vertr...@schrodinger.com Date: Tuesday, April 13, 2010 4:47 pm Subject: Re: [PyMOL] Label size in different scenes To: Vitaly Vostrikov vvos...@uark.edu Cc: pymol-users@lists.sourceforge.net Vitaly

[PyMOL] Label size in different scenes

Hello, I am learning movie-making in Pymol, and I have a question about label size. I have a script with one state and several scenes, and I would like to introduce titles for each scene. I create pseudoatoms for each scene and label them, but because of the different length of text, I would

Re: [PyMOL] Label size in different scenes

Vitaly, You can set label_size per object: set label_size, -0.35, pseudo1 set label_size, -0.50, pseudo2 I recently ran into similar issues. My solution was to make use of the mdo command. Try help mdo and check out the PyMOLWiki page http://www.pymolwiki.org/index.php/Mdo. Cheers, -- Jason

Re: [PyMOL] Label size in different scenes

Jason, Thank you very much - it worked perfectly! I did not realize it is possible to apply that for individual objects. Vitaly - Original Message - From: Jason Vertrees jason.vertr...@schrodinger.com Date: Tuesday, April 13, 2010 1:58 pm Subject: Re: [PyMOL] Label size in different

Re: [PyMOL] Label size in different scenes

, Thank you very much - it worked perfectly! I did not realize it is possible to apply that for individual objects. Vitaly - Original Message - From: Jason Vertrees jason.vertr...@schrodinger.com Date: Tuesday, April 13, 2010 1:58 pm Subject: Re: [PyMOL] Label size in different scenes

[PyMOL] label a stereo .png image in pymol

Hello all I have made a stereo image in pymol and photoadobeshop. But, i would like to label the image file which should like a stereo image label. how that can be done in the pymol. I can do it in photoadobeshop .problem lies her that i am not sure is the labels are really stereo or not? can

Re: [PyMOL] label a stereo .png image in pymol

. Using this trick ensures that the labels appear in the correct depth. HTH Carsten From: peter hudson [mailto:peter.hudson.pe...@gmail.com] Sent: Monday, September 07, 2009 12:30 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] label a stereo .png image in pymol

Re: [PyMOL] Label coordinates

a to do item. Cheers, Warren -Original Message- From: Folmer Fredslund [mailto:folm...@gmail.com] Sent: Thursday, July 09, 2009 6:33 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Label coordinates Dear all, Is there a way to get the coordinates for manually shifted

[PyMOL] Label coordinates

Dear all, Is there a way to get the coordinates for manually shifted labels? What I want to do is to include the label positions in my script instead of moving the labels each time I update my figure. Thanks in advance, Folmer Fredslund

[PyMOL] label transparency

Dear All, Does anyone now if it's possible to alter the transparency level of a label? I have an object that is scripted to fade in and out, and I would like to bring the labels in and out at the same speed, but can't seem to find a setting that works. Thanks in advance, Neil. Neil

Re: [PyMOL] label transparency

: [PyMOL] label transparency Dear All, Does anyone now if it's possible to alter the transparency level of a label? I have an object that is scripted to fade in and out, and I would like to bring the labels in and out at the same speed, but can't seem to find

Re: [PyMOL] label with arbitrary string

Dear Tsjerk, Marius, and all -- Thanks for your answers. Both methods worked perfectly. I personally like the one from Tsjerk, as I can play a little bit more with the font. Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home

Re: [PyMOL] label with arbitrary string

Dear all -- On 30 Jul 2008, at 01:03, DeLano Scientific wrote: Richard, label (residue 200 and name ca), My favorite C_alpha The command you provided works as written, so what are you asking exactly? Is is that you want us to add a GUI way of doing this? Related to labeling, I was

Re: [PyMOL] label with arbitrary string

Hi Leo, AFAIK you can't do it with Pymol, as it would require additional fonts. Also, it seems tough to me to position to label properly with respect to the camera. But you have plenty control with convert/imagemagick (see http://www.imagemagick.org/Usage/annotating/). That will allow you to

Re: [PyMOL] label with arbitrary string

Hello Leo, You could use Unicode to get the special characters you were taking about. angstrom = u\u00C5 angstrom_utf8 = angstrom.encode ('utf-8') label (residue 200 and name ca), Distance: 8+angstrom_utf8 To see the label bigger use set label_size, 20 You can get the unicode charts from here

Re: [PyMOL] label with arbitrary string

Dear All, Can someone advise me how to insert a label with an arbitrary string, e.g. label (residue 200 and name ca), My favorite C_alpha Thanks for your help, Richard Baxter

Re: [PyMOL] label with arbitrary string

-Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Richard Baxter Sent: Tuesday, July 29, 2008 4:31 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] label with arbitrary string Dear All, Can someone

[PyMOL] label in Greek letters

Hi All users, I am a PyMOL ver.0.99rc6 (Win and Linux) user. Now I want to label with chain ID ( A, B, G,... for alpha, beta, gamma,...) in Greek letters. I have tried it following http://www.pymolwiki.org/index.php/Label#UTF8_Fonts , but the output corresponds to \316\261 has not been printed.

[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

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

-Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Seth Harris Sent: Thursday, February 23, 2006 10:45 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] label positions, centered, left, or right Hi

[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

Re: [PyMOL] label alternate conformations

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 Cheers, -bob On 12/7/05, Seth Harris set...@gmail.com wrote: Hi, I'm writing a small script to visit alternate conformations,

Re: [PyMOL] label alternate conformations

Hi Bob, Good to hear from you. I didn't know about alt as a selection, so in the end that gave the answer... Your example, which I find quite clever, didn't exactly match my goal, though, so just to clarify: Rather than distinguishing residues with alternate conformations from those normal ones

[PyMOL] label

Hi, I am back with a small prob! may be i am missing something in command line Q: How to label residue in cartoon selection using command line. Sincerely sn __ Do you Yahoo!? The all-new My Yahoo! - What will yours do? http://my.yahoo.com

[PyMOL] label is not displayed after raying

Hi, I wonder if anyone has had the similar problem. I can see both the label and dash at normal window. After raytracing there is only a yellow dotted line between two atoms without the distance. How can I make the distance shown on the raytracing picture? Thanks! Happy new year! Eric

[PyMOL] label wizard

Hello people, This is a labeling wizard. It allows you to click atoms and have a label show up near the atom position. If the atom is a C-alpha the label is slighly different. More info is shown in the prompt area. To use it, put the attached file in