Re: [PyMOL] Pymol not opening files

Hi Shivani - PyMOL's defer_builds_mode setting can improve performance when loading large trajectories. You can type `set defer_builds_mode, 3` on the PyMOL command line or adjust it via the Settings > Edit All menu. Hope that helps. Cheers, J

Re: [PyMOL] [Help]About indentifying interaction between residues

Hi Nikita - To me this looks like the cartoon representation for missing residues, which is controlled by the cartoon_gap_cutoff setting. If you either `hide cartoon` or `set cartoon_gap_cutoff, 0`, does it go away? Usually the dashed line wou

Re: [PyMOL] File attachments

Hi Istvan - Most of the time a PDB or other data attachment is not necessary. Or if it is, someone from the community may ask you to send it to them individually (and confidentially) to help you offline. Instead, you can try to describe the problem or issue you're having, possibly including an i

Re: [PyMOL] centerofmass command gives error

Hi Petro - It looks like that structure has a deuterium atom. Assuming you're interested in the non-deuterated molecule, you can convert it to a hydrogen and the command will work. ``` alter elem D, elem="H" rebuild print(cmd.centerofmass("polymer")) ``` Or if you want to stick with Python API s

Re: [PyMOL] Get/edit molecule title?

Hi Petro - This is the object's "title" attribute, and can be accessed using the Properties Inspector in the top right part of the GUI, as well as read or edited via the `get_title ` or `set_title

Re: [PyMOL] Nonsense mutagenesis

Hi Jevin - Depending on how far the termination codon mutation is from the end, it may work to just delete residues from 415 onward. However, if this would delete a substantial chunk of the protein, the real structure of the truncated polypeptide may differ significantly from the crystal structur

Re: [PyMOL] How to show orientation axis in Pymol

Hi G.V. - See also: https://pymolwiki.org/index.php/Axes Hope that helps. Cheers, Jared On Thu, Jun 23, 2022 at 8:03 PM Florian Nachon wrote: > Hi, > > Quite easy using CGO : https://pymolwiki.org/index.php/Cgo_arrow >

Re: [PyMOL] set_view based on origin and a vector

Hi Wei - Fun problem! Not a "smart" way to do it, but I think functional, using pseudoatoms and orient to set the view angle: ``` # Create an origin pseudoatom ori_coords = [0.4017522, 23.15367207, 6.68992345] cmd.pseudoatom("ori", pos=ori_coords) color red, ori show nb_spheres, ori # Second ps

Re: [PyMOL] Pymol-Alignment Module

Hi Ecem - If I understand correctly, you first want to align on one set of residues and calculate their RMSD, then to calculate the RMSD for the remaining residues without moving the structures. This is straightforward using PyMOL's internal command line. ``` # Create two selections called "sel1

Re: [PyMOL] CGO object code structure

until you set another `cgo.ALPHA` value by the same method. Hope that helps. Cheers, Jared On Mon, Feb 14, 2022 at 10:04 AM Jared Sampson wrote: > Hi Marcelo - > > No I don't believe so. In PyMOL, a CGO `CONE` is a fixed-length list of > floats. You can see in the cgo.p

Re: [PyMOL] CGO object code structure

lor lists? > > Best regards, > -- > Marcelo > > Em dom., 13 de fev. de 2022 às 21:42, Jared Sampson < > jared.samp...@columbia.edu> escreveu: > >> I forgot to add that the transparency can be handled by e.g. >> >> set cgo_transparency,

Re: [PyMOL] CGO object code structure

I forgot to add that the transparency can be handled by e.g. set cgo_transparency, 0.5, my_cgo_object Cheers, Jared On Sun, Feb 13, 2022 at 9:38 PM Jared Sampson wrote: > Hi Marcelo - > > Looks like you have the right format for `CONE`. This should really be in > th

Re: [PyMOL] CGO object code structure

Hi Marcelo - Looks like you have the right format for `CONE`. This should really be in the Wiki...and apparently is not. I've just made a couple of pages, others can of course feel free to elaborate: https://pymolwiki.org/index.php/CGO_Shapes https://pymolwiki.org/index.php/Load_CGO You may al

Re: [PyMOL] How to label atom at proper positions?

Hi sunyeping, Try this: set label_position, [0, 0, 5] The 5 here moves the label 5 Å closer to the viewer along the viewport Z axis. See also: https://pymolwiki.org/index.php/Label_position Hope that helps. Cheers, Jared On Tue, Jan 18, 2022 at 5:15 AM sunyeping via PyMOL-users < pymol-

Re: [PyMOL] Getting angle between z axis and a molecules principal axis

Hi Yogesh - You may be able to do something similar to the antibody elbow angle script on the PyMOL Wiki (and PyMOL-scripts GitHub repo) using rotation matrices aligning various subunits to determine the principal axis. Or if you already have a way of calculating the principal axis, you can use Ch

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 ve

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 object-spec

Re: [PyMOL] renumber

ate: June 15, 2020 at 3:57:24 PM To: Jared Sampson Cc: pymol-users@lists.sourceforge.net Subject:  RE: [PyMOL] renumber Jared,   Are you saying it cannot be done within PyMOL? The ccp4 option is well known.   Thanks.   From: Jared Sampson Sent: Monday, June 15, 2020 2:41 PM To: Og

Re: [PyMOL] renumber

Hi Vaheh - Try `pdbset` from the CCP4 suite. http://www.ccp4.ac.uk/html/pdbset.html#renumber ``` pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF renum 1 chain H renum 1 chain L end EOF ``` Hope that helps. Cheers, Jared From: Oganesyan, Vaheh Reply: Oganesyan, Vaheh Date: June 15, 2

Re: [PyMOL] Scenes

Hi Tim -  One way to do this would be to duplicate the object before mutating and keep an "old" and "new" version as separate objects in the session.  Then you can enable one or the other as you like in your scenes. Hope that helps, Cheers, Jared From: Waybright, Timothy (NIH/NCI) [C] via Py

Re: [PyMOL] Holes in dots

Hi Jason -  This happens when there is an overlap with another atom's dots, for example where there is an H-bond or vdW contact.  One workaround would be to extract that residue you're showing in dots into a new object, so it doesn't have anything else in the object to interfere with it. Hope

Re: [PyMOL] Compare two structures with the same connectivity butdifferent stereochemistry?

Hi Peng -  You probably want to use `pair_fit` here, to align on a conserved core of atom pairs between the two models.  However, two complicating issues here are 1) equivalent atoms are not listed in the same order in the .mol2 files, and 2) they don't have atom names, which makes selecting th

Re: [PyMOL] broken DNA cartoon

Hi Adam -  That's a fun one.  It appears that most of these O3' atoms are not bonded to the P atom of the following nucleotide, which you can see if you show the DNA chains as sticks.  Creating a bond via `bond atom1, atom2` results in a normal cartoon.  Fortunately, the DNA chains are sequenti

[PyMOL] Accessing vertex normals from surface representation within PyMOL session

Hi all - Is it possible to access surface triangle mesh position and normal values on a per-selection basis within a PyMOL session?  I know it's possible to get these by writing out and parsing .obj files, but to do this for an entire protein surface in a per-atom/residue fashion would be ineff

Re: [PyMOL] Calculate the angle between two domains

Hi Yikan - Check out: https://pymolwiki.org/index.php/Angle_between_domains Hope that helps. Cheers, Jared On November 27, 2019 at 4:02:34 AM, Zhang Yikan via PyMOL-users (pymol-users@lists.sourceforge.net) wrote: Hi all, I am a beginner of the PyMol script. I have 200 pdbs(names, C_1, C_2,

Re: [PyMOL] Re. Pymol Ray problem

Hi Changdev -  Try the following command, which will save a ray-traced PNG image with transparent background (which is what is represented by the checkerboard pattern):     png myfigure.png, ray=1 Alternatively, you can adjust the ray background setting:     set ray_opaque_background, 1 Hope

Re: [PyMOL] Get surface coordinates

Hi Pedro -  The COLLADA option exports unlabeled mesh objects so I couldn't figure out which one is acceptor or donor. Yes, you're correct about that.  This is due to the fact that COLLADA export uses geometry after it is prepared for ray tracing, which doesn't know about object names (see the

Re: [PyMOL] feature request

Hi Thomas -  When I said it's easy to implement, I was only thinking of object color. Among the various cases you describe, the "dominant color" is probably the most important one, as it might not be obvious to the user that object color can be different from atom colors. Indeed, I was among th

Re: [PyMOL] feature request

bel_color match the residue color. I vaguely remember something like this discussed x number of years ago, but do not remember why not. Could label become property of the object and not just a property of a session?   Thank you.     From: Jared Sampson Sent: Tuesday, October 1, 2019

Re: [PyMOL] feature request

Hi Thomas and Vaheh -  This is indeed an interesting idea.  I was thinking about this in terms of implementation, and what the edge cases might be.  I wonder what would be the mechanism for assigning the color if the object is not just a single color.   Would it be the color that is the dominant

Re: [PyMOL] How to label secondary structures in pymol

Hi sunyeping -  Yes, it is possible.  You can pick one atom to label in each SS element.  See this old thread: https://sourceforge.net/p/pymol/mailman/message/30823352/.  You can also adjust the label position/size/style using the various label  settings as well.  I would normally direct you to

[PyMOL] Errors in "Label" page on PyMOL Wiki

Hi PyMOLers - I'm currently not able to access the label page on PyMOL Wiki, which prints out a string of PHP errors. Weirdly, it appears to be specific to that page, as others (off the top of my head, I visited load an

Re: [PyMOL] PDB post-processing and TER records

Hi James - Glad you got it working. > chains_array = ["A", "B"] If you want a list of chains without having to hard-code them, try the `get_chains` command. ``` chains_array = cmd.get_chains() ``` > cmd.load('${pdb}') > cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"') Alternatively,

Re: [PyMOL] counting number of standard amino acids in PDB

D_multi_0434.pdb, tmp CmdLoad: "./NpXynWT_apo_340K_MD_multi_0434.pdb" loaded as "tmp". PyMOL>sel = 'tmp and polymer.protein' PyMOL>print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom]))) Selector-Error: Invalid selection name "pol

Re: [PyMOL] counting number of standard amino acids in PDB

( set( [(i.chain,i.resi,i.resn) for i in cmd.get_model(selection).atom] ) ) " ? пн, 24 июн. 2019 г. в 16:17, Jared Sampson : > > Hi James - > > Do any of the options from this previous BB discussion help? > > https://sourceforge.net/p/pymol/mailman/message/284669

Re: [PyMOL] counting number of standard amino acids in PDB

Hi James -  Do any of the options from this previous BB discussion help? https://sourceforge.net/p/pymol/mailman/message/28466955/ Cheers, Jared On June 24, 2019 at 8:13:47 AM, James Starlight (jmsstarli...@gmail.com) wrote: Dear Pymol Users, that is not very related to pymol question but

Re: [PyMOL] selection of residues in protein using plane perpendicular to Z-axis

Hi Divya -  It's not entirely clear what you're trying to do from your description.  Are you looking to select residues near the plane, or perhaps use the plane to divide residues into "of interest" and "not of interest"?  I think PyMOL can be useful here, but the approach will likely be differ

Re: [PyMOL] Greetings

Hi Shahzad -  In your session file, these residues are part of a protein structure, so "bringing them closer together" (e.g. with the `translate` command) would distort the geometry of the protein and I would advise against it. I would recommend simply adjusting the camera position to zoom on t

Re: [PyMOL] Seeing more H-bonds than expected

Hi Neena -  PyMOL shows all the potential H-bonds, but not all of them will be formed at all times. Any single proton can only participate in one H-bond at a time, but remember a crystal structure is an average structure based on the ensemble of states present in the protein crystal (or on the

Re: [PyMOL] auto focus after creating

Hi again, Michael -  This can be adjusted either globally via the `auto_zoom` setting: set auto_zoom, off or when loading a PDB with the `load` or `fetch` commands: load my_structure.pdb, zoom=0 fetch 1xyz, async=0, zoom=0 Here I also include `async=0` as you would in a

Re: [PyMOL] rename/assign residue names

Hi Michael - Assuming you already have your atoms selected in a selection called e.g. `sele` and you want the new residue name to be e.g. `XYZ`, you can achieve this on the PyMOL command line: alter sele, resn='XYZ' save XYZ.pdb, sele Hope that helps. Cheers, Jared On March 27, 2019 at 8:36:1

Re: [PyMOL] fix cartoon backbone

Hi Adam - The characters between the object names and the chain IDs are the segment IDs.   You can remove them by setting them to the empty string using `alter`: alter all, segi="" Hope that helps. Cheers, Jared On March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.adam.steinb...@gmail.com)

Re: [PyMOL] how to make selected residues blurry?

Hi Yeping - The `set_view` command sets the view matrix for the camera in PyMOL. Once you have the view you want set up in the viewport, you can copy the matrix to the system clipboard using the “Get View” button in the top GUI window and paste it into your .pml script, or print it to the con

Re: [PyMOL] how to make selected residues blurry?

Hi Yeping  -  I had replied to your first email (on 11/30) with a similar suggestion to Paul's of using the `cartoon_transparency` setting, but now after looking at the original figure you're trying to replicate more closely, I realize that there isn't actually any transparency in that figure a

Re: [PyMOL] how to make selected residues blurry?

Hi Arthur - The `transparency` setting affects only surface representations.  I believe you're looking for `set cartoon_transparency, 0.8, sele`.    https://pymolwiki.org/index.php/Cartoon_transparency Hope that helps. Cheers, Jared On November 30, 2018 at 3:41:57 AM, sunyeping via PyMOL-user

Re: [PyMOL] How do I make two grouped sets of dashes different lengths/widths?

Hi Kelvin - Try this syntax: # Create a new example molecule fab A, ala # Create the dashes using the `dist[ance]` command and two atom selections dist dash1, name H, name O dist dash2, name N, name 1HB # Add the dashes to a named group group group1, dash1 group group2, dash2 # Change the widt

Re: [PyMOL] allign multiple freme in pymol

Hi ABhik -  You'll want to have a look at the `split_states` command.  Something like the following should get you going.  Note the embedded multiline `python` block.  # Using 1nmr as a sample structure fetch 1nmr, async=0 split_states 1nmr, prefix=model python # starting at state 2, align each

Re: [PyMOL] urgent Help

Hi As,  You can start with this:     select my_ligands, organic and if that gives you other unwanted molecules (buffers, ions, etc), you can try to narrow the selection by chain, residue name/number, etc.:     select my_ligands, organic and chain B and resn ATP+ADP+AMP Hope that helps. Cheer

Re: [PyMOL] Collada export with instances?

Hi Gary and Thomas -  As Thomas mentioned, the sphere/cylinder/etc. primitives described in the COLLADA 1.5 spec as ("boundary representation") elements would be the best option for spheres and basically all other PyMOL representations except for molecular surfaces.  Unfortunately COLLADA 1.5

Re: [PyMOL] loading two objects in same pymol window

add a title in PyMOL screen? I want to show some information about my objects there (distance, area, ...) Thank you very much, Amir On Fri, May 25, 2018 at 7:49 AM, Jared Sampson wrote: Hi Amir -  It looks like you're overwriting obj1 with obj2.  Try giving them different names

Re: [PyMOL] loading two objects in same pymol window

Hi Amir -  It looks like you're overwriting obj1 with obj2.  Try giving them different names, e.g. "segment1" and "segment2" and you should be able to display both objects. Hope that helps. Cheers, Jared On May 24, 2018 at 5:10:59 PM, Amir Hossein Sharifzadeh (amirsharifza...@gmail.com) wro

Re: [PyMOL] Anaglyph stereo output from command line

Hi Cody -  I can confirm that I see similar behavior on 2.1.0 (stereo rendered properly from the GUI but not in batch mode) but the issue is not limited to just anaglyph stereo.  Rather, (admittedly not having tested all stereo_mode options) it seems stereo in general doesn't get rendered as ex

Re: [PyMOL] record and replay session?

Hi Gary - In the session you want to record, before performing the actions or commands, type: ``` log_open log.pml ``` You can also optionally provide the full path to the log file.   Then to replay the recorded instructinos in the new session (here assuming the same working directory): ```

Re: [PyMOL] Export vmrl as single object

Hi Gianluca -  Based on the way sphere export is set up for VRML2 (and similarly for COLLADA), with each sphere being a separate object, to my knowledge it is not currently possible to do what you're talking about within PyMOL.  You can probably achieve something like what you want on the Blend

Re: [PyMOL] Chi torsion angles measurements on multiple structures

Hi Baptiste -  You can loop through your loaded objects within a Python code block for this.   This works for me with a different set of related structures: ``` python dihedral = ['N', 'CA', 'CB', 'CG'] for obj in cmd.get_names():     residue = "/{}//A/288/".format(obj)     angle = cmd.get_dihedr

Re: [PyMOL] how to get session to include CGO graphics objs?

ed to all commands. Cheers, Thomas > On Mar 29, 2018, at 9:54 PM, Gary Oberbrunner > wrote: > > Thanks for the idea Jared, but no, still nothing but atoms. > > On Thu, Mar 29, 2018 at 3:31 PM, Jared Sampson > wrote: > Hi Gary - > > `cmd.fetch()`

Re: [PyMOL] how to get session to include CGO graphics objs?

Hi Gary -  `cmd.fetch()` runs asynchronously by default, meaning `cmd.show()` might execute before the structure is actually loaded.  Try amending to: cmd.fetch(mol_id, async=0) Does that make a difference? Cheers, Jared On March 29, 2018 at 2:18:29 PM, Gary Oberbrunner (ga...@darkstarsystem

Re: [PyMOL] exporting graphics objects?

Hi Gary - I’m admittedly not very familiar with Pymol2glmol, but the choice will depend on what kind of integration you want. If you’re looking for a static 3D representation that can be rotated around but not otherwise altered, COLLADA could be ok. I wrote the code for that exporter as part of

Re: [PyMOL] definition of isomesh level parameter

Hi Wolfram - The "level" parameter corresponds to sigma level.   https://pymolwiki.org/index.php/Display_CCP4_Maps Hope that helps. Cheers, Jared On March 8, 2018 at 11:07:41 AM, wtempel (wtem...@gmail.com) wrote: Hello all, even though I have some intuition about what the "level" parameter o

Re: [PyMOL] highlight a domain with another color

mean overlap them based on their similar sequence that I know the read ?  Thanks Mohammad  On Fri, Jan 26, 2018 at 3:53 PM, Jared Sampson wrote: Hi Mohammad -  If you know the residue numbers at the domain boundaries, you can do this at the command line with, e.g.: color red, chain A and resi

Re: [PyMOL] highlight a domain with another color

Hi Mohammad -  If you know the residue numbers at the domain boundaries, you can do this at the command line with, e.g.: color red, chain A and resi 1-100 color cyan, chain A and resi 101-200 etc. Hope that helps. Cheers, Jared On January 26, 2018 at 4:48:43 PM, Mohammad Goodarzi (mohammad.

Re: [PyMOL] pymol software

Hi Rex - Open-Source PyMOL is freely available.  You can find installation instructions on the PyMOL Wiki:  https://pymolwiki.org/index.php/Linux_Install  https://pymolwiki.org/index.php/MAC_Install  https://pymolwiki.org/index.php/Windows_Install Hope that helps, Cheers, Jared On January 10,

Re: [PyMOL] object not in list

e right. Im using PyMol 2.0.6. On Wed, Dec 27, 2017 at 10:45 AM, Jared Sampson wrote: Hi Ricardo -  On recent versions of PyMOL, there should be a scroll bar associated with the object list.  What version of PyMOL are you using?  If it is older, might I suggest trying out the recentl

Re: [PyMOL] object not in list

Hi Ricardo -  On recent versions of PyMOL, there should be a scroll bar associated with the object list.  What version of PyMOL are you using?  If it is older, might I suggest trying out the recently released PyMOL 2?  https://pymol.org/2/ Alternatively, if you know the name of the PDB file, th

Re: [PyMOL] How to select an atom of a particular state

Hi Cavi -  This should do it: select delta, resi 11 and resn ARG and name CD and state 76 or, using a selection macro: select delta, ARG`11/CD and state 76 If you want to show all the states simultaneously to highlight differences from state 76, you can also use: set

Re: [PyMOL] show dashes lines in cartoon to connect loops not resolved in structure

Hi Hari -  The `cartoon_gap_cutoff` setting does this.   https://pymolwiki.org/index.php/Cartoon_gap_cutoff Cheers, Jared On November 2, 2017 at 6:04:12 AM, hari jayaram (hari...@gmail.com) wrote: Hi , One of the features I like in Chimera is that breaks in the protein chain due to unresolved

Re: [PyMOL] distance wizard

Hi Leigh -  How are you getting the coordinates?  This works for me: ``` import math # Show more digits for the distance label set label_distance_digits, 10 # Make an alanine residue fab A, ala # Get coordinates from 2 atoms o = cmd.get_coords("/ala///1/O")[0] h = cmd.get_coords("/ala///1/H")[

Re: [PyMOL] Removing unwanted molecules

ove (all and not polymer) and not resn 6TA Hope that helps, Cheers, Jared > > Thanks > Mohammad > > > > > > > On Thu, Jun 22, 2017 at 3:35 PM, Jared Sampson <mailto:jared.samp...@columbia.edu>> wrote: > Hi Mohammad - > > If you click

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

) >cmd.hide('everything', 'all and not %s_%s%s' % (bare_name, > resname, resnumber)) >cmd.zoom('%s_%s%s' % (bare_name, resname, resnumber), 5) >cmd.png('%s_%s%s.png' % (bare_name, resname, resnumber), ray=1) Also, to get

Re: [PyMOL] Using API to select resi, and return some information within a certain distance

Hi Ahmad - Here are a few suggestions: > I'm still a bit new to the API so I'm not sure which commands to use. > At least I know I will start with cmd.select(string name, string > selection). > > How can I tell Pymol to: > > 1) look within a certain radius distance, and return resi's within >

Re: [PyMOL] on PDB display and calculation

Hi Smith - Check out the `orient` and `clip` commands. http://www.pymolwiki.org/index.php/Orient <http://www.pymolwiki.org/index.php/Orient> http://www.pymolwiki.org/index.php/Clip <http://www.pymolwiki.org/index.php/Clip> Cheers, Jared — Jared Sampson Graduate Student D