Re: [PyMOL] Deprecation of MMTF-format files for the PDB archive

Jose, I have a few questions about the BCIF format. Adding pymol-users because there might be interest there as well (at least among developers). First, at PDBe, where is the link for downloading BCIF files for a given structure? I only see this, for example, at https://www.ebi.ac.uk/pdbe/entry/

[PyMOL] open source installation on Windows broken?

At https://pymolwiki.org/index.php/Windows_Install the process fails for 3. Download the appropriate wheel files , which is a dead link. Does anyone know how to run open source PyMOL on Windows OS? Bob Hanson

[PyMOL] BCIF

Seeing as MMTF is being deprecated, I am wondering if efforts are underway to allow PyMOL to read the BinaryCIF format? Bob Hanson >From July 2024 the PDB file archive will not be offered in the compressed > MMTF format anymore. Users are strongly encouraged to switch to the BinaryCIF > format

Re: [PyMOL] how to convert .pse to html?

Albert, I just note that JSmol reads PyMOL PSE files directly - fully JavaScript/HTML5 - and allows interactive viewing of them in JavaScript as well as all the functionality of Jmol; nothing to change in terms of the PyMOL file. Just load it. Of course, not every capability of PyMOL is reproduced

Re: [PyMOL] 3D printing

On Tue, Oct 4, 2016 at 11:28 AM, Spencer Bliven wrote: > I've done a bit of 3D printing of proteins. I found links in the previous > thread VRML2 export and edu pymol > helpful. > > STL is the best supported format for the printers, but s

[PyMOL] 3D printing

Can someone give me a summary of capabilities and limitations in PyMOL re 3D printing? For example: Q: What output file types are supported? (WRL, X3D, STL[ASCII/binary], other) Q: Does the generation of these include algorithms for ensuring closure or for stitching together objects in order to

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

To finish this thread -- Jmol and JSmol can now read (basic) PyMOL 1.8 PSE files that have set dump_binary, 1 for faster loading and smaller file sizes. Jmol only implements a small, basic range of PyMOL functionality, of course. https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.6/Ve

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

Almost have it. Having trouble fitting all that into 120 bytes, though. I'm good through bytes 96-99, visrep. Somehow, though I count 124 bytes total, not 120 (which is clearly the case in the PSE file). What is sizeof(AtomInfo_1_8_1) ? I calculate: ... 100-105 (six booleans) 106-111 (six characte

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

Ah, that is what I needed. For some reason that file is not in the download I unzipped. Much more sensible! Bob On Mon, Aug 8, 2016 at 3:18 PM, Thomas Holder wrote: > On 08 Aug 2016, at 16:01, Robert Hanson wrote: > > > I see this in 1.8.2.1: > > > > #define

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

U (will indeed write an unused NULL pointer), at the time it > was work in progress for a specific use case which didn't require ANISOU. > > Cheers, > Thomas > > On 08 Aug 2016, at 11:32, Robert Hanson wrote: > > > I do like the compactness of that and the quicker lo

Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

for "AtomInfoTypeConverter" if you're > interested in the details. > > The default (in 1.8.2) is to save PyMOL 1.7.6 compatible PSE files, and > with the "pse_export_version" setting you can also export for older PyMOL > versions. > > Cheers, > Tho

[PyMOL] dump_binary and PyMOL 1.8 PSE files

Thomas, In reading PyMOL PSE files into Jmol I have recently run into the problem with some of these files (version 1.8.2.3). Jmol has no problem reading the standard Pickle format, but there seems to be an option in PyMOL to serialize binary data structures as BINSTRING or SHORT_BINSTRING format

Re: [PyMOL] The Wiki appears outdated or in error

In case you are interested, Jim, Jmol will read (most/some) PyMOL session files, and Jmol can then create both an idtf for generating a u3d file, and a small sample TeX file also that can be used to create a PDF containing it. I had some interest in u3d back in 2009, when I wrote this exporter. Yo

Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]

Ioannis, I suggest using the CIF file from EBI instead: http://www.ebi.ac.uk/pdbe/static/entry/download/1hho-assembly-1.cif.gz It looks good to me -- just one model. For reference, the RCSB site is using Jmol and is simply loading 1HHO itself and constructing the assembly *in situ *using the sy

[PyMOL] status of Uppsala EDS server?

Does anyone know the status of http://eds.bmc.uu.se? Is it gone forever? Does anyone know the replacement URL for getting electron density maps and difference maps? (Which I think is at EBI, right?) Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St

Re: [PyMOL] Version question -- PSE session file format

ith partial=1, it will also not store the viewport. > > Cheers, > Thomas > > On 23 Dec 2015, at 19:12, Robert Hanson wrote: > > > I have a question about the PSE file format. > > > > Newer PSE files, perhaps those created using PyMOL 1.8, seem to have no >

[PyMOL] Version question -- PSE session file format

I have a question about the PSE file format. Newer PSE files, perhaps those created using PyMOL 1.8, seem to have no indication of the desired viewport width and height. These were in the "main" dictionary item. Is there any way in these new files to find out the original viewport size? Bob --

Re: [PyMOL] JyMOL vs JSMol

Don't worry. No apology necessary. It's a closely held secret that JSmol can do this. In any case, trust me, you will find plenty that JSmol cannot handle. There are many mysteries of the PSE format that I could only guess at. Enjoy! ​ --

Re: [PyMOL] JyMOL vs JSMol

I guess I should chime in here. JSmol does read (some fraction of) PyMOL session files. To be sure it has not been a priority to keep up to date with all the amazing PyMOL capabilities, but certainly as a proof of concept it has worked well, and it would be great to collaborate on this to improve i

Re: [PyMOL] Problems loading new mrc-format electron density files into pymol

>From Steven Ludtke (EMAN2): We'll get it fixed in today's daily release. On Tue, Oct 6, 2015 at 7:37 AM, Michael F. Summers wrote: > Colleagues: > > In the past, I was able to load MRC format electron density maps into > pymol without problems. However, files I’ve received from collaborators,

Re: [PyMOL] Superimpose small non-protein molecules?

Looks like PymolWiki is down. On Tue, May 5, 2015 at 1:59 PM, Osvaldo Martin wrote: > Hi Jorge, > > You are right align is only for proteins. You can use the Fit > command > > Cheers, > Osvaldo. > > On Tue, May 5, 2015 at 3:38 PM, Jorge Fernandez de Cossi

Re: [PyMOL] sulfated tyrosine's losing connection

actually -- I see there are just CONECT records for all the HETATMs, as usual. Nothing odd about that. But, nonetheless, in this case those CONECT records are not there. The point is that it has nothing to do with PyMOL. ​

Re: [PyMOL] sulfated tyrosine's losing connection

This unusual file has all the backbone bonds indicated with CONECT records -- except the missing links you note. I'm guessing that PyMOL is respecting that, and that it could be an RCSB file error. CONECT 9606 9593 9607 CONECT 9607 9606 CONECT 9608 9609 ... CONECT 1674 1661 1675 CONECT 1675 1674 C

Re: [PyMOL] CGOs

Great. Thanks very much. The ones perhaps missing there are: #define CGO_INDENT 0x18 #define CGO_RESET_NORMAL 0x1E #define CGO_PICK_COLOR 0x1F And I think #define CGO_LIGHTING 0x0B50 may be an internal flag, not a CGO command.

Re: [PyMOL] CGOs

OK, that explains it. I think I made that one up. It was a while ago that I worked on this. :) I see the list at https://github.com/speleo3/pymol/blob/master/modules/pymol/cgo.py Thanks​, David. Bob -- Dive into the World

Re: [PyMOL] CGOs

O objects. You can have > a look in modules/cgo.py and in the example scripts in examples/devel/ in > the pymol directory to get some more information. If there is something > specific you want to do, please let us know. > > Cheers, > > Tsjerk > > > On Sun, Dec 21, 2014

Re: [PyMOL] CGOs

I'm looking for something that is relatively comprehensive. There are far more commands than VERTEX, CYLINDER, CONE, and SPHERE, I think. -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! In

[PyMOL] CGOs

Happy holidays! Q: Is there a resource that describes the syntax for compiled graphical objects in PyMOL? I see http://pymol.sourceforge.net/newman/user/S0500cgo.html, but that is pretty minimal. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St

Re: [PyMOL] View Matrix operation

I don't think this is possible. Those 9 numbers simply tell you the orientation. There is much more to it than that. Perspective, camera position, x-y translation, screen dimensions, for example. Some of these are in other PyMOL settings. On Wed, Nov 19, 2014 at 6:14 AM, Feitsma, L.J. wrote: >

[PyMOL] mmCIF -- multicharacter chain labels

What's the trick to loading mmCIF files with multi-character chain IDS? Maybe I just need to upgrade? (Using PyMOL 1.6.0.0) What I see now is just the first character of _atom_site.auth_asym_id Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

My only real objection is that WebGL is not supported on iOS in browsers. Beyond that, I probably just don't know enough about it to do it right. On Wed, Feb 12, 2014 at 1:50 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Bob, > > On 10 Feb 2014, at 20:43,

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

So JmolData.jar can read a .pse file as is (with lights, > transparences, hidden no-polar hydrogens, colors, ray, etc)? Sounds good. > > Thanks a lot to you. > > Regards, > Riccardo Volpe > > > *ChemBioScripting | X3D PyMOL Molecule Viewer > <http://chembioscrip

Re: [PyMOL] Corrupted IDTF file from small molecule (sticks representation)

So in the mean time, Riccardo, I guess what you are already using: xxx.pse -- JmolData.jar --> idtf is your best bet. Q: What sort of size of PDF file are you seeing in the end? Q: Do you see this a practical and useful in some way? If so, in what way? Bob Hanson --

Re: [PyMOL] minimum rotation between views

Jonathan, this is called the quaternion difference, but I don't know how you get access to quaternions in PyMOL. If you could, you would just take the difference between the two quaternion representations of the views and get it's angle for the corresponding axis-angle. Jason, are there standard P

Re: [PyMOL] new "metals" keyword

see http://chemapps.stolaf.edu/jmol/docs/#atomproperties for several suggestions. On Tue, Aug 13, 2013 at 10:56 AM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Greetings, > > this is a quick announcement that we added the "metals" keyword to the > selection language (SVN code revisio

Re: [PyMOL] Reducing the surface rendering load for JSmol export

Nick, if these are just molecular surfaces, there is nothing to do in PyMOL. The PSE files have only an indication of which atoms to create the surface for, not the surface itself. Jmol/JSmol reads the PSE files directly, determines what molecular surface to create, and uses its own algorithms. Ri

Re: [PyMOL] PyMOL 1.6 pre-release announcement

(yes, I meant "forward compatibility" there) Jason, in our 100+ PyMOL session files that we can now read into Jmol we have a few files that don't seem to have backward compatibility to PyMOL 1.3 from the open source version 1.6.0.0. Mostly it has to do with CGOs and measurements. Should I just sen

Re: [PyMOL] PyMOL 1.6 pre-release announcement

That would be a problem with all programs -- unless there is a SAVE mode that is "compatible with version " (as, for example, MS Word has). One cannot expect backward compatibility, I think. Bob Hanson On Wed, Jun 19, 2013 at 4:18 PM, David Hall wrote: > I still have this problem: > sessi

Re: [PyMOL] Cartoon transparency

I must say, 'cartoon skip' does not do what I thought it would do. fetch 1RV1 cartoon skip, i. 55 # now a helix section is turned into a loop cartoon skip, i. 56 # now there is a break, but two non-helix ends cartoon skip, i. 57 # now there is a break, with two non-helix ends I guess I understan

Re: [PyMOL] Possible hydrogen addition bug

Just adding that N1, C2, and N3 in that ring are all sp2 hybridized. So the H on the adjacent N is also in the wrong place. Q: How is PyMOL determining ligand atom hybridization, by the way? Not using the ligand CIF file at PDB, I guess? Bob Hanson On Fri, Jun 7, 2013 at 10:51 AM, Matthew Baum

Re: [PyMOL] scenes and atom-wise colors

throwing me off. For my purposes, it just means that I have to be careful to use only the COLOR command if I want scenes to reproduce changes in color. Might be nice to explain that on the wiki. (Or, of course, maybe I missed it there) Bob On Thu, Jun 6, 2013 at 9:47 AM, Robert Hanson wrot

[PyMOL] scenes and atom-wise colors

I guess I still don't understand exactly what a scene is: "scene" saves and restores scenes. A scene consists of the camera view, all object activity information, all atom-wise visibilities, all atom-wise colors, all representations, the global frame index, and may contain a text

Re: [PyMOL] Cartoon transparency

That would not work if you were trying to show selected individual ribbon segments translucent, I think. Right? >From what I can tell, here is the list of settings that you can assign a selection. Notably missing is cartoon_transparency and ribbon_transparency. Perhaps because a cartoon object can

Re: [PyMOL] settings

olors. > But a scene does store settings in the sense that there are, at least for colors, for example, _!c_scene_xxx_sticks "settings". How does that fit in, then? I'll look into that. > Hope that helps. > definitely! > > Cheers, > Thomas > > On Jun

Re: [PyMOL] scenes and states

face > representation only in one state, such that looping over the states, the > surface would suddenly pop up for one. > > Hope it helps, > > Tsjerk > > > On Mon, Jun 3, 2013 at 2:38 PM, Robert Hanson wrote: > >> Questions: >> >> Can two objects be

[PyMOL] scenes and states

Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Robert M. Hanso

[PyMOL] settings

I'm trying to understand settings. I see that there are at least these levels of settings: - global - object - state - unique atom/bond Are there more? I'm unclear on when one overrides another. It looks to me that the general "getSetting" methods have the option of up to three levels of setting

Re: [PyMOL] PyMOL measurements

ic_measures, 1 > > In newer versions of PyMOL this is enabled by default. > > Cheers, > > -- Jason > > > On Fri, May 31, 2013 at 8:27 AM, Robert Hanson wrote: > >> Is there a way to tie measurement ends to specific atoms, so that when >> th

[PyMOL] PyMOL measurements

Is there a way to tie measurement ends to specific atoms, so that when the structure is tweaked, those measurements update automatically? -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr I

[PyMOL] surfaces involving more than one object

PyMOL questions about surfaces: Simple enough to create a surface for one object. What about for only a portion of the object? How to do each of these? -- closed surface ignoring a selected set of atoms -- open surface not ignoring any atoms, but also not displaying their part Is the rule, "

[PyMOL] PyMOL session file reader for Jmol

Hello, PyMOL users, The driving force behind these last four months of Jmol/JSmol development has been e-publication. The goal has been to produce a means of e-publishing working interactive biomolecular models that are ubiquitously accessible (i.e. no Java, no WebGL). We achieved that goal for J

Re: [PyMOL] new to list -- simple questions

Thank you, Tsjerk, that's helpful. To date, we are successfully interpreting all of the following: -- atoms with labels -- bonds -- standard PyMOL rendering, including: -- lines -- sticks -- nonbonded (stars) -- nb_spheres -- cartoons of vari

[PyMOL] new to list -- simple questions

Hello, PyMOL users! I'm new to this list. Some may recognize me as the current principal developer of Jmol. Until recently I hadn't explored PyMOL much, mostly because I'm not myself a biochemist. For about three months now, though, Jaime Prilusky (Weizmann Institute) and I have been working on a