Pymol 1.8.x now fetches mmCIF files by default and shows missing residues in Sequence View

Long time Pymol users will be familiar with the fetch command by which it retrieved the selected file from the Protein Data Bank (PDB). Up until version 1.8, Pymol fetched the PDB version of the file by default over the mmCIF option, which the biomolecular crystallography community has long been advocating due to some deficiencies in the legacy PDB file format. Now however, Pymol fetches the mmCIF version by default and has a new default behaviour as well. When viewing the sequence bar,* Pymol now show the residues that were missing in the crystal structure, whether due to insufficient resolution or electron density. These are now displayed in grey lettering in the sequence bar (Figure 1).

Figure1. Pymol imports mmCIF files now by default with the fetch command, and displays missing residues as described in the metadata

There are also significant differences in how water molecules are listed. Previously water molecules were associated with each subunit or chain within the PDB file. In figure 2 I have loaded a second copy of the 3e90 structure which I had downloaded as a .pdb file. I had to rename it to 3e90a.pdb otherwise Pymol would have assumed it was a second state of the molecule which I did not want. You can see clearly here that for the PDB version, the water molecules associated with chain A are listed after the amino acids.

Figure2. Second copy of crystal structure manually loaded from a previously downloaded PDB file.

Similarly the water molecules and ligands associated with the PDB file are shown at the end of chain B (Figure 3). Whereas the initially loaded mmCIF file puts them all at the end of the line as separate objects, along with the extracted ligands and salts (Figure3).

Figure 3. in mmCIF files, ligands and water molecules are listed as separate chains, whereas with PDB files that are associated with a protein chain

 

I have not yet worked out a way to undisplay those missing residues short of deleting them, and they can cause issues when trying to align different structures. For example in Figure 4, the alignment of the missing residues in Box A with all the water molecules of chain A doesn’t make a lot of sense. On the other hand, the small Box B shows  how the mmCIF file conveys useful information about the residues that are missing in that portion of the PDB version of the structure.

Figure 4. Alignments in Pymol can be problematic when missing residues “align” with water molecules

 

This way of displaying missing residues quickly gets confusing when overlaying multiple structures, in the case of Figure 5, multiple versions of the NS2B/NS3 protease from West Nile Virus. For the moment I would recommend downloading the PDB files individually as PDB files and hold off switching to mmCIF if Pymol is your principle viewer.

Figure 5. Using mmCIF versions for multiple alignments with several deletions represented by grey lettering can become confusing

 

Test Platform: MacBook Pro (2011), MacOS El Capitan 10.11.3, Pymol v. 1.8.4.0

*To turn the sequence bar on you can either press the S button third from the right at the bottom of the screen, or use the seq_view command.

The sequence bar toggle button

 

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Posted in Chem, mmCIF, mmCIF files, modeling, Pymol, software | Leave a comment

When in Pymol, don’t call your model “model”

Sometimes it pays to read the blurb that loads in a textport when software loads.

Folks, there is an inherent problems when viewing your Swissmodel results in Pymol. Like many people I usually look away from the screen when I boot a program as I know it will often take a few seconds while either a boot screen appears, or more commonly with molecular modelling programs, a bunch of text scrolls by in the terminal, or in a textport window somewhere in the GUI.

Turns out that in the case of Pymol I should have been paying a bit more attention. I am an enthusiastic user of Pymol and may be guilty of proselytising a bit in it’s favour on Twitter. When Pymol boots, a lot of information scrolls by in it’s textport

 

Pymol boot screen

 

As a part-time homology modeller I use a range of software, and recently I’ve been using Swissmodel frequently. I like it quite a lot as it’s:

  1. Free
  2. Easy to use
  3. Web-based and frequently updated
  4. Gives good models as starting points for more rigorous study

However for years there’s been one aspect of results from Swissmodel that have been infuriating. When you download your results you get a lovely html-based nest of folders containing the different models produced. Unfortunately it names every model “model.pdb”. Not even model1.pdb, model2.pdb…

Swissmodel output files

When you load any of these results in Pymol a whole bunch of operations are blocked. You cannot use the “actions” menu, or even “Show Cartoons”. Over the years I’ve used a couple of workarounds. The simplest is to rename the model to something more useful. It should have dawned on me that there was something intrinsically wrong with the name model.pdb but I didn’t bother to pursue it.

Using the Pymol Actions dropdown to extract the selection to a new object

If I forget beforehand to rename* the file I simply used to use the Pymol “extract object” feature to take the entire molecule out of the file “model”, and then continue work. Now if I had bothered to look more closely at the textport I would have seen that:

Executive-Warning: name “model” collides with a selection language keyword.

Update: It is of course easy to rename model.pdb using the “set_name” command in pymol to something that allows you to keep working, rather than going through the trouble of extracting into a new object as I had been doing. The correct syntax is:

set_name model, newname

It doesn’t help to know this now of course, I still have to use a workaround. It would just be nice if there was an option to have the 16 different models that Swissmodel produced in this case named something different (like model1, model2, model3…

POSTSCRIPT. I hope that this brief post doesn’t sound like too much of a whinge. I aim to write a bit more about Swissmodel, which is an excellent resource for people looking at getting into homology modelling in particular in the near future. If you have any questions about today’s post, or about Swissmodel, leave a comment or you can always send me a Tweet @MartinStoermer over on Twitter.

POSTSCRIPT. I saw this great tip from Cult of Mac for bulk renaming files with renumbering in the Mac Finder, which I didn’t know about. It works great, even on nested files in folders.

bulkrenamerenumber

The inbuilt bulk rename/renumber tool in the MacOS Finder

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Major upgrade to WebCSD – The small molecule crystal structure database

[Update 16th June: Added Note about Pymol 1.8.4]

The new version of WebCSD has arrived and with it, a few new important features, such as improved substructure searching, and advanced text searching. The Cambridge Crystallographic Data Centre (CCDC) houses the the Cambridge Structural Database (CSD), a repository of over over 875,000 small molecule structures from x-ray and neutron diffraction analyses.

Growth in the CSD. Graphic copyright The Cambridge Crystallographic Data Centre http://www.ccdc.cam.ac.uk. The Cambridge Structural Database, C. R. Groom, I. J. Bruno, M. P.
Lightfoot and S. C. Ward, Acta Cryst. (2016). B72, 171-179 DOI:
10.1107/S2052520616003954

Traditionally, use of the CSD has been by institutional licensing of the desktop client Conquest, and by downloading periodic updates. The current release is May 2017. Recently a Java/Web interface WebCSD has become available for use, which contains fewer features compared to Conquest, but which is useful for accessing structures if you are out of the office or working from home. Unfortunately, I frequently had problems with the previous version which used to throw up lots of erroneous Java errors on Mac, claiming that the user had an out-of-date Java version. Happily this annoying bug seems to have gone with the new version.

Java Error with WebCSD v1.1.2 on Mac

Another confusing thing about the old WebCSD was that it used a different login system from the CCDC data deposition interface, requiring crystallographers or IT departments to maintain separate logins. In the new version you log in with your data deposition username/password at the main CCDC home page. The first thing you will notice is that the new CCDC home page now has two large button options:
Deposit structures and Access Structures.

new CCDC home page

Choosing Access structures takes you to the new WebCSD text and structure search interfaces in a familiar tab format.

Text Query Interface in the new WebCSD

Substructure search in the new WebCSD

I first gave it a quick try in text mode looking for structures of my current favourite mushroom toxin cyclic peptide α-amanitin. The results page has all the structures preselected in a tickbox format and encouragingly there is a “Download Selected” button.

Hits Page in WebCSD

This may not seem like a big deal but one of my major gripes with previous versions of WebCSD was that it was not possible to do a bulk download of hits. For that you have to use the Conquest interface, something that is impractical to do off-site.

So finally you can download all the hits, but currently only as a multiCIF file. This is not the easiest option but better than nothing. I’m currently trying to find reliable ways to convert or read multiCIFs. Pymol loads them all but only puts bonds in for the first entry (see pictures below). Update: Newer versions of Pymol (I used 1.8.4) read in all the files in a multiCIF correctly.

MultiCIF files opened in Pymol (v.1.6). First entry shows bonds, later entries just show atoms.

New versions of Pymol (v.1.8.4). show all atoms and bonds correctly*

Schrödinger’s Maestro only reads only first of a multiCIF file. The CCDC’s own software Mercury reads them all into the viewer window, from which you can select and export the files in a variety of formats, but you still can’t bulk export them all to another format.

Amanitin hits from WebCSD displayed in Mercury

I next tried searching for a substructure, a cyclic octapeptide equivalent with four thiazoles. Excuse the drawing, I’m still coming to grips with the interface and rotating etc. This came up with one hit, which happens to be a symmetric compound with four prolines occupying the remaining four amino acid positions. (Link to paper)

Substructure search interface. Had trouble finding rotate or cleanup tools

Nicely, there is a JSmol rotating 3D model of the structure as well. This hit also shows how this class of modified peptide macrocycles frequently bind solvent molecules and metal ions, In this case I have caught the rotating JSmol at the right angle to see a nice molecule of acetonitrile bound in the centre of the macrocycle.

WebCSD substructure hit interface

This has been only a very short overview of the new version. Stay tuned for anything else I discover. In particular one of the best things about new version is that is much much faster. I look forward to the products continued evolution, particularly the ability to extract hits to SD files, which is a standard feature of the desktop version.

*I should note that multiCIF files often contain coordinates for disordered atoms and these may display weirdly in Pymol. Pymol uses distances to estimate bonds, so some downloaded structures may appear to have chemically unfeasible connectivities.

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New initiative: The Molecular Sciences Software Institute (MolSSI), based at Virginia Tech. via @ACSPublications

“A new computational chemistry software institute, the first of its kind funded by the National Science Foundation, aims to bring software development in the field up to speed with rapid advances in computer hardware.

The Molecular Sciences Software Institute (MolSSI), based at Virginia Tech, celebrated its launch with a reception on Tuesday at the American Chemical Society national meeting in San Francisco.”

I haven’t had a good look at this yet, I just saw this over at the ACS Meetings page. This looks like a really interesting initiative from the NSF. I can’t see any current job openings on the site, the last round closed in November 2016 and the Fellowships in February 2017. Something to keep an eye out on for when the next round opens.

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ChemDraw, Chem3D dropped from iOS App store

☹️ I missed this one back in January, but I could sense it was coming. CambridgeSoft have dropped the iOS apps ChemDraw, Chem3D, and CDSL from the App Store. (admittedly I hadn’t heard of the last one at all). Together with this, the “Flick2Share” feature has been killed off. I never really used Flick2Share but it seems that PE are putting all their efforts in the sharing space into the updated ChemDraw Cloud, which I also haven’t really used yet. I hope to get around to fully evaluating ChemDraw Cloud at some point and reviewing it here.

deathofcdapps

ChemDraw, Chem3D, CDSL iOS Announcement © Cambridgesoft / Perkin-Elmer

I’m sad that the iOS apps are gone, particularly ChemDraw. I like the ability to quickly share structures to social media, particularly seeing as the desktop versions struggle to easily produce GIFs that retain resolution in web browsers, especially  on Twitter, and in 3rd Party Twitter clients,

[Update 2 March] However, if you have downloaded the apps to your iPad they will continue to function. Testing this morning on my rapidly ageing iPad3 the last-downloaded versions (ChemDraw 2.01, Chem3D 2.02) worked OK, except that on startup you may see an oblique message to the effect that “a sharing option could not be enabled”. I forgot to screenshot it but I presume this means Flick2Share.

 

So here is a summary of what still works. ChemDraw:

  1. Drawing, editing, saving, and (some) exporting of structures
  2. Save picture to Camera Roll
  3. Dropbox export (PDF, PNG, CDXML) works fine as previously
  4. Twitter export
  5. Export via email

What doesn’t work:

  1. Flick2Share

 

img_1207

Twitter sharing in ChemDraw for iPad still works

 

Chem3D was always a somewhat limited product compared to the desktop version, and never gained any additional features after my original mini review. This limitation was somewhat compensated for by virtue of being free. Importing structures could only be done through iTunes or downloaded protein structures from the PDB. Chem3d for iPad is a viewer application only. There are no molecular mechanics options available at all, and analysis options are few. But after a brief test the list of what works and what doesn’t is as follows:

  1. Viewing and importing of structures from the PDB
  2. Save picture to Camera Roll
  3. Twitter export
  4. Email export

What doesn’t work:

  1. Flick2Share
  2. Dropbox Export
Chem3D Twitter export also still works.

Chem3D Twitter export also still works.

Actually I don’t recall Dropbox export ever working for Chem3D, whereas it works fine for ChemDraw. As of this morning choosing Dropbox as the export function simply flips you out to the Dropbox app, if installed, to the default root directory listing page, and no option to name the file or specify a location. It just sits there until you go back to Chem3D. Nothing is ever written to Dropbox. Personally I have always preferred Pymol for visualising proteins for use online and in print,  so the loss of Chem3D for iPad isn’t as big of a deal for me as ChemDraw.

I was happy to pay around $10 for ChemDraw when it came out so I’m disappointed that it’s been abruptly dropped. It’s a peculiar strategy for CambridgeSoft/PE who evidently see ChemDraw Cloud as the future, particularly as everyone else in the app space seems to be trying to drive people away from web services and onto apps. Witness the endless pop-ups in Safari on every other web page imploring you to download and view their content in their app. An annoying UI “feature” that I earnestly implore Apple to kill ASAP.

When these apps originally appeared I saw them as principally teaching tools, given the reduced set of features and lower price point. With tablets becoming common in schools I saw possibilities for teachers and students flicking structures back and forth in pop quizzes  etc. A few people have contacted me wondering about this too, but I have absolutely no idea of what the uptake of this was in schools. Obviously PE has that information and made a business decision to drop it. I’m not yet convinced that ChemDraw Cloud is going to fit that school usage demographic either. In it’s current form its seems placed more towards the higher, content creation end of the user spectrum.

Posted in Chem, ChemDraw, Chem_Comp, iPad, tablet, Twitter | Tagged , , , , , , , | Leave a comment

ChemDraw 16.0.1, a maintenance release

chemdrawchain

Cambridgesoft/PerkinElmer announced a ChemDraw maintenance release of ChemDraw and ChemOffice 16.0.1. Apparently designed principally to address usability on the Mac platform.

ChemDraw 16.0.1 Announcement © Cambridgesoft / Perkin-Elmer

ChemDraw 16.0.1 Announcement © Cambridgesoft / Perkin-Elmer

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ChemDraw 16, a second look: Running under MacOS Sierra

[Update March 1. ChemDraw 16.0.1, ChemDraw 16.0.1 press release principally addressing stability and usability issues on the Mac platform has been released.]

A quick update on my earlier post. I have managed to get ChemDraw 16 running on MacOS 10.12.1 Sierra. I installed Sierra on an external USB self powered hard disk, so performance is a bit slow but the important details are as follows:

It works!

It works!

I have not tested all functionality of ChemDraw 16 under Sierra for the moment. But for me, the most important question, “Does round trip editing work with Word 2011, PowerPoint 2011 under Sierra?” can be answered with a big “YES”. Here is a pic of a structure from the previous post pasted back into ChemDraw 16 from Word. The structure is editable, and can be transferred back to Word (or PPT). But please note, this is not supported yet by CambridgeSoft. Officially Sierra is not supported. It’s just that the features I have tested on one machine work.

ChemDraw 16 under MacOS Sierra

ChemDraw 16 under MacOS Sierra

On this Sierra boot disk I have now also updated the copies of Pages, Keynote and Numbers to their Sierra release versions however disappointingly Round Trip Editing (RTE) still does not work on my test platform. So to summarise, neither the El Capitan versions of Pages (v 5.6.2) or Keynote (v 6.6.2) or their Sierra release versions, Pages 6.0.5 or Keynote 7.0.5 support RTE. Office 2011 does.

P.S. I have not tested RTE on OpenOffice of any flavour as I have a thing about Java. Also if anyone else has read this far, pasting ChemDraw structures into a Google Doc does not work. Docs doesn’t recognise the clipboard contents. You can do it by  inserting a graphic (PNG etc) sure, but the editable features that make a ChemDraw structure work aren’t incorporated, so why would you even?

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