How to view structures in ChimeraX and PyMOL

TW001 · 30 May 2022 15:25

On Windows computer:

I found that Jalview requires a path to ChimeraX or PyMOL to be specified - otherwise, Jalview cannot find the program/app file and it is not possible to view structures.
For PyMOL, when I specify the correct path Jalview still sends notification that it cannot find the program/app file, and then PyMOL opens without the .pdb file.
For ChimeraX, when I specify the correct path the ChimeraX viewer window opens in Jalview and is blank, and ChimeraX opens without the .pdb file.

On Mac computer:

PyMOL worked perfectly.
ChimeraX: exactly the same problems.

jalviewadmin · 30 May 2022 15:54

Hi Thomas - thanks for posting. There are a few things that could be going wrong here for you, so please bear with us!

I also just noticed you have edited your message… so I’ve also edited my reply below:

You say the problem is on Windows - can you tell us which version of windows ? The Jalview Console (open via Jalview’s Tools menu’s Java Console entry) reports the platform info at the top. Once you have this open, please also change the Log Level to ‘TRACE’ - so Jalview outputs more information when you try to view the structures.
If Jalview is popping up a dialog warning you it cannot locate the Pymol executable even after you have provided the path, then it might be that some special characters need to be escaped. Did you try double clicking the text box and navigating to Pymol.exe (or bin/pymol) via the file chooser ?
It sounds like Jalview managed to locate and launch ChimeraX correctly - but that Jalview didn’t give ChimeraX the PDB file. If you can cut and paste any errors you can see in ChimeraX’s reply log into a message, that will help us work out what’s going on.

If you can send me the contents of the Jalview Java Console after trying to configure and view with Pymol and ChimeraX that would be really helpful also.

Hopefully we can get work out what the problem is …
Jim.

PS. There might be a problem with the PDB file (unlikely, but worth mentioning) - for instance, if you are trying to view the ‘1A70’ structure that is loaded via the Jalview project, this actually won’t work with the current version of Jalview due to a bug (JAL-4015)

You can work around this problem by clicking the ‘Fetch from 3D Beacons’ button in the structure chooser’s dialog, or picking one of the “PDBe …” options from the drop down menu to download the 1A70 structure again from the PDBe.

If you are having problems with a PDB file that you have on a shared drive, there might be other issues - again, the Jalview Java console log will help us diagnose.

jalviewadmin · 30 May 2022 16:04

all done - please take a look!

TW001 · 30 May 2022 17:12

–Reply to no. 1–

I copied and pasted the Java console in the different situations. I inserted spaces in hyperlinks because hyperlinks not allowed in this post.

Windows

Java console after trying to view structure in PyMOL:

Jalview Version: 2.11.2.2
Jalview Installation: Source git-commit:62fb9a3042 [releases/Release_2_11_2_Branch]
Build Date: 15:43:43 19 April 2022
Java version: 1.8.0_322
amd64 Windows 10 10.0
Install4j version: 9.0.5
Install4j template version: 2.11.2.0_F188884b4_C2040e7e728
Launcher version: 1.8.3-1.2.12_JVL
LookAndFeel: Windows (com.sun.java.swing.plaf.windows.WindowsLookAndFeel)
Getdown appdir: C:\Users\TW43969\AppData\Local\Jalview
Java home: C:\Users\TW43969\AppData\Local\Jalview\jre
ERROR - Failed to start PyMOL with XMLRPC, response was:
INFO - PyMOL started with XMLRPC on port 0
ERROR - Failed to read PyMOL XMLRPC port number
ERROR - Failed to launch PyMOL!
WARN - Request to http:// 127.0.0.1:0 returned java.net.ConnectException: connect: Address is invalid on local machine, or port is not valid on remote machine

Java console after trying to view structure in ChimeraX:

Jalview Version: 2.11.2.2
Jalview Installation: Source git-commit:62fb9a3042 [releases/Release_2_11_2_Branch]
Build Date: 15:43:43 19 April 2022
Java version: 1.8.0_322
amd64 Windows 10 10.0
Install4j version: 9.0.5
Install4j template version: 2.11.2.0_F188884b4_C2040e7e728
Launcher version: 1.8.3-1.2.12_JVL
LookAndFeel: Windows (com.sun.java.swing.plaf.windows.WindowsLookAndFeel)
Getdown appdir: C:\Users\TW43969\AppData\Local\Jalview
Java home: C:\Users\TW43969\AppData\Local\Jalview\jre
https:// www. ebi. ac. uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(text:101)+AND+molecule_sequence:%5B’’+TO+*%5D+AND+status:REL&sort=overall_quality+desc
query >>>>>>> jalview.fts.core.FTSRestRequest@31a75c08
Chimera REST API started on port 56010
Jalview ChimeraListener handler started on http:// localhost:53911/jalview/chimera1
CIR resolver set to https:// cactus. nci. nih. gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53 2021-02-10 09:12
java.vendor: Java: Temurin
java.version: Java 1.8.0_322
os.name: Windows 10
Access: ALL
memory: 127.1/365.4
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
reading 905 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty “modelInfo” or getProperty “auxiliaryInfo” to inspect them.
Default Van der Waals type for model set to Jmol
905 atoms created
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Jmol 15.1.53 2021-02-10 09:12 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,
and we thank the CMBI for maintaining it to the extent that it was easy to
re-engineer in Java for our purposes.

Second generation DSSP 2.0 is used in this analysis. See Int. J. Mol. Sci. 2014, 15, 7841-7864; doi:10.3390/ijms15057841.

All bioshapes have been deleted and must be regenerated.

Time for creating model: 9 ms

Mac

Java console after viewing structure in PyMOL:

Jalview Version: 2.11.2.2
Jalview Installation: Source git-commit:62fb9a3042 [releases/Release_2_11_2_Branch]
Build Date: 15:43:43 19 April 2022
Java version: 1.8.0_202
x86_64 Mac OS X 10.16
Install4j version: null
Install4j template version: null
Launcher version: 1.8.3-1.2.12_JVL
LookAndFeel: Quaqua Leopard FileChooser-only LAF (ch.randelshofer.quaqua.subset.QuaquaLeopardFileChooserLAF)
Getdown appdir: /Applications/Jalview.app/Contents/Resources/app/.
Java home: /Applications/Jalview.app/Contents/Resources/app/jre/Contents/Home
https:// www. ebi. ac. uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(text:101)+AND+molecule_sequence:%5B’’+TO+*%5D+AND+status:REL&sort=overall_quality+desc
query >>>>>>> jalview.fts.core.FTSRestRequest@76bf229b
INFO - PyMOL started with XMLRPC on port 9123
INFO - PyMOL XMLRPC started on port 9123
CIR resolver set to https:// cactus. nci. nih. gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53 2021-02-10 09:12
java.vendor: Java: AdoptOpenJdk
java.version: Java 1.8.0_202
os.name: Mac OS X
Access: ALL
memory: 247.4/1225.3
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
reading 905 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty “modelInfo” or getProperty “auxiliaryInfo” to inspect them.
Default Van der Waals type for model set to Jmol
905 atoms created
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Jmol 15.1.53 2021-02-10 09:12 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,
and we thank the CMBI for maintaining it to the extent that it was easy to
re-engineer in Java for our purposes.

Second generation DSSP 2.0 is used in this analysis. See Int. J. Mol. Sci. 2014, 15, 7841-7864; doi:10.3390/ijms15057841.

All bioshapes have been deleted and must be regenerated.

Time for creating model: 17 ms

Java console after trying to view structure in ChimeraX:

Jalview Version: 2.11.2.2
Jalview Installation: Source git-commit:62fb9a3042 [releases/Release_2_11_2_Branch]
Build Date: 15:43:43 19 April 2022
Java version: 1.8.0_202
x86_64 Mac OS X 10.16
Install4j version: null
Install4j template version: null
Launcher version: 1.8.3-1.2.12_JVL
LookAndFeel: Quaqua Leopard FileChooser-only LAF (ch.randelshofer.quaqua.subset.QuaquaLeopardFileChooserLAF)
Getdown appdir: /Applications/Jalview.app/Contents/Resources/app/.
Java home: /Applications/Jalview.app/Contents/Resources/app/jre/Contents/Home
https:// www. ebi. ac. uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(text:101)+AND+molecule_sequence:%5B’’+TO+*%5D+AND+status:REL&sort=overall_quality+desc
query >>>>>>> jalview.fts.core.FTSRestRequest@93ec274
Chimera REST API started on port 56203
Jalview ChimeraListener handler started on http:// localhost:56158/jalview/chimera1
CIR resolver set to https:// cactus. nci. nih. gov/chemical/structure
Operating headless display=null nographicsallowed=true
(C) 2015 Jmol Development
Jmol Version: 15.1.53 2021-02-10 09:12
java.vendor: Java: AdoptOpenJdk
java.version: Java 1.8.0_202
os.name: Mac OS X
Access: ALL
memory: 390.5/1117.3
processors available: 8
useCommandThread: false
The Resolver thinks Pdb
reading 905 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty “modelInfo” or getProperty “auxiliaryInfo” to inspect them.
Default Van der Waals type for model set to Jmol
905 atoms created
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Jmol 15.1.53 2021-02-10 09:12 DSSP analysis for model 1.1 - null

W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637

We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,
and we thank the CMBI for maintaining it to the extent that it was easy to
re-engineer in Java for our purposes.

Second generation DSSP 2.0 is used in this analysis. See Int. J. Mol. Sci. 2014, 15, 7841-7864; doi:10.3390/ijms15057841.

All bioshapes have been deleted and must be regenerated.

Time for creating model: 37 ms

–Reply to no. 2–

The pymol.exe file appears to be located in a folder that is not visible in the file navigation app. I found the location of pymol.exe by following the shortcut that is found in the Start Menu folder.

–Reply to no. 3–

Here is the ChimeraX log, which is basically the same on Windows or Mac:

remotecontrol rest startUCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
REST server started on host 127.0.0.1 port 62967
Visit (hyperlink - deleted by Tom) for CLI interface

I noticed that on both Windows and Mac, if I click “open” in ChimeraX it is already in the Jalview folder.

jalviewadmin · 31 May 2022 07:57

Hi Thomas - thanks. It looks like the path is the problem for Pymol - a trick we discovered (and should put in the docs) is that if you paste the path into the File Browser app that pops up when you double click the text box (rather than direct into the text box), then hit return, the file browser app will show you the pymol directory so you can select the executable directly.

As to why ChimeraX is failing - I’m not sure. I can’t see errors.

I’ve messaged you on the University of Dundee’s Teams app - it might be best if we meet virtually so you can show me what’s going on.

TW001 · 31 May 2022 08:38

I was not able to do that trick as you described. I unhid the hidden folder in the file navigation app (outside of Jalview), and then was able to directly select the .exe file for PyMOL from Jalview. No change from before - the same problem occurs. I checked the file>open option in PyMOL, and as I found for (ChimeraX on both Windows and Mac) it was already in the Jalview folder. This suggests a similar problem for all the scenarios, except PyMOL on Mac because that is working fine.

jalviewadmin · 31 May 2022 10:59

I’ll connect with you on MS Teams to see what’s going on. None of the debug logs suggested there was anything untoward, except I would normally expect a bit more output from Jmol as it processes the PDB file. I’m sure it is something straightforward to fix…