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Re: [chimerax-users] 2D plots and graphs for protein-ligand interactions
by Tom Goddard 13 Sep '22

13 Sep '22

So the chimerax-daily command is installed in a separate location from the production releases. So if you install both, you will have a /usr/bin/chimerax and a /usr/bin/chimerax-daily. The bug in the installation process was in the post-install script, so the command is already there. That particular bug has to with with integrating ChimeraX in the system menus and no effect on starting ChimeraX from a terminal. You might see a similar error when installing the next chimerax-daily -- that will not have that bug :-). -- Greg On 9/9/2022 10:41 AM, Tom Goddard wrote: > Greg Couch our Linux expert would have to answer that question. > > Tom > >> On Sep 9, 2022, at 1:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> P.S. Are there other possibilities to install chimera-daily in a distinct directory from the chimerax stable release not to overlap between the both ? >> >> Il giorno ven 9 set 2022 alle ore 10:07 Enrico Martinez <jmsstarlight(a)gmail.com <mailto:jmsstarlight@gmail.com>> ha scritto: >> Thank you Tom! >> Actually I faced the problem with the installation of the chimerax-daily on the ubuntu-20.04 >> (currently I am using the 1.4 version realized in june 2022). Here is the error of the installation: >> >> root@Perfetto-7920-Tower:/home/enrico/Downloads# dpkg -i ./chimerax-daily.deb >> (Reading database ... 322925 files and directories currently installed.) >> Preparing to unpack ./chimerax-daily.deb ... >> Deregister desktop menu and associated mime types >> Remove Python cache files >> Unpacking ucsf-chimerax-daily (2022.09.08ubuntu20.04) over (2022.09.08ubuntu20.04) ... >> Setting up ucsf-chimerax-daily (2022.09.08ubuntu20.04) ... >> Install desktop menu and associated mime types >> Traceback (most recent call last): >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py", line 724, in init >> run(sess, cmd) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38, in run >> results = command.run(text, log=log, return_json=return_json) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run >> result = ci.function(session, **kw_args) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/cmd.py", line 23, in linux_xdg_install >> install(session, verbose=verbose, system=system) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py", line 428, in install >> generate(session, info, system, verbose) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py", line 421, in generate >> from chimerax.core import localized_app_name >> ImportError: cannot import name 'localized_app_name' from 'chimerax.core' (/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__init__.py) >> dpkg: error processing package ucsf-chimerax-daily (--install): >> installed ucsf-chimerax-daily package post-installation script subprocess returned error exit status 70 >> Processing triggers for man-db (2.9.1-1) ... >> Errors were encountered while processing: >> ucsf-chimerax-daily >> >> >> Il giorno ven 9 set 2022 alle ore 00:07 Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> ha scritto: >> Hi Enrico, >> >> As Elaine says, ChimeraX isn't a plotting package, so it doesn't let you set colors, sizes, scales, ..., of plots. You could save the plot ChimeraX makes with Python, but I don't think it is very useful to do in an automated way because the aspect ratio of the plot will probably be poor and you cannot control it in a script. At any rate, for reference here is Python that would save the image >> >> from chimerax.core.commands import run >> plot = run(session, 'crosslinks histo #1.1') >> plot.save_plot('histogram.png') >> >> This will need a September 9, 2022 or newer daily build because I just made the "crosslinks histogram" command return the plot, before it did not return it. >> >> The figures in the paper were made interactively in ChimeraX on a high resolution display and just a screen capture was used to save an image. Although as Elaine notes the right-click context menu on those plot windows has a "Save Plot As..." menu entry that will save at 300 dots per inch resolution. >> >> Tom >> >> Example histogram of hydrogen bond lengths for pdb 7qfc saved with the context menu entry "Save Plot As..." >> >> <histogram.png> >> >>> On Sep 8, 2022, at 9:10 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> The main advantage of these plots inside ChimeraX is that they are interactive with the 3D structure (e.g. you click something on the plot, it does something in the 3D window). They weren't meant for making figures for hundreds of molecules in scripts. >>> >>> So, there are no options to customize plot appearance, and the only way to save the histogram currently is by interactively using the context menu on that window, as mentioned in the help: >>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram>> >>> >>> If you wanted to make your own plots with everything about the appearance customized, currently you would have to write python scripts to dump the data and then use your own favorite plotting program to generate images. >>> Best, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>>> On Sep 8, 2022, at 1:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> Thanks a lot, Elaine! >>>> Actually crosslink hist #1 works very well! >>>> Could you please specify would it be possible to plot the histogram >>>> (using batch chimera-x execution) or alternatively add it directly to >>>> the produced png image? >>>> I did not find any possibility to save the plot or to customize its >>>> appearance (color of the bars etc). >>>> Cheers >>>> Enrico >>>> >>>> Il giorno mer 7 set 2022 alle ore 17:52 Elaine Meng >>>> <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> ha scritto: >>>>> >>>>> Hello! >>>>> The chain contacts diagram shown in Fig 4b is made with the "interfaces" command. Then you can use context menu on that contacts diagram to make the interface-residue plot in Fig 4d. Please see the "interfaces" help for details on both of those. >>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>> >>>>> >>>>> The histogram plot in Fig 5b is made with the command "crosslinks histogram" but first you have to have some crosslinks, or other pseudobonds such as from finding H-bonds or contacts. Then in the "crosslinks histogram" command you specify the pseudobond model to plot their distances. See "crosslinks histogram" help: >>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram>> >>>>> >>>>> Also for a more detailed example see the "Interactive H-bond Histogram" feature highlight, which includes a script (.cxc file): >>>>> <https://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram <https://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram>> >>>>> >>>>> I hope this helps, >>>>> Elaine >>>>> ----- >>>>> Elaine C. Meng, Ph.D. >>>>> UCSF Chimera(X) team >>>>> Department of Pharmaceutical Chemistry >>>>> University of California, San Francisco >>>>> >>>>> >>>>>> On Sep 7, 2022, at 2:18 AM, Enrico Martinez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>>> >>>>>> Dear ChimeraX users! >>>>>> I am dealing with the analysis of protein-ligand interactions in a >>>>>> single PDB structure. I am looking for any tools implemented in >>>>>> Chimera-X, which could be used to analyse the interactions (besides >>>>>> the hbond and contact tools giving info in the log files). >>>>>> I wonder to know which commands and corresponded ChimeraX tools could >>>>>> be used to produce the 2D contact diagrams shown on the Fig.4 as well >>>>>> as python graphs demonstrated on the Fig.5 in the Chimera-X article: >>>>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/> >>>>>> >>>>>> Many thanks in advance! >>>>>> Cheers >>>>>> Enrico >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >>> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >

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Saving obj files
by Daniel VillanuevaAvalos 12 Sep '22

12 Sep '22

Hello, I am exporting molecules in the backbone view from chimera x as obj files, but only the points are saving and not the faces. When I import the file to another 3D software, only points show up. How can I save the faces too? Thank you, Daniel.

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Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)
by Tom Goddard 12 Sep '22

12 Sep '22

Hi Asmahan, Ok, probably you used ChimeraX 1.3 since 1.4 was not released in December 2021. So of course Model_1_multimer_pae.json goes with Model_1_multimer_unrelaxed.pdb. And Model_5_multimer_relaxed.pdb is the energy minimized version of Model_5_multimer_unrelaxed.pdb and in that older ChimeraX it only energy minimized the best scoring model so model 5 is the best scoring one. The best_model.pdb file is a copy of Model_5_multimer_relaxed.pdb. Tom > On Sep 12, 2022, at 1:07 PM, Asmahan Alghamdi <Asmahan.Alghamdi(a)nottingham.ac.uk> wrote: > > Hi Tom, > Thank you very much for your time and help. > > I used ChimeraX 1.4 December 2021 on my laptop. The type of files I have got are as follows: > > Best model file , then three files for each model except model 5 in this particular prediction > > Model_1_multimer_pae.json > Model_1_multimer score > Model_1_multimer_unrelaxed > > The same for model2,3,4 > > But 5 with extra file that is: model_5_relaxed > > After that, a list of sequence files > > Best regards > Asmahan > > Get Outlook for iOS <https://aka.ms/o0ukef> > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, September 12, 2022 8:03:22 PM > To: Asmahan Alghamdi <stxamalg(a)exmail.nottingham.ac.uk> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?) > > Hi Asmahan, > > I'm not sure how you ran your AlphaFold prediction. Currently ChimeraX AlphaFold predictions creates JSON PAE files that match the 5 predicted models > > af111_unrelaxed_rank_1_model_4.pdb > af111_unrelaxed_rank_1_model_4_scores.json > af111_unrelaxed_rank_2_model_5.pdb > af111_unrelaxed_rank_2_model_5_scores.json > af111_unrelaxed_rank_3_model_3.pdb > af111_unrelaxed_rank_3_model_3_scores.json > af111_unrelaxed_rank_4_model_2.pdb > af111_unrelaxed_rank_4_model_2_scores.json > af111_unrelaxed_rank_5_model_1.pdb > af111_unrelaxed_rank_5_model_1_scores.json > > The file names have both the scoring order (rank 1 best, rank 5 worst). If you ran AlphaFold on your local machine it might put out > > relaxed_model_1_multimer.pdb > relaxed_model_2_multimer.pdb > relaxed_model_3_multimer.pdb > relaxed_model_4_multimer.pdb > relaxed_model_5_multimer.pdb > result_model_1_multimer.pkl > result_model_2_multimer.pkl > result_model_3_multimer.pkl > result_model_4_multimer.pkl > result_model_5_multimer.pkl > > where the .pkl files contain the PAE data. These are not in score ranked order but you can find the score ranked order from another file AlphaFold writes > > ranking_debug.json > > There are other ways to run AlphaFold that give different output files. You'd have to show your list of output files to advise further. > > Tom > > >> On Sep 12, 2022, at 2:37 AM, Asmahan Alghamdi via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> >> Dear ChimeraX users support, >> Thanks for making AlphaFold such accessible and user friendly tool that has added a great deal to my protein-protein investigations. >> >> I have modelled a number of protein complexes a long while ago effortlessly. However, i need to get the PAE for the best model only, so I managed to know which model is the best because from file name but the pae.json file does not. >> >> Just I am wondering if there is a way to know which json file is associated with the best model? >> >> Thanks a lot. >> Asmahan >> >> Get Outlook for iOS <https://aka.ms/o0ukef> >> From: Asmahan Alghamdi <stxamalg(a)exmail.nottingham.ac.uk <mailto:stxamalg@exmail.nottingham.ac.uk>> >> Sent: Thursday, June 23, 2022 9:39:46 AM >> To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>; ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>; Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?) >> >> Thank you very much, I will try that and see how it goes. >> >> your help is much appreciated. >> Asmahan Alghamdi >> >> >> Get Outlook for iOS <https://aka.ms/o0ukef> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Thursday, June 23, 2022 12:52:50 AM >> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>; Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> >> Cc: Asmahan Alghamdi <stxamalg(a)exmail.nottingham.ac.uk <mailto:stxamalg@exmail.nottingham.ac.uk>> >> Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?) >> >> Hi Asmahan, >> >> I added an outputFile option to the "alphafold contacts" command so the pairs of close residues and their PAE value can be written to a file. This will be in tomorrow's ChimeraX daily build. >> >> alphafold contacts /B to /C output contact_pae.txt >> >> and the output_pae.txt file looks like >> >> /B:24 /C:30 4.30 >> /B:56 /C:9 9.84 >> /B:68 /C:32 1.48 >> ... >> >> with chain identifier and residue number for both residues and their PAE value. >> >> Elaine is right that the PAE values are in a file produced by AlphaFold. For ChimeraX AlphaFold predictions using Google Colab the file is JSON format (text) like >> >> ~/Downloads/ChimeraX/AlphaFold/prediction_20/best_model_pae.json >> >> If you run your own installation of AlphaFold with multimer or monomer_ptm presets the PAE data is in Python pkl format (binary) like >> >> alphafold_output/result_model_1_multimer_v2_pred_0.pkl >> >> Each of these files have a matrix of all residue by all residue PAE values. It is not too convenient to get the values for specific residues out of such a file unless you write some code. That is why I made ChimeraX do it for you. >> >> Tom >> >> > On Jun 22, 2022, at 1:43 PM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Dear Asmahan Alghamdi , >> > I am guessing you are talking about the AlphaFold PAE values. These are output by the AlphaFold calculation into a file. What you see as a plot using ChimeraX was already read from that file. So you don't need to export it, you just need to find the file that already exists. >> > >> > I am not sure where this file is stored, or whether it is in some "temp" location. We will get back to you on that. >> > >> > I should also clarify that a PAE value by itself is not a measure of how likely the residues are in contact. It is the predicted error in the relationship between the two residues in the Alphafold-predicted structure, where some pairs of residues are close together like a contact, but many more are far apart and not in contact. Although the "alphafold contacts" command does draw lines between residues that are close together based on a cutoff value, the presence of a line does not mean a contact is predicted with high confidence unless its coloring also shows a favorable PAE value. >> > >> > I hope this helps, >> > Elaine >> > ----- >> > Elaine C. Meng, Ph.D. >> > UCSF Chimera(X) team >> > Department of Pharmaceutical Chemistry >> > University of California, San Francisco >> > >> > >> >> On Jun 22, 2022, at 1:21 PM, Asmahan Alghamdi via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> >> >> Dear Chimerax team, >> >> >> >> Thanks a lot for the extremely useful software that has been helping a great deal in improving my protein complex investigations. >> >> >> >> Recently I succeeded in using version 1.5 to determine contacts and the correlated confidence but exporting that list of contact not clear to me yet although searched within software guide and tutorials available online. >> >> >> >> Your help would be much appreciated in this respect. >> >> >> >> Thanks in advance >> >> Asmahan Alghamdi >> >> The university of Nottingham >> > >> > >> > _______________________________________________ >> > ChimeraX-users mailing list >> > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> > Manage subscription: >> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >> > >> >> This message and any attachment are intended solely for the addressee >> and may contain confidential information. If you have received this >> message in error, please contact the sender and delete the email and >> attachment. >> >> Any views or opinions expressed by the author of this email do not >> necessarily reflect the views of the University of Nottingham. Email >> communications with the University of Nottingham may be monitored >> where permitted by law. >> >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > > This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please contact the sender and delete the email and > attachment. > > Any views or opinions expressed by the author of this email do not > necessarily reflect the views of the University of Nottingham. Email > communications with the University of Nottingham may be monitored > where permitted by law. > > >

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Export list of contacts
by Asmahan Alghamdi 12 Sep '22

12 Sep '22

Dear Chimerax team, Thanks a lot for the extremely useful software that has been helping a great deal in improving my protein complex investigations. Recently I succeeded in using version 1.5 to determine contacts and the correlated confidence but exporting that list of contact not clear to me yet although searched within software guide and tutorials available online. Your help would be much appreciated in this respect. Thanks in advance Asmahan Alghamdi The university of Nottingham Get Outlook for iOS<https://aka.ms/o0ukef> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

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inquiry about label the residues of pseudo bonds
by Jiaqiao Zhou 12 Sep '22

12 Sep '22

Dear Chimerax users, I am trying to analyze the results of AF2 predictions. I used the "alphafold contacts" command to the interfacing residues, then several pseudobonds are displayed. "label sel pseudobonds" shows the length of the bonds, but I want to show the residue name the number that makes the pseudobonds. Actually, I found that in the label mode of right mouse, it shows the residue name and the number. However, I have to do it one by one. So I am wondering if there are any easier ways. Another question is about the "alphafold contacts" command itself, I want to know the definition of "distance of residues". Is it the distance of the centroid, the average distance of heavy atoms of the residues. or some other ways of determining the distance between two residues? Thanks in advance.

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How to update the bonding status in a molecular trajectory?
by 洪冉 12 Sep '22

12 Sep '22

Dear ChimeraX developers and users, I tried to use ChimeraX to visualize my MD trajectory and I found some bonds were stretched very long and weird, see below In VMD, I could fix this phenomenon using updatebond features, could anybody tell me how to enable this feature in ChimeraX? Many thanks in advance. Ran hong hongran(a)ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000

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Failure in installing daily build version
by jq 10 Sep '22

10 Sep '22

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morphed model
by Krishnan Raman 09 Sep '22

09 Sep '22

How do we get the morph player after reopening the saved session with a prexisting morphed model ? thanks Krishnan Raman CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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2D plots and graphs for protein-ligand interactions
by Enrico Martinez 09 Sep '22

09 Sep '22

Dear ChimeraX users! I am dealing with the analysis of protein-ligand interactions in a single PDB structure. I am looking for any tools implemented in Chimera-X, which could be used to analyse the interactions (besides the hbond and contact tools giving info in the log files). I wonder to know which commands and corresponded ChimeraX tools could be used to produce the 2D contact diagrams shown on the Fig.4 as well as python graphs demonstrated on the Fig.5 in the Chimera-X article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/ Many thanks in advance! Cheers Enrico

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Create Complete Oligomers
by Samuel Kyobe 09 Sep '22

09 Sep '22

Dear ChimeraX We have a protein NLRX1 which functions as a trimer, however only the terminal component of this trimer has been experimentally resolved (3UN9) and in alpha fold the complete monomer of NLRX1 has been predicted (Q86UT6). Is it possible to build a complete trimer of NLRX1 starting with the partial X-ray resolved structure as a reference using ChimeraX and the alphafold model. We would like to use the complete structure for MD studies. Thank you Samuel

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