- ChimeraX-users - RBVI Mailing Lists

protein void volume or enclosed space
by Vitali James 21 Nov '24

21 Nov '24

Dear Chimera support, Is it possible to calculate the enclosed space, channel volume or void space with the x-ray structure in chimera or chimera x. best, James

3 4

help browser and embedded pdf's
by John Monroe Heumann 21 Nov '24

21 Nov '24

Hi, Am I correct that ChimeraX help browser currently can not automatically open links to pdf's (requiring you to download the file instead)? If so, would this be a reasonable enhancement request or do the pdf reader licensing requirements make it impractical? Thanks! -jh-

3 5

ChimeraX on a tablet ?
by GOVAERTS Cédric 20 Nov '24

20 Nov '24

Hi ChimeraX team I wanted to know if ChimeraX can run on a tablet, either Ipad (M2 or M4 chips) of a Windows tablet (either Intel or Qualcomm Snapdragon) ? Obviously not for using it as main workstation, but rather check structural features while on the move. Thanks Cedric - Prof. Cedric Govaerts, Ph.D. Biochemistry & Structural Biology Universite Libre de Bruxelles - Campus Plaine. Building BC, Room 1C4 203 - Phone :+32 2 650 53 77 Boulevard du Triomphe, Acces 2 1050 Brussels - Belgium

3 6

Adding a Covalently Bound PLP to an AlphaFold Model
by Omar De Bei 20 Nov '24

20 Nov '24

Dear ChimeraX Community, I’m reaching out for advice on what is likely a simple issue, but I’m stuck and would greatly appreciate your input. I’m currently working on a PLP-dependent enzyme and have generated its structure using AlphaFold3. Unfortunately, AlphaFold3 does not include PLP as a preset ligand. To address this, I’m attempting to manually add the PLP to the predicted structure based on homology with other PLP-dependent enzymes. Here’s where I’m facing trouble: The PLP forms a covalent bond with a lysine residue in the active site. After aligning my AlphaFold-predicted structure with the PDB structure of a homologous enzyme, I managed to position the PLP within the predicted structure. However, the lysine residue is not in the correct orientation to form the covalent bond. I’ve tried changing the lysine’s rotamer to improve the position, but it’s still not quite right. I was considering performing a local minimization of the structure to refine the geometry, but I’m unsure how to do this in ChimeraX. Does ChimeraX offer a tool or feature for local minimization that could help in this scenario? If so, could you guide me on how to proceed? Thank you in advance for your help! Best regards, Omar

2 1

Bundle Sample Code
by Lou Holland 19 Nov '24

19 Nov '24

Hello, I work with Jon Agirre at the University of York and am about to start work on developing a privateer bundle for ChimeraX for glycan validation. I have been working through some of the very helpful tutorials and was planning to work through this page as I started building the bundle: https://www.rbvi.ucsf.edu/chimerax/docs/devel/writing_bundles.html I tried to download the sample code ( https://www.cgl.ucsf.edu/chimerax/cgi-bin/bundle_sample.zip) linked in the "Bundle Sample Code" section so that I could use it as a starting point to edit for the privateer bundle, but it seems that the sample code is not currently available. Is this something that you can help with? Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

2 2

Question about commercial license for ChimeraX
by Gleb NOVIKOV 18 Nov '24

18 Nov '24

Dear ChimeraX Development Team, I hope this message finds you well. I am writing as an enthusiastic user of your remarkable software, which has been instrumental in both my academic and educational pursuits. Recently, I was approached by a small company interested in commissioning visualizations as part of a collaborative effort. I would like to inquire whether you offer a specific commercial license suitable for such freelance engagements. Additionally, I would be delighted to contribute to your website by sharing some of my visualizations of molecular systems, should this be of interest to your team. Thank you very much for your time and consideration. I look forward to your response. Best regards, Gleb

2 4

Question the lattest ChimeraX-1.9
by Enrico Martinez 18 Nov '24

18 Nov '24

Dear ChimeraX users! I am testing the new ChimeraX 1.9 release, via creating a short movie demonstrating an X-ray structure with basic features (without molecular dynamics). I noticed that my computer (using an Apple Silicon chip) gets quite hot during the frame rendering process (prior to encoding). In the previous release (1.8), the resource usage didn't seem as intense. Have there been any changes or optimizations in the new version that could explain this increased resource demand? Thank you in advance! Enrico

2 1

Fuzzy colour boundaries in protein cartoon
by James Lingford 18 Nov '24

18 Nov '24

Dear ChimeraX team and users, Is there a way to set colours of individual atoms to have a fuzzy boundary with the surrounding cartoon colour? Example picture attached. Normally, colouring individual atoms will create a solid line between one colour and the next. But is there a setting to change this? Many thanks

2 1

Modelling of missed loop fragments in multi-chain structure
by Enrico Martinez 18 Nov '24

18 Nov '24

Dear Chimera-X users! I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit: open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard which very slowly produces 5 models of the chain A. The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ? Many thanks in advance Enrico

3 15

adding a hydrogen to side chain of Glu
by Chang Jang 15 Nov '24

15 Nov '24

Hi ChimeraX users, I am building a customer peptide containing Glu, Ala, Lys using Build Structure. Once I built it, I added hydrogens. But, one oxygen in the side chains of Glu does not have a hydrogen added. How would I fix the structure? Thanks, Chang

2 2

2 different clipping planes, 1 per model?
by Vincent CHAPTAL 15 Nov '24

15 Nov '24

Hi, I wonder if it is possible to have 2 different clipping planes, 1 per model? It would be nice to show an helix as a surface within a domain like this. Thanks Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

2 1

the artifacts of the PBC of the MD trajectory
by Enrico Martinez 14 Nov '24

14 Nov '24

Dear Chimera-X users ! I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)? Many thanks in advance Enrico

4 10

AlphaFold 3 source code released today
by Tom Goddard 11 Nov '24

11 Nov '24

AlphaFold 3 source code was released today AI protein-prediction tool AlphaFold3 is now open source <https://www.nature.com/articles/d41586-024-03708-4> https://github.com/google-deepmind/alphafold3 It is for non-commercial use only, and they require you to submit a form and get approved (2-3 days) to get the parameters. Tom

1 0

color bfactor by alphafold palette
by Agnieszka Obarska 11 Nov '24

11 Nov '24

Hi, I’ve just would like to let you know that we’ve noticed recently that alphafold palette in ChimeraX is not consistent with original AlphaFold coloring. Please see the slide attached. On the left there is a model colored by the “color bfactor pal alpha” command in ChimeraX while on the right there is the same model colored according to AlphaFold coloring scheme. Best, Agnieszka

5 16

New user -have queries
by karan kohli 11 Nov '24

11 Nov '24

Hi, Thank you for developing Chimera X, a tool that can help novices like myself to make in silico predictions. I am new to the world of silico protein interaction prediction. I am looking to use Chimera X to predict interaction between the antibody clones our company generated and the target protein. This should be doable with Chimera X right. I I am not sure how to do it. I am trying to follow the below video., But I am struggling to enter my ab sequence as it contains two chains (heavy and light). https://www.youtube.com/watch?v=TMcjEecFHaI I would really appreciate some help. Thank you, Karan

2 1

isolde write phenixRsrInput – how to restrain ligands?
by Shahid, Taha (Dr.) 08 Nov '24

08 Nov '24

Hi Tristan, I am trying to phenix real-space refine a structure containing AMPPNP, which I have modelled very accurately with ISOLDE. I create inputs using the isolde write phenixRsrInput command, including the restrainPositions true and includeHydrogens true arguments (which normally works perfectly). However, in this case, the Rsr output yields AMPPNPs with bond-length RMSZs > 2, although this is not the case in the input model itself. Would you be able to advise as to how I can potentially restrain the AMPPNP heavy atoms from the ISOLDE model as well? I am not a phenix expert, so not having to create these manually would be ideal. Perhaps a phenix command that will automatically generate an appropriate restraints file (to append to the isolde write phenixRsrInput command or phenix.real_space_refine itself), and/or lines that may be added to the real_space_refine.eff file created by ISOLDE? Any help would be immensely appreciated. Best regards, Taha

3 3

Re: [Chimera-users] Write out SeqRes entry
by Eric Pettersen 07 Nov '24

07 Nov '24

Hi David, For PDB output, ChimeraX should output SEQRES records for each chain as long as either: (A) the chain had sequence information in the original input file (e.g. SEQRES records), or (B) the chain has no missing-structure pseudobonds. I not the author of the mmCIF I/O part of ChimeraX, but I believe the criteria is different in that the chain has to have its "full_sequence_known" attribute set to true. You can do this "by hand" with the command (assuming your structure is model #1) "setattr #1 chains full_sequence_known true". --Eric Eric Pettersen UCSF Computer Graphics Lab P.S. There are different lists for Chimera vs. ChimeraX questions. I have cc'ed the ChimeraX list on this. > On Nov 6, 2024, at 10:54 AM, David Bhella via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera/ChimeraX team, > > I have a model for an asymmetric unit of a virus capsid that has three chains of the same capsid protein – but I am having trouble depositing my model in the PDB because it only has a seqres entry for one of the three chains (B). Whatever I do, chimeraX will only write entries for that chain. Is there a way to force chimeraX (or any other program) to write the seqres card for each chain correctly? > > Thanks > D > > David Bhella > Professor of Structural Virology > Director, Scottish Centre for Macromolecular Imaging > Associate Director, MRC - University of Glasgow Centre for Virus Research > +44 (0)141 330 3685 <tel:+441413303685> > > > > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

3 2

Command to measure the Atomic to Map fit quality
by Roden Deng Luo 06 Nov '24

06 Nov '24

Hi ChimeraX Team, I wonder if there is a command that can measure the fit quality of an atomic structure to a volume map. I imagine the metric could be the sum of the density of all atoms or a correlation. Something like: fit_quality #ModelID in #VolumeID (similar to: rmsd #1 to #2). Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

4 6

Error saving a chimeraX session for large MD trajectory
by Enrico Martinez 06 Nov '24

06 Nov '24

Dear ChimeraX users! Dealing with the session contained loaded md trajectory of 10000 snapshots for a quite big system I got the following error trying to save this session File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101, in provider_save saver_info.save(session, path, **provider_kw) File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 922, in save session.save(output, version=version, include_maps=include_maps) File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 651, in save fserialize(stream, data) File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 76, in msgpack_serialize stream.write(packer.pack(obj)) ^^^^^^^^^^^^^^^^ File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack File "<stringsource>", line 69, in cfunc.to_py.__Pyx_CFunc_8chimerax_4core_10_serialize_object__lParenobject__rParen_to_py_3obj.wrap File "src/_serialize.pyx", line 253, in chimerax.core._serialize._encode_ext File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack File "<stringsource>", line 69, in cfunc.to_py.__Pyx_CFunc_8chimerax_4core_10_serialize_object__lParenobject__rParen_to_py_3obj.wrap File "src/_serialize.pyx", line 226, in chimerax.core._serialize._encode_ext File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack ValueError: bytes object is too large ValueError: bytes object is too large File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack *See log for complete Python traceback.* Would it be possible to reduce the number of frames loaded as coordset e.g. closing the last 6000 frames ? Many thanks in advance! Enrico

2 4

Generating quantitative values for electrostatic potential and molecular lipophilicity potential
by mishra.ananya.163＠gmail.com 06 Nov '24

06 Nov '24

Dear Sir/Madam, I hope this message finds you well. My name is Ananya, and I am an undergraduate student working on a project analysing protein structures. I am currently exploring the tools available in ChimeraX to measure structural parameters of protein models. I find the visualization features for surface electrostatic potential and molecular lipophilicity potential especially valuable for my research, as they provide essential insights for my analyses. However, I have encountered some difficulty in locating a way to export quantitative values for these surface properties. Could you please advise if there is a method within ChimeraX to generate and export these values? Thank you for your time and I would greatly appreciate any guidance you could offer. Hope you have a great day ahead! Best regards, Ananya

3 8

integration of US-align into ChimeraX
by Chengxin Zhang 06 Nov '24

06 Nov '24

Dear ChimeraX developer. I am the developer of the US-align tool for protein and nucleic acid structure alignment. We currently offer a command line tool and a plugin for PyMOL. We are asked by the community to make a ChimeraX plugin. I have used ChimeraX for cryo-EM structure analysis before and know that there is a related tool called matchmaker. However, I do not know where to start to implement a matchmaker-like plugin for US-align in ChimeraX. Can you give me some recommendations and/or point me to a developer I can work with? Thanks. Chengxin Zhang, PhD Research Assistant Professor Department of Computational Medicine & Bioinformatics University of Michigan, Ann Arbor, MI

2 1

Variables and conditional statements in the command line
by Roden Deng Luo 05 Nov '24

05 Nov '24

Hello again, Are variables and conditional statements possible in the command line in any way? Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

Troubleshooting the match function
by Christman, Nick 04 Nov '24

04 Nov '24

Hello, My name is Nick Christman and I am a microbiology PhD student at Indiana University. I am using ChimeraX to visualize and compare some small proteins (minor pilins) and it has been working great. I have run into an issue that I am hoping you can help me resolve. I want to use the match function to compare various different minor pilins. Each minor pilin has a somewhat unique structure, and I am trying to make the case that certain minor pilins from one organism are homologous to other minor pilins from a different organism. I have noticed that the match function provides different results from session to session. This concerns me and makes me question how much I can trust the results provided by chimeraX. Along with different spatial matching, the calculated RMSD values differ greatly. Is there a way I can make these matches more consistent? Like dictating a set starting point for matching? Thanks for your time! Nick Christman (He/Him) Dalia Lab Indiana University

2 1

setzoom command in Chimera X
by Vitali James 04 Nov '24

04 Nov '24

Dear Chimera support, There was a some old code to set the zoom in the chimera. I would like to set the same frame size of different models and different views in chimerax. How it can be done in chimeraX. best, James

2 1

Tool docking
by Eric Pettersen 01 Nov '24

01 Nov '24

Hi all, Starting with tomorrow’s daily build (but not the 1.9 release candidate or [eventual] production release), most tools can no longer be docked into the top or bottom areas of the main window, just the sides. This should prevent a lot of accidental grief from accidentally docking a tool into the toolbar area. This policy can be overridden by the tools themselves if typical use of that tool might involve docking into the top or bottom areas. Initially, two tools override the policy: the sequence viewer can be docked anywhere (since you might want it as wide as possible), and the tool created by the buttonpanel command can be docked into the top area, so that it can be placed next to the toolbar. If there are other tools that can really benefit from being docked into the top or bottom areas, please let me know. --Eric Eric Pettersen UCSF Computer Graphics Lab

2 2