November 2024 - ChimeraX-users - RBVI Mailing Lists

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