June 2023 - ChimeraX-users - RBVI Mailing Lists

Selecting segments overlapping atomic model
by kizziah4＠uab.edu 16 Jun '23

16 Jun '23

Is there some degree to which a segment must overlap an atomic model to be selected with "Over Sel. Atoms"? Can it be changed? I frequently use Segment Map to create custom masks for focused refinement and classification and for signal subtraction. I tend to use reference atomic models to expedite this process, but I am having problems selecting segments overlapping atomic models (compared to older versions of Chimera). I am on Windows 10 with ChimeraX version 1.5 (2022-11-24). I have experienced the same on Ubuntu-20.04 with ChimeraX v1.6.1. For example, I have an unsharpened map estimated at 4.8A resolution from RELION and an atomic model of the same structure downloadeded (via ChimeraX) from the PDB. After deleting some unneeded chains and duplicating others, fitting the model into the map using simulated density (4.8A resolution, 0.77 correlation), segmenting the map at a low threshold that covers all (but a couple of loops) of the atomic model, ungrouping the segments once for granularity, selecting the entire atomic model, and clicking "Over Sel. Atoms", no segments are selected. If I try repeating the process with the backbone only (0.80 correlation), no segments are selected. I have succeeded in some cases by ungrouping all segments ~4 times, but in this particular case it only selects a few segments corresponding to parts of some alpha helices.

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Question about MatchMaker with nucleic acids
by Leonardo BETANCURT ANZOLA 14 Jun '23

14 Jun '23

Hello, I’m currently using ChimeraX to compare different DNA binding proteins and would like to align them using match maker and the DNA helix. The problem is that the structures do not have the same DNA sequence and that is the parameter the MM uses to align. Would it be possible to align DNA using only the phosphate-sugar backbone of the molecule? In that case I’d like to tell chimera which phosphates should one aligned to which. Thank you, Leo B.

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Isolde installation in chimeraX
by Chiara Rapisarda 14 Jun '23

14 Jun '23

Hi, I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara

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Missing or invalid "sequence" argument: Sequences argument
by Adetoun Adeniji-Adele 14 Jun '23

14 Jun '23

Hello, I was trying to use the AlphaFold predict function earlier and received the following error. Missing or invalid "sequence" argument: Sequences argument "MNGIDIAVVTDDPAILKSVHERYPDGSKHSIELEHGHNVHIFVRTATLVLSSYIRDNEAIAVLGYSNVHESSMRAILESSPGVAHMNSALGQLIGAQWVVAIRKGAVRIQGTVSGLSRVYWSKRGSRFVASNRSRELARLLGSELDPTQVAFRTIHPMQHPFTSSSCWKDLEGVLPGEYLEVTGRSSPRTERWWTPATSYRSLEDGANETAAALFSVVRNQLSDHSAASCDISGGLDSSSIAAIAANAAKSGETHTVLHGTTSVSRDEFNSDADWAIELSKSLKLDSHSFLSWNDMPKEYDDLDALASYDLDEPSIASISHSRFTHLINVARSKGSQVHLTGFGGDELFIGSPTFCVDLFKTQPLLSARLLLTYRAMYRWTFRSLVRPLTTPMSYQQWMRTKSLSTDRSTLRIPPLSWGFHGVIPPWITRDARHSMYDHVRSASSATFPLAPTPGRHFELENLYQCARLFRTMSDIVSQTSGVLLVAPMLEQAVVEAAISVRTPERLTPHKYKPVLTHATRGLLPAVVAERQTKGGEDTDAAIGFSENISAIRELWDESRLASLGIVDGDYLSNALRRPDSAEFDDCAIAKTLATELWLRSLEK,MPVVGAMAIPSKTRISATERLRLASALSLGKALSHLPPGLLRRSMTAFAAKARPASYREAEAAVVSITQYSKASAGPGSCLQRSISVCILMRLDGRWPTWCVGVPSKPPFRAHAWIEAGGQIVAELGDMNSYSRLMTISTHAERTE" is not a chain specifier, alignment id, UniProt id, or sequence characters I am not sure what the message means and can't seem to find others who have had similar error messages. Any help would be appreciated. Best, Adetoun

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No chains in AtomicStructure
by Dominik Sordyl 13 Jun '23

13 Jun '23

Hi, I have created a python plugin that uses AtomicStructure() class to create a model based on the pdb file and custom trajectory file. The problem is that after creating the structure (adding residues and atoms) it has no chains. Due to this issue, I cannot use some of the ChimeraX features (e.g. rainbow coloring) - at least I think this is the reason. While adding new residues one has to specify the chain_id, but even if I do it those chains are not created automatically. Do I have to create chains separately or there is something that I am missing here. Would be grateful for your help. Best, Dominik

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How to play volume series in chimeraX?
by Rayees Mattoo 12 Jun '23

12 Jun '23

Hi, I want to play a volume series in chimeraX. There is an option "volume series" in chimera but could not find the equivalent option in chimeraX. Also, is it possible to 'movie record' the volume series while it is playing? Any suggestion would be helpful. Best

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Triangle attention for alphaFold2
by Cheng Fei Phung 10 Jun '23

10 Jun '23

Hi, This might not be directly related to use of ChimeraX gui software that this mailing list is targeted for. Might I ask if anyone have any suggestions for the use of triangle attention module in https://twitter.com/salmon_shitake/status/1663176260632346624 ? Regards, Phung Cheng Fei feiphung(a)hotmail.com

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sym command
by postmaster＠cgl.ucsf.edu 09 Jun '23

09 Jun '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: sym command Date: June 9, 2023 at 11:55:38 AM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Dear All, I am trying to generate symmetric copies of the atomic structure in a filament map and I get the following error sym #1 group c6*h,39.1,19.3,7,-1 coord #2 (atomic structure is #1 and the map is #2) error - Expected a keyword What is incorrect in the command. Stay safe & Regards Anindito Sen. Ph.D <> Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

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ChimeraX not able to install for ubuntu22
by himanshi singh 07 Jun '23

07 Jun '23

Greetings! Kindly find the attached screenshot for installing in ubuntu22, it says dependencies unmet. Kindly guide me. Thankyou Regards Himanshi PhD candidate IIT Kanpur India

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ChimeraX .cxs session file
by Moustafa, Ibrahim M. 06 Jun '23

06 Jun '23

Dear ChimeraX, I have a ChimeraX session .cxs file that was created a while ago. I wonder if there is a way to open the file to see the actual commands, parameters used in that session. Is there is tool/way to read .cxs file? Thank you for your help. Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927

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