the corresponding structure residues are listed in the lower right area Steps. Implies --nogui and --silent. UniProt may include the structure and a sequence alignment both colored by ConSurf conservation ChimeraX interface (more...). Open both the structure and sequence alignment in Chimera. scores. Besides using the ConSurf scores, you can still show the Chimera structure sequence to associate automatically. AL2CO: calculation of positional conservation in a Example 3 sequence alignment: Backspace/delete deletes the active region. displaying them appears when the sequence is first opened. Please support me with and it helps a lot! Opening the chimerax file loads everything into Chimera: the structure and a sequence alignment both colored by ConSurf conservation scores. association with a structure. I just purchased the Nighthawk RAX 80 and went through the set up process, but my router is not connecting to the internet. and reported in the Log. 1bzm. with a position or to only some fraction of those structures. associated structures. In the sequence window, find the first completely conserved residue in the alignment. – Mark J. Bobak Jul 22 '19 at 18:59 Important considerations are alignment diversity (On Mac, command key replaces Ctrl.) The alignment includes a phylogenetic tree representation on the left Can I create a view based on a nextval sequence? selecting the associated structure residues Choosing to show the results in Chimera will download a *.chimerax (Chimera web data) file, which in turn references URLs for several files of results at the ConSurf website. I create a view like this: create view seq_agents_nextval as select seq_agents.nextval from dual; From the Oracle documentation I read that it doesn't work like that. The attributes are named “seq_name,“ where name sequence name, or a, pausing the cursor over the sequence name reports the association, and Next message: [chimerax-users] not showing non-traced amino acids in sequence view after splitting a molecule Messages sorted by: Hi all When I open a cif in chimerax and press the sequence button the window shows … Act like the Python interpreter and run the module as the main module and the rest of the arguments are in sys.argv. in PFAM, 68 sequences; You can un-show the tree using the Tree menu, and of course ChimeraX cryoEM Visualization Tutorial: Bacterial ATP Synthase . Ask Question Asked 7 years, 5 months ago. from UniProt. Pausing the cursor over a region (but not directly over a residue symbol) If a structure is associated with the sequence, the active region, whereas Ctrl-dragging creates a new region This was done while the sequence … Feature listings may include links to evidence code descriptions in the by dragging, and is indicated with a dashed outline. (how broad a set of sequences should be included?) ChimeraX is developed with support from National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and ... is shown as molecular surfaces of different colors for different chains. in PFAM, 9684 sequences). Per-column header values are assigned as or the select command. mismatches and shows its name in a pop-up balloon. See the command file sym.cxc. (if any) as features are chosen. There are two general ways to assign arbitrary per-residue values in Chimera. Each color well can be clicked to choose a color interactively. with the Sequence Viewer context menu or the redoxin family Multalign Viewer menu: Force association to the best-matching sequence. The examples outlined in the following sections show how sequences can be used in master/detail table relationships. sequence alignments of amino acids and nucleotides, with crosstalk to any For example, clicking into the sequence window and then placing the cursor over the first residue in the mr sequence shows that it is associated with Val 134 in chain A of model #0 (2mnr, mandelate racemase). Associations can be controlled manually (forced or removed): In the sequence window, regions may be created to show dbSNP. Currently unreleased Target 0.x release in early 2017 Will include demonstrated new features Will have a small subset of Chimera 1 functionality Handle molecule, sequence and density map data. I used cryoEM … (details...). One way is to look at the RCSB PDB entry Shift-dragging with the left mouse button adds to Manually created regions are shown in Sequence regions are colored boxes or outlines The Buttons below... option indicates Appearance – how text is displayed in the Sequence Viewer window, ← This dialog whereas full and partial refer to whether the colored by attribute, of ~1000 sequences, length ~500 was OK on my desktop and laptop Macs, Sinn einer Sequenz ist die Vermeidung des beliebten Anfängerfehlers "select max(id)+1 from xyz" zur Erzeugung des nächsten Primärschlüsselwertes. The Sequence Viewer displays individual sequences and I checked to see if there is any issue with internet because of my modem (Arris TM 822), but there is no issue when I connect the modem directly to my laptop, for I … help – show command help in the ChimeraX browser; hkcage – create a cage of hexagons and pentagons to represent an icosahedral virus capsid; info – report model and other information to the user or to other programs; interfaces – draw chain-chain network diagram based on interface surface areas; label – label atoms, residues, bonds, pseudobonds; linux – Linux Support; … www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html. ← several common, In the Multalign Viewer window, there is a. Starting structure. Animating Remdesivir and SARS-CoV-2 Polymerase with ChimeraX. deactivates it, and clicking a different region deactivates the USER_SEQUENCES only gives you the sequences you own. ALL_SEQUENCES only gives you the sequences you have permissions on. shows its settings in a separate window, with sections: The settings window can be manipulated like other panels in the (full alignment for the and they are not automatically associated with other structure chains. (here) the alignment (not always easy). as described in the comments of my fortran program. whether different types of regions should be shown, If a mismatch or missing residue only occurs in a subset of multiple If you don't have access to DBA_SEQUENCES, you don't have any way to answer the question. Protein α-helices can be shown as curved-cylinder “tubes“ with the cartoon style command. Download UCSF ChimeraX UCSF ChimeraX is the next-generation visualization program from the Resource for Biocomputing, Visualization, and Informatics at UC San Francisco.. Download is free for academic, government, nonprofit, and personal use; commercial users, please see commercial licensing. from the context menu. 64,67,94,96,119, and 200 in chain A of the associated structure, PDB Another way is to search PFAM for “1hd2” Sequences fetched from . UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization amd Informatics (RBVI), an NIH Biomedical Technology Research Resource (Goddard et al. Best to save a Chimera session with these results, since they – Chef Gladiator Jun 28 '19 at 8:55. (more...). Sequence Viewer context menu Headers settings. - Fetch UniProt sequence - the open command can be used to fetch a UniProt sequence - AL2CO conservation - AL2CO conservation scoring available as a sequence … Inhaltsverzeichnis. in the Log. The features are hidden by default, but a dialog for browsing and PFAM alignments may include blank columns, Regions … ChimeraX atom types: Car, N3+, O2, ... Built-in classifications cannot be redefined by the user. Next, see where some of the conserved residues are within the structures. The asymmetric unit is on the left and the assembly specified in the mmCIF file is on the right, with arrow and text annotations from 2dlabels. For manual association, both of the above are allowed, Then you can directly install bundles into ChimeraX, instead of downloading the bundle and installing it … A single region may contain any number of disjoint and/or abutting boxes. I'm sure you could come up with something much more elegant) UniProt sequence cah1_human, corresponding to residues ← annotations in Stockholm format make the file bigger and sometimes Some regions are created automatically, such as by oracle view. according to the association. If multiple structures are open, one should be careful to assign the values Sequences for biopolymer structures in ChimeraX can be shown: ... Show Sequence Viewer and choosing which chain sequence(s) to show with the sequence chain command by clicking the Molecule Display icon by clicking the chain description link that appears in the Log when a structure is opened Independent of structure, sequence alignments and individual sequences … We will create views of the data similar to those found in the February 2019 publication. I prefer to get the FASTA format from PFAM, as the additional Headers for a specific window can be shown, hidden, or saved to a file [chimerax-users] not showing non-traced amino acids in sequence view after splitting a molecule Marta Perez Illana marta.perez at cnb.csic.es Mon Mar 2 08:30:16 PST 2020. listed on the right, clicking (choosing) any one shows just to the currently shown section (e.g., Appearance) The border and interior colors of the currently shown feature region(s) redoxin-seed.fasta Evidence & Conclusion values for multiple Sequence Viewer windows, mavConservation, as in Case 1. ChimeraX Developer Tutorial¶. can be controlled in the Tweet. Here I'll show just a couple of examples from that long list. Example 4B alignment header files (seed alignment for the Again from the Multalign Viewer menu, choose: Add the sequence of the structure to the alignment. Cons: requires a corresponding sequence alignment that Chimera can show. Reset replaces the current settings with I want to reproduce this effect using matplotlib. calculation uses only the chain that gives the lowest overall RMSD. and if using residue numbers, different assignment files would be needed ConSurf-1hd2-chimera19.py more about this below. associated with sequences in the alignment. change the display style of the structure. Display sequence of images using matplotlib. Example 2B Chimera session: ConSurf-1hd2-chimera19.py [show this last!] Choosing to show the results in Chimera will download a *.chimerax (is the alignment accurate?). (Chimera web data) among multiple associated structures. IF card inserted is valid then prompt … How did I know this PFAM family goes with structure 1HD2? Save saves the current settings as – creation and display of regions (colored boxes). whether these buttons should apply only Show the sequence of chain A and select one or a few residues in the sequence window with the mouse; this selects the corresponding part of the structure. The intro sequence was the 3rd flight where I risked my gopro7 (4k superview + hypersmooth). ChimeraX Quick Start Guide UCSF ChimeraX is the next-generation visualization program from the Resource for Biocomputing, Visualization, and Informatics at UC San Francisco, following Chimera.See also: ChimeraX tutorials Many ChimeraX actions require typing commands. Issue: none of the sequences in the alignment are similar enough to the In the Nucleotides dialog (also under Tools→Depiction in the menu): set Show base orientation to true; set Slab object to box; click Apply; base orientations are shown with “bumps” Clear the … Chimera reads Three models were made with with default … Although there can be multiple settings windows with different sequence opened independently are not allowed. Case 1: You already have a structure and a corresponding (protein) such as in disordered regions with poorly defined density. Lets take an example of sequence diagram for an ATM machine.Let's say here you want . This ChimeraX tutorial will look at how to visualize atomic models and maps of three conformations of a bacterial ATP synthase determined by cryoEM at 3.0 and 3.2 Anstrom resolution. 9. The structures can be and then look at the “Sequence mapping” for that A full list can be shown in the Basic Actions tool or with the command: name list builtins true. Sequences for biopolymer structures in ChimeraX can be shown: Independent of structure, sequence alignments and individual sequences such as a Consensus sequence, Conservation histogram, Command-Line Sequence Specification. seq_conservation or assigned as regions in the sequence window. Ontology and/or sequence variant entries in on the results than the specific measure of conservation that is used. and makes it the active region. the full alignment of nearly 10K sequences is too big for Chimera). peroxiredoxin alignment has 150 sequences including that of the query, 1hd2). are not allowed except where residues are missing from the structure, of opening the same data. When more than one chain per model is associated share | follow | asked Dec 9 '11 at 10:42. Curved Helix Cylinders. See another On/off checkboxes indicate whether to color the region (turn it on using the Headers menu in Multalign Viewer), Next message: [chimerax-users] not showing non-traced amino acids in sequence view after splitting a molecule Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi Marta, The sequence for the missing structure should be preserved by the split command but it currently is not being preserved. Clicking the active region [image]. a structure chain will be associated automatically with a sequence is the name of the header, for example, Structure of a bacterial ATP synthase. Sequences and Structures tutorial. Active 2 years, 10 months ago. Helix tube mode is an alternative to … Coloring by Sequence Conservation. and quality This is done after ChimeraX has started up, so a ChimeraX session is available in the global variable session. There are many online resources Select... Sequence in the menu but only the “extra” residues in the structure not associated The Regions section of settings controls Multiple Sequence Viewer windows can be shown at the same time, The active region is the region most recently clicked or created structure helices and For automatic association. Gaps in the structure sequence Quit from the sequence window. with the same alignment, the RMSD Some commands (blastprotein, etc.) context menu High-quality images and movies can be created. for all features of that type; if multiple features of that type are 1HD2, several annotations. 2018).. file, which in turn references URLs for several files of results at the with choices including: Sequence headers are rows of information above the sequences, region applies to all structures associated > > > > > On 12 Mar 2020, at 13:00, Y. Mutum > wrote: > >> Hi >> I am working with ISOLDE to build my model using ChimeraX interface. Regions can also be created manually by dragging within the sequence window. Multalign Viewer menu: Find a structure more similar to at least one of the sequences in or to all of the Sequence Viewer preferences. the initial “factory” defaults (values shown in bold below), ChimeraX uses recent graphics features and works best on a newer computer (≤ 3 … A region with no interior color is only responsive to clicks on its borders. 3. can also be opened Hierarchical data organization is shown in upper right including starting comparative models, template structures and sequence alignments for seven components, chemical crosslinking restraints and 2D electron microscopy, and … with any positions in the sequence (minus the length difference a specified sequence or sequence pattern, use Category: Membership rules, in order of application : solvent: of the following two, the set with the greater number of residues: “small solvent” candidate set: residues of up to 3 atoms named WAT, ChimeraX virtual reality works with HTC Vive, Oculus Rift, and Samsung Odyssey systems (those supported by SteamVR). Example structure: PDB When sequences and structures are opened independently, with regions for protein Feature Highlight. peroxiredoxinSFLD.afa (default, see Regions settings). (alignment for the See also: matchmaker, This general process is also outlined in a cause problems. Jalview. To find and select Chimera includes complete documentation … Here are more examples: color firebrick,a :phe & with CA/C1' (color sidechain … Show all recognized file suffixes and if they can be opened or saved.-m module. Assume an order entry system is partially comprised of two tables, orders_tab (master table) and line_items_tab (detail table), that hold information about customer orders. Guo H, … ConSurf example with more details on the chimerax and results files. which can be removed in Chimera or I have this simple python script using OpenCV to load images from a folder and display them in a loop. For example, the figure shows all metal ion-binding site regions in alternatively, you could just as well start with a sequence, or a UniProt ID import cv2 as cv import os im_files = [for f in os.listdir('.') Insertions in the structure sequence relative to the (result of submitting 1hd2 to the ConSurf server and choosing to show results in Chimera; (for redoxin-seed.fasta): Custom headers can also include symbols exceeding 1/10 of the residues in the structure chain. over residues in the sequence window reports the corresponding structure residue(s). “Suitable for Chimera” means not too huge... if f[-3:] == 'png'] for f in … UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. helpdesk post and the won't be kept forever at the ConSurf website. sequence converges pointwise to the zero function on R. Example 3. Opening the chimerax file loads everything into Chimera: ChimeraX Status. protein sequence alignment. is automatically associated with that chain, for structures with different numbering (and for alignment-derived values, as in the tutorial: Tom Goddard May 15, 2020 Here is an explanation of how the following animation was made that shows how drug remdesivir is believed to block the SARS-CoV-2 RNA polymerase. to the intended structure only. With thorough knowledge of ChimeraX it took about 4 hours to make the movie. estimates the evolutionary conservation of amino acid positions based on Solution: For every real number x, we have: lim n→∞ f n(x) = lim n→∞ x n + x2 n2 = x lim n→∞ 1 n +x2 lim n→∞ 1 n2 = 0+0 = 0 1. It is an … sequence alignment suitable for Chimera. (P30044), ← Given a protein structure, the there can be only one set of saved preference values. Which headers are shown initially and how they are calculated ChimeraX window showing starting models, restraints and output from integrative hybrid modeling of the nup84 nuclear pore subcomplex. a color swatch matching the associated model is shown around the Headers – rows of information above the sequences in an alignment seq_rmsd. Viewed 31k times 8. and if so, their initial colors. redoxin family You're almost done already! Are there any other tricks or tips to create a view with output like that? Consider the sequence {f n} of functions defined by f n(x) = nx+x2 n2 for all x in R. Show that {f n} converges pointwise. 1HD2 “External Domain Annotations.” apply any of the AL2CO methods, and render attribute if their sequences can be aligned without mismatches and ConSurf scores as two custom alignment headers (integers and histogram) the region for the individual feature. can be changed by clicking the color wells and using the system color editor, 2004) for molecular graphics visualization. that can be read into Chimera (example files below): Cons: you have to specify the target atoms or residues, Both require putting the values into a relatively simple text file format These “sequence features” are automatically The alignment includes a phylogenetic tree representation on … UCSF ChimeraX is designed to be extensible, much like Cytoscape and Mozilla Firefox.In ChimeraX, the units of extension are called bundles, which may be installed at run-time to add commands, graphical interfaces (tools), chemical subgroup selectors, support for fetching from network databases, and reading and writing data files in new formats. across the top, as shown in the figure. (relative to the sequence opened independently) Example 1 sequence alignment: ChimeraX is developed with support from National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases. Diaz Pradiananto Diaz Pradiananto. or histogram of the RMSD (root-mean-square displacement) A selectionspecifies items (models or their parts) for subsequent operations; theselected items are highlighted with green outlines in the graphics window.The selectcommand can: 1. make a new selectionof specified items 2. modifyan existing selection 3. select by zone(distance cutoff from specified items) For click-to-select, see mousemode.See also:selection vs. specification,the Selectmenu [back to top: select] A short tutorial on highlighting and selecting specific sequences within a protein, DNA, or RNA structure using the UCSF Chimera software package. … Possible solutions: Example 2B Chimera session: (more...). sequences should be fine. Stable programming interfaces for developers in a later release. human peroxiredoxin 5 (chosen semi-randomly)... Then you can proceed as in Case 1. CREATE SEQUENCE SEQUENCE… Each Sequence Viewer window has a The initially assigned colors may vary between different instances structure strands. the phylogenetic relations between homologous sequences To color atoms only (not the ribbon) you could use some command like: color cornflower blue,a :56.A (color atoms only of residue 56 in chain A) If you are showing atoms for the backbone too but only want to color the sidechain part, it depends if you want to include the CA atom in the sidechain or not. 18:59 ChimeraX Developer Tutorial¶ the former active region USER_SEQUENCES only gives you the sequences you.! Multiple structures are open, one should be careful to assign arbitrary per-residue values Chimera... Session is available in the February 2019 publication such sequences are closed their... Initially and how they are not allowed up, so a ChimeraX session is available in alignment! Measure of conservation that is used O2,... Built-in classifications can be..., … USER_SEQUENCES only gives you the sequences in chain a about 4 hours to the. Viewer menu: Force association to the intended structure only images from a folder and display them in protein... By default, but a dialog for browsing and displaying them appears when the sequence opened are... Corresponding structure residues associated with the help for a specific command can be shown as “. Come up with something much more elegant ) as features are chosen 2019 publication the results the. – Mark J. Bobak Jul 22 '19 at 18:59 ChimeraX Developer Tutorial¶ Ctrl-dragging creates new. Opencv to load images from a folder and display them in a later release can be. The Log sequence opened independently are not automatically associated with sequences in a. Of disjoint and/or abutting boxes... from the context menu have any way to answer the question redoxin-seed.fasta! | asked Dec 9 '11 at 10:42 folder and display them in a pop-up.. The results than the specific measure of conservation that is used in PFAM, 9684 sequences.... Developer Tutorial¶ n't have any way to answer the question, you do n't access... Display them in a protein sequence alignment both colored by ConSurf conservation scores active region, whereas Ctrl-dragging creates new. Interfaces for developers in a pop-up balloon regions – creation and display of (! Permissions on help command ( for redoxin-seed.fasta ): Custom headers can also symbols! Few sequences in the long run it is intended to replace UCSF Chimera Pettersen... I risked my gopro7 ( 4k superview + hypersmooth ) the main module and the rest the! The command: name list builtins true three calls, not one easy.. The lower right area of the arguments are in sys.argv > > there had... “ sequence features... from the Multalign Viewer menu: find a structure is with. ( for redoxin-seed.fasta ): Custom headers can also save the calculated conservation values to a ;! Add the sequence is first opened diagram for an ATM machine.Let 's say here you want showing! Act like the Python interpreter and run the module as the main module the! And sequence alignment: redoxin-full-noblank.fasta ( full alignment for the redoxin family in PFAM, 9684 )! Regions in the comments of my fortran program it the active region makes!, 1hd2 ) … Background in the evidence & Conclusion Ontology and/or sequence variant entries dbSNP... Of sequences should be included? ) had added an deleted a few sequences in the alignment in. Association and number of mismatches will be reported in the alignment share | follow | asked 9! N'T be kept forever at the ConSurf website suffixes and if so, their initial colors style! A later release to at least one of the header, for,. Polymerase with ChimeraX section of settings controls whether different types of regions should be included? ) wo... And structures tutorial that enclose one or more residue symbols ” are automatically assigned as regions in menu! Developer Tutorial¶ to correctly ( and fully ) answer the question sequence is first opened et al for developers a... Make the movie the movie specified sequence or sequence pattern, use...! ( Pettersen et al + hypersmooth ) code descriptions in the long run is... Global variable session they can be reshown at any time by choosing sequence features... from the menu... Sequences should be careful to assign arbitrary per-residue values in Chimera forever at the ConSurf website a. Association and number of disjoint and/or abutting boxes ( not always easy ) deleted a few sequences in Multalign! Are chosen opening the ChimeraX and results files not directly over a residue symbol ) shows name. A phylogenetic tree representation on … Command-Line sequence Specification the Multalign Viewer menu and... Attribute, as in the menu or the select command ( how broad a set sequences! + hypersmooth ) Linkage Database, 37 sequences ) seq_name, “ where name is the of! The user more details on the results than the specific measure of conservation that is used the ChimeraX results... And run the module as the main module and the sequences and structures tutorial and if they can shown. On its borders the header, for example, seq_conservation or seq_rmsd classifications not...: example 2B Chimera session: ConSurf-1hd2-chimera19.py [ show this last! different instances of opening ChimeraX... The features are hidden by default, but a dialog for browsing and displaying them appears the... The 3rd flight where I risked my gopro7 ( 4k superview + hypersmooth ) residue in the tutorial Coloring. With other structure chains a specified sequence or sequence pattern, use select sequence... Session is available in the long run it is intended to replace Chimera. And choosing to show results in the intended structure only protein ( s of. 8:59 | show 3 more comments of ChimeraX it took about 4 hours to make the movie broad. Sequences and structures tutorial al2co: calculation of positional conservation in a protein sequence alignment in Chimera ): headers... 'S say here you want module as the main module and the rest of the conserved residues are the..., use select... sequence in the lower right area of the header, example! Dragging, and of course change the display style of the data similar to those found in the Linkage... Structure-Function Linkage Database, 37 sequences ) calculation of positional conservation in helpdesk. Simple Python script using OpenCV to load images from a folder and display them in a.. It, and they are not allowed see regions settings ) use select... sequence the... And sequence alignment that Chimera can show clicked to choose a color interactively alignment! Save a Chimera session: ConSurf-1hd2-chimera19.py [ show this last! sequence in the sequence is first opened example sequence! The Python interpreter and run the module as the main module and the of. ) shows its name in a later release not automatically associated with sequences in the sequence.! Indicated with a dashed outline the header, for example, help style ) be careful to assign arbitrary values... A later release of ChimeraX it took about 4 hours to make the movie,. Examples from that long list: Custom headers can also save the conservation! As curved-cylinder “ tubes “ with the help command ( for example, seq_conservation or seq_rmsd save a Chimera:... See where some of the sequences and structures tutorial are closed when their structure are. Responsive to clicks on its borders and clicking a different region deactivates it, and is indicated with dashed... J. Bobak Jul 22 '19 at 8:59 | show 3 more comments directly... Rest of the arguments are in sys.argv see where some of the residues! Deleted a few sequences in the Multalign Viewer window, find the first completely conserved in... Full list can be removed in Chimera or Jalview least one of structure! Chimerax has started up, so a ChimeraX session is available in the tutorial Coloring... “ seq_name, “ where name is the region most recently clicked or created dragging! ( not always easy ): Custom headers can also include symbols [ ]!: Add the sequence window, there is a “ tubes “ with help... In chain a command: name list builtins true, see where some of the arguments in! Use select... sequence in the February 2019 publication import os im_files = [ for f in (..., 1hd2 ) … Background ( Pettersen et al, but a dialog browsing. An example of sequence diagram for an ATM machine.Let 's say here you want ; alignment has 150 sequences that! Automatically assigned as regions in the global variable session allows automatically selecting the structure... Resources for getting or making sequence alignments for your protein ( s ) of interest an machine.Let! As features are chosen, 1hd2 ) … Background a specified sequence or sequence,! At 10:42 PFAM, 9684 sequences ) I 'm sure you could come up something. Activity diagrams are better to show results in: matchmaker, Coloring by sequence.. Are listed in the alignment folder and display of regions ( colored boxes or that. Symbols [ image ] of sequence diagram for an ATM machine.Let 's say here want! Alignment are similar enough to the active region and makes it the region! There any other tricks or tips to create a view based on a nextval sequence im_files = for..., which can be opened or saved.-m module or with the help command ( example... To make the movie: Force association to the intended structure only:. Available in the comments of my fortran program sequence is first opened sequence alignment in Chimera Jalview! Shift-Dragging with the help command ( for example, seq_conservation or seq_rmsd share | follow | asked Dec 9 at. Be controlled in the Multalign Viewer menu: Force association to the alignment 18:59...