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October 6, 2011, [pymol] assign secondary structural regions.
Sometimes I displayed the cartoon view of a protein in PyMOL as the figures shown below that I don’t really see the helix and strands.
It often happens when I merged 10 or 20 structures into a NMR ensemble file. All 20 structures are aligned but the secondary structural regions are not clearly displayed in PyMOL (commands: set all_states, on )
PyMOL provides two simple means to quickly draw helices and strands on the target proteins.
1. use command “dss”.
Simply type “dss” in the command line, PyMOL automatically calculates, rebuilds and draw the secondary structural regions. If the “all_states” is turned on, all structures will also be displayed properly. Here are two figures show the results of “dss” with single and all 20 states of my target protein.
The command “dss” provides simple but quick way to draw helical and strand regions, however, using other programs such as “DSSP” or “STRIDE” to clearly define the regions of helices and regions is highly recommended.
2. Use command “alter”
As I just said, “dss” doesn’t work perfectly. In this example case, I found length of first two sheets are not long enough, and the loop is a bit longer. I can use command “alter” to manually assign the secondary structural regions of my target proteins.
alter 3-9/, ss=’H’ alter 12-18/, ss=’H’ rebuild
The above 3 lines are the commands I typed in and the sheets are now longer (see the right up corner). To change the length of loop and sheets, just type alter xx-yy/, ss=’L’ , and alter aa-bb/, ss=’S’ , respectively.
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Automated Family-Wide Annotation of Secondary Structure Elements
- First Online: 04 April 2019
Cite this protocol
- Adam Midlik 3 , 4 ,
- Ivana Hutařová Vařeková 3 , 4 , 5 ,
- Jan Hutař 3 , 4 ,
- Taraka Ramji Moturu 3 ,
- Veronika Navrátilová 6 ,
- Jaroslav Koča 3 , 4 ,
- Karel Berka 6 &
- Radka Svobodová Vařeková 3 , 4
Part of the book series: Methods in Molecular Biology ((MIMB,volume 1958))
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Secondary structure elements (SSEs) are inherent parts of protein structures, and their arrangement is characteristic for each protein family. Therefore, annotation of SSEs can facilitate orientation in the vast number of homologous structures which is now available for many protein families. It also provides a way to identify and annotate the key regions, like active sites and channels, and subsequently answer the key research questions, such as understanding of molecular function and its variability.
This chapter introduces the concept of SSE annotation and describes the workflow for obtaining SSE annotation for the members of a selected protein family using program SecStrAnnotator.
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Acknowledgments
This work was supported by ELIXIR CZ research infrastructure project (MEYS) [LM2015047 to A.M., I.H.V., J.H., K.B., and R.S.V.]; Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 [LQ1601 to A.M., R.S.V., and J.K.]; ELIXIR-EXCELERATE project, which received funding from the European Union’s Horizon 2020 research and innovation program [676559]; ELIXIR-CZ: Budování kapacit [CZ.02.1.01/0.0/0.0/16_013/0001777]; Ministry of Education, Youth and Sports of the Czech Republic [project CZ.02.1.01/0.0/0.0/16_019/0000754 to V.N. and K.B.]; and Palacky University Olomouc [IGA_PrF_2018_032 to V.N.]. A.M. is a “Brno Ph.D. Talent” scholarship holder funded by Brno City Municipality.
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Adam Midlik, Ivana Hutařová Vařeková, Jan Hutař, Taraka Ramji Moturu, Jaroslav Koča & Radka Svobodová Vařeková
Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
Adam Midlik, Ivana Hutařová Vařeková, Jan Hutař, Jaroslav Koča & Radka Svobodová Vařeková
Faculty of Informatics, Masaryk University, Brno, Czech Republic
Ivana Hutařová Vařeková
Faculty of Science, Department of Physical Chemistry, Regional Centre of Advanced Technologies and Materials, Palacký University, Olomouc, Czech Republic
Veronika Navrátilová & Karel Berka
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Midlik, A. et al. (2019). Automated Family-Wide Annotation of Secondary Structure Elements. In: Kister, A. (eds) Protein Supersecondary Structures. Methods in Molecular Biology, vol 1958. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9161-7_3
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DOI : https://doi.org/10.1007/978-1-4939-9161-7_3
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Can pymol show cartoon (secondary structure) for a pdb of multiple frames?
I am using pymol to visualise the secondary structure of protein using its cartoon representation. The pdb file comes from a simulation, which contains multiple frames. After loading the pdb , its secondary structure (e.g. sheet, helix) could not been recognised. Surprisingly, if only one frame is kept, its secondary structure could be seen. So how to enable secondary structure recognition for a pdb file with multiple frames?
An example of the pdb file with multiple frames is shown below.
- protein-structure
- 3d-structure
- $\begingroup$ I suspect that the PDB is malformed. Is it available online somewhere so I can take a look at it? Alternatively, could you post and excerpt of the HELIX and/or SHEET records from the file? $\endgroup$ – canadianer Commented Feb 2, 2018 at 18:52
- $\begingroup$ I notice that the ATOM records don't contain a chain identifier. I'm not sure if that would prevent PyMol from recognizing the secondary structure elements. $\endgroup$ – canadianer Commented Feb 2, 2018 at 18:59
- 1 $\begingroup$ @canadianer the chain ID is not the problem, as it works for a single frame $\endgroup$ – lanselibai Commented Feb 2, 2018 at 19:06
- $\begingroup$ Okay... Does an NMR model with multiple conformers display correctly (5VKV, for example)? $\endgroup$ – canadianer Commented Feb 2, 2018 at 19:10
- $\begingroup$ So it must be this particular PDB. If there's anything wrong with the portion of the file you've posted, I don't know what it is. Does the file with multiple models have HELIX/SHEET records? $\endgroup$ – canadianer Commented Feb 2, 2018 at 19:20
It seems that if no HELIX record is present in the PDB, PyMol attempts to assign secondary structure itself. For whatever reason, it does not do this if multiple MODEL s are present. You should be able to use the dss command to force PyMol to calculate secondary structure in a PDB with multiple MODEL s.
- $\begingroup$ Thanks for this, it was so easy to get this "fixed"! Works like charm. $\endgroup$ – Marcin Magnus Commented Nov 18, 2021 at 9:44
- $\begingroup$ @MarcinMagnus You’re welcome! $\endgroup$ – canadianer Commented Nov 18, 2021 at 16:56
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STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins
STRIDE is a software tool for secondary structure assignment from atomic resolution protein structures. It implements a knowledge-based algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignments in maximal agreement with crystallographers' designations. The STRIDE web server provides access to this tool and allows visualization of the secondary structure, as well as contact and Ramachandran maps for any file uploaded by the user with atomic coordinates in the Protein Data Bank (PDB) format. A searchable database of STRIDE assignments for the latest PDB release is also provided. The STRIDE server is accessible from http://webclu.bio.wzw.tum.de/stride/ .
INTRODUCTION
Identification of secondary structure elements is a major step in the characterization of a newly determined protein structure. It serves as a basis for virtually all subsequent analyses, including visualization, structure comparison and classification, homology modelling, threading and sequence alignment. To a large extent, our visual notion of proteins is based on cartoon diagrams showing α-helices and β-strands as cylinders and arrows, respectively.
Several automatic tools for secondary structure assignment from known atomic coordinates are available [reviewed in ( 1 )]. The most widely used method, DSSP ( 2 ), defines secondary structure elements as repeating elementary hydrogen bonded patterns. Hydrogen bonds between peptide units are assigned if the electrostatic interaction energy between C=O of one residue and N–H of another residue is <−0.5 kcal/mole. The DEFINE algorithm ( 3 ) compares inter-atomic distance matrices of structural fragments to idealized reference distance masks typical for a particular secondary structure type, while P-Curve ( 4 ) is based on quantification of backbone curvature using differential geometry. More recently, an improved version of DSSP, called DSSPcont, has been developed which takes into account the structural variations in proteins ( 5 ).
Our method, STRIDE ( 6 ), was developed with a specific goal to accurately reproduce secondary structure designations created by human experts. It is thus a knowledge-based approach which uses, as training data, a carefully verified set of secondary structural elements defined by crystallographers who have deposited structures in the Protein Data Bank (PDB) ( 7 ). The main difference between STRIDE and DSSP is that STRIDE considers both hydrogen bonding patterns and backbone geometry. The hydrogen bond energy is calculated using an empirical energy function which takes into account the distance between the donor and the acceptor and the deviations from linearity of the bond angles ( 8 , 9 ). A weighted product of hydrogen bond energy and torsion angle probabilities for α-helix and β-sheet is used to determine the start and stop positions of secondary structure elements based on empirically optimized recognition thresholds.
The source code of STRIDE has been freely accessible from the FTP server of the European Bioinformatics Institute since 1995 ( ftp://ftp.ebi.ac.uk/pub/software/unix/stride/src ). It is also available as part of several molecular graphics packages and websites [e.g. Visual Molecular Dynamics (VMD) ( 10 )]. Here, we report a dedicated STRIDE web server and a database of secondary structure assignments.
STRIDE WEB SERVER AND DATABASE
The STRIDE web server, written in the python programming language, makes accessible all functions implemented in the STRIDE software and also provides several additional visualization tools (Figure (Figure1). 1 ). It accepts as input atomic coordinates in standard PDB format, which can be either uploaded or pasted into a web form. The STRIDE home page offers the following options.
Available views of the secondary structure assignment created by STRIDE from the sample structure 456c. Center top, original STRIDE output; left, contact map; right, Ramachandran plot; bottom, cartoon representation of secondary structure.
Basic secondary structure assignment . A secondary structure assignment in text form is produced. Its header section gives general information about the structure (author, compound, etc.) as well as a secondary structure summary which lists locations of identified secondary structure elements. Then follows a detailed per residue assignment of secondary structure states complemented by information on backbone dihedral angles and solvent accessible area computed according to Eisenhaber et al . ( 11 , 12 ).
Graphical representation of secondary structure assignment . A cartoon representation similar to the ‘wiring diagram’ of the PDBsum web server ( 13 ) is produced. Technically, this representation is generated not as a rendered image or postscript file, but rather in the form of an html table incorporating both individual graphical items and the protein sequence. The table is constructed by parsing the output of STRIDE and assigning an image to each structural state. An interactive point-and-click interface reveals detailed per residue information.
Contact map . A contact map is derived from a symmetric square matrix of distances between all C-α atoms in a given protein. An interactive mouse-sensitive image indicates distances below a certain threshold defined by the user, typically 6 Å.
Ramachandran plot . No secondary structure web server is complete without a Ramachandran plot ( 14 ) representing the distribution of ϕ and φ torsion angles in a given protein. The allowed areas for α-helix and β-sheet are shown in the background of the plot. They are taken from a recent update of the Ramachandran map by Lovell et al . ( 15 ). The orange line is the border for the core region of favourable angles. Gold limits the region of disfavoured but allowed angles. Like the contact map, this image is also mouse sensitive and gives additional information on the residue that is pointed at.
Database of STRIDE assignments . A complete database of STRIDE secondary structure assignments is calculated from each weekly update of PDB ( 7 ). Individual entries can be accessed either by PDB code or through a text search interface allowing for the construction of logically structured queries.
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IMAGES
COMMENTS
Secondary Structure Determination. As is typical with PyMOL, the secondary structure assignment engine is ad hoc and empirically tuned to produce desirable aesthetics. Though there are some phi/psi's that are clearly helix/sheet and others that are clearly not, there are certain regions of phi/psi space were the assignment is subjective or ...
"dss" defines secondary structure based on backbone geometry and hydrogen bonding patterns. ... With PyMOL, heavy emphasis is placed on cartoon aesthetics, and so both hydrogen bonding patterns and backbone geometry are used in the assignment process. Depending upon the local context, helix and strand assignments are made based on geometry ...
1. use command "dss". Simply type "dss" in the command line, PyMOL automatically calculates, rebuilds and draw the secondary structural regions. If the "all_states" is turned on, all structures will also be displayed properly. Here are two figures show the results of "dss" with single and all 20 states of my target protein.
Polar Contacts in PyMol. Using the actions [A] button for an object or selection you can display Hydrogen bonds and Polar Contacts. [A]->find->polar contacts-><select from menu>. The command behind the menus is the dist ance command called with the additional argument mode=2. Parameters that control the the identification of H-bonds are defined as.
PyMOL> cd <path to assignment directory>/pdbs PyMOL> load hras.pdb When you load a structure, the default visualization is an all-atom depiction. While there are times ... Note: You may nd it useful to color by secondary structure. C !by ss !Helix Sheet Loop 2.1 Backbone Geometry Next, we will take a closer look at the typical secondary ...
5.4.1 Secondary Structure Assignment by PyMOL. It is reassuring that the secondary structure assignments between PyMOL, the PDB, and DSSP are so similar because PyMOL employs a completely different method to the other two. PyMOL's method is based on the torsional angles of each C α atom.
The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. The abbreviation is only mentioned once in the 1983 paper describing this algorithm, [2] where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins.
Dssp. Included in psico. This command or function is available from psico, which is a PyMOL extension. Module. psico.editing. dssp is a wrapper for the popular DSSP program, which computes secondary structure. The command updates PyMOL's ss atom property.
Secondary structure assignment (SSA) consists of the set of SSEs found in a protein structure (each one described by its chain, start, end, and type) and optionally the β-graph. SSA can also refer to the process by which the SSEs and the β-graph are found. ... PyMOL: PyMOL is a commonly used molecular visualization tool. It is typically ...
Sst. Included in psico. This command or function is available from psico, which is a PyMOL extension. Module. psico.editing. sst is a wrapper for the SST secondary structural assignment web service. The command updates PyMOL's ss atom property. SST does minimum message length inference of secondary structure based on C-alpha atom positions.
Alternatively, is there a manual series of Pymol commands to directly assign secondary structure for a protein for insertion into the .pml script file? Even better, is there a separate program that can assign secondary structure and then allow you to save the revised PDB file with the secondary structure assignments inserted into the PDB output.
From PyMOL Wiki Jump to navigation Jump to search import pymol pymol . stored_ss = [] cmd . iterate ( 'all' , 'pymol.stored_ss.append(string.ljust(ss,1))' ) print string . join ( pymol . stored_ss )
This is the list of all PyMOL commands which can be used in the PyMOL command line and in PML scripts. The command descriptions found in this file can also be printed to the PyMOL text buffer with the help command. Example: PyMOL>help color ... The list of arguments for a command (the "usage") can be queried on the command line with a ...
Alternatively, is there a manual series of Pymol commands to directly assign secondary structure for a protein for insertion into the .pml script file? Even better, is there a separate program that can assign secondary structure and then allow you to save the revised PDB file with the secondary structure assignments inserted into the PDB output.
2. I am using pymol to visualise the secondary structure of protein using its cartoon representation. The pdb file comes from a simulation, which contains multiple frames. After loading the pdb, its secondary structure (e.g. sheet, helix) could not been recognised. Surprisingly, if only one frame is kept, its secondary structure could be seen.
PyMOL> cd <path to assignment directory>/pdbs PyMOL> load hras.pdb When you load a pdb file, the default visualization is acartoondepiction of the structure. You can toggle between different depictions of the same structure by hiding the current depiction and thenshowingadifferentdepiction.
However, PyMOL does have a reasonably fast secondary structure alignment algorithm called "dss". Please be aware that due to the subjective nature of secondary structure assignment in borderline cases, dss results will differ somewhat from DSSP. SYNTAX dss selection EXAMPLE dss 1dfr. If you are visualizing an animation, you may wish derive ...
STRIDE is a software tool for secondary structure assignment from atomic resolution protein structures. It implements a knowledge-based algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignments in maximal agreement with crystallographers' designations.
Dear PyMol users! I'm working with the big pdb ensemble wich lack information about the secondary structure ( deleated header region) I want to find possible way to assign secondary structure for all pdb's in my ensemble ( like A-> assign sec.str for specified pdb). Finally I want to deleate some common SS region is the whole insemble -e.g all ...
The architecture and the folding pattern of most of the proteins are supported by their secondary structures, so an accurate assignment for the prediction of secondary structure elements (i.e ...
To: pymol-***@lists.sourceforge.net Subject: [PyMOL] about secondary structure assignement: help Dear Pymol Users, i am working with some pdb files with no secondary structures assignments embedded on it. Then when i try to see my molecules on cartoon diagrams, i see the secondary structure different to another programs, VMD for example.
The original question was >I am using PyMOL and it requires secondary-structure-assigned pdb file for >the correctly assigned secondary structure. >I have successfully ran DSSP for the assignment of the secondary structure >but don't know how to add this information to pdb file. >Does anyone know how to do? >Is there any program to do this ...
> Alternatively, is there a manual series of Pymol commands to directly assign > secondary structure for a protein for insertion into the .pml script file? alter atom_selection, ss='L' (or 'H' or 'S', I think) > Even better, is there a separate program that can assign secondary structure > and then allow you to save the revised PDB file with ...