Re: [ccp4bb] [ccpem] Making thioester bond in Chimera/ChimeraX
Hello Firdous, Probably the problem is that mol A and mol B are two different models. You can't add a bond in Chimera or ChimeraX until after combining them into one model first. ChimeraX combine command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> ChimeraX bond command or Build Structure tool, Adjust Bonds section: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> For the best chance of getting an answer to a question about ChimeraX, please use the chimerax-us...@cgl.ucsf.edu <mailto:chimerax-us...@cgl.ucsf.edu>address: <https://rbvi.ucsf.edu/chimerax/docs/contact.html> I hope this helps, --Eric Eric Pettersen UCSF Computer Graphics Lab > From: Collaborative Computational Project in Electron cryo-Microscopy > mailto:cc...@jiscmail.ac.uk>> on behalf of Firdous > Tarique mailto:kahkashantari...@gmail.com>> > Date: Thursday, November 9, 2023 at 12:27 PM > To: cc...@jiscmail.ac.uk <mailto:cc...@jiscmail.ac.uk> <mailto:cc...@jiscmail.ac.uk>> > Subject: [ccpem] Making thioester bond in Chimera/ChimeraX > > Hi > > Does anybody know how to make thioester bonds in Chimera or ChimeraX ? > > I am unable to make a bond between Cys321 in mol A with Gly1 in mol B > (S-glycyl-L-cysteine) using Chimera or ChimeraX. > > I tried Isolde in ChimeraX and Build Structure in Chimera to make a bond > between selected atoms but so far have been unsuccessful. I don't know if I > am missing something. > > Any help would be appreciated. > > Thanks > > Firdous > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] CCP4BB Digest - 13 Feb 2021 to 14 Feb 2021 (#2021-51)
> On Feb 14, 2021, at 4:00 PM, CCP4BB automatic digest system > wrote: > > Date:Sat, 13 Feb 2021 20:24:07 -0500 > From:Nicholas Larsen <mailto:nicholas_lar...@h3biomedicine.com>> > Subject: Re: Bug in mmCIF handling of UNK residues? > > I hope this doesn't confuse the discussion, but my understanding was "UNK" > stood for "unknown" residue and this will cause errors. UNK naming > convention is the default output of Schrodinger when generating ligand PDB > files. Coot will display the PDB containing "UNK" as a residue, but if you > try to use the CIF file to real-space refine, the ligand will blow up. I > found that renaming the residue in the output PDB and regenerating the CIF > file with the corrected RESID name solved the problem. So in > my experience, the problem is the name "UNK" and this just needs to be > switched to something else. Has anyone else seen this? > Nick The PDB defines UNK as unknown amino acid. UNL is unknown ligand. N is unknown nucleic acid. --Eric Eric Pettersen UCSF Computer Graphics Lab To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] strict structure based alignment
On Jul 13, 2012, at 4:00 PM, Christian Roth wrote: I want align a couple or protein structures by secondary structure matching to one target and want get a kind of aminoacid alignment file e.g. what residue fit the other, without adjustments due to sequence based alignments. I tried Strap, but as far as I understood it, it takes also the sequence into account. I tried also Rapido, but this does only a pairwise comparison. Superpose does align it nicely (ccp4 based or Coot based) but there seems to be no option to print the sequence alignment in a file and it is again just a pairwise comparison . Is there an other program which does something similar? If you use UCSF Chimera (www.cgl.ucsf.edu/chimera), you can use the MatchMaker tool to superimpose the structures. MatchMaker allows you to adjust the weight of sequence similarity vs. secondary structure matching, so you can just make the sequence similarity 0% and the secondary structure 100%. With the structures superimposed, you can use the Match-Align tool to generate a sequence alignment based solely on the proximity of residues to one another in space. Be warned that Match-Align will be very slow for 10+ structures, but is fine for half a dozen or so. The generated alignment will be displayed in a window that will have a File menu where you can save the alignment to a variety of common formats. --Eric Eric Pettersen UCSF Computer Graphics Lab
Re: [ccp4bb] Tool for calculating RMSD
If you open the structures in Chimera, the measure rotation command will report the transformation matrix as well as the screw axis and shift/rotation along/around the screw axis needed. There are also options to that command for actually depicting the screw axis and/or rotation. www.cgl.ucsf.edu/chimera www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 22, 2012, at 4:00 PM, Jeremy Tame wrote: Yes, LSQKAB does, but not the equivalent screw axis (which exists by Chasles theorem). I think a screw axis may well be the best way to describe the rigid body movement which began the thread. A simple distance and angle (2 numbers) are easier to understand, and often of more biological relevance, than RT matrices, for example in the case of relative domain motions. On Jun 20, 2012, at 5:20 PM, Mark J van Raaij wrote: LSQKAB (superpose in CCP4i GUI) also outputs in its log-file the translation parameters and rotation matrix it used to superpose the structure.
Re: [ccp4bb] residuewise rmsd for multiple chain superposition
On Feb 21, 2012, at 4:00 PM, sreetama das wrote: Is there any software which will print the RMSDs (residue wise, and not chain wise) for more-than-2 chains (having similar/ same sequences) superposed together? In UCSF Chimera you can use the Match-Align tool to create a structure-based sequence alignment (or you can open an alignment file if you already have one). The the alignment will show per-residue RMSD as a bar chart across the top of the alignment (if you opened your own alignment file you'd have to use the Headers-RMSD menu entry to show the bar chart). You can save the numeric RMSD values to a file with Headers-Save. Also, Match-Align will report a couple of additional normalized RMSD scores, namely Structural Distance Measure and Q-score. Chimera home page: www.cgl.ucsf.edu/chimera Match-Align page: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchalign/matchalign.html sequence aignment viewer: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/framemav.html --Eric Eric Pettersen http://www.cgl.ucsf.edu/home/pett And isn't sanity really just a one trick pony anyway? I mean all you get is one trick, rational thinking, but when you're good and crazy, oooh oooh oooh, the sky is the limit!-The Tick
Re: [ccp4bb] Putting Text into Movies
On Feb 21, 2012, at 4:00 PM, Jacob Keller wrote: is there a good way to put text labels into movies from pymol or otherwise? It would be helpful for conveying some ideas... As Jason pointed out, PyMOL has some useful facilities for this. Chimera has a tool for placing standalone text and arrows called 2D Labels. The arrows and text can be any color and the text can also be various sizes, styles (italics, etc.) and typefaces (serif etc.), all on a per-character basis. You can place text and arrows interactively with the mouse or via commands. Text can also be faded in or out as a movie plays/records. A pretty nice example use of 2D Labels in the DNA basics movie on this page: http://crc.nd.edu/index.php/cyberinfrastructure/visualization/80 Chimera home page: www.cgl.ucsf.edu/chimera 2D Labels page: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/2dlabels/2dlabels.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] secondary structure output
On Jan 24, 2012, at 4:00 PM, Ed Pozharski wrote: I am looking for a program/server that would determine secondary structure from a pdb file and then output a new pdb file with HELIX/SHEET records. I have a model for which pymol fails to produce correct secondary structure. DSSP and STRIDE identify the secondary structure correctly but I'd need to convert their output myself to either pdb header or pymol script. So I wonder maybe something like that already exists. If you open the PDB in Chimera and the PDB lacks HELIX/SHEET records, Chimera will use DSSP to compute the secondary structure and if you then save a new PDB file (File-Save PDB) the saved file will have the appropriate HELIX/SHEET records. You can get Chimera from www.cgl.ucsf.edu/chimera . --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] Software for showing crystal packing
On Dec 3, 2011, at 4:00 PM, Yuri Pompeu wrote: Hello everyone, Whats a good software for showing crystal packing and unit cell, axes , etc... I know pymol and coot will do it but would love to hear other possibilities/ideas. Chimera's Unit Cell tool can do this. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] Superpositions: Deviation by Residue
On Nov 28, 2011, at 4:03 PM, Jacob Keller wrote: Let me refine my question (sorry for my lack of clarity): is there a program that will output the distances between the corresponding ca's of a superposition on a residue-by-residue basis, and not just a global RMSD value (doubtless these numbers are part of the superposition algorithm itself)? I want to plot these values as a function of residue number to show which parts of the structures deviate more or less from each other. If you use the MatchMaker tool in UCSF Chimera to make the superposition, it has an option to show the corresponding sequence alignment. The sequence alignment will have an RMSD header running across the top, which is a bar graph of the RMSD values. You can the alignment's Headers-Save... menu item to save the numerical values to a file if you want. If you already have the structures superimposed on your own, you can use Chimera's Match-Align tool to create a superposition-based sequence alignment, and do the same thing with its RMSD header. Some links: Chimera home page: http://www.cgl.ucsf.edu/chimera alignment tool's RMSD header: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/multalignviewer.html#assessment --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] [CCP4] identify a rotation centre: domain rotation
Perhaps this video would be helpful: http://www.cgl.ucsf.edu/chimera/videodoc/AlignDomains/index.html The axis point shown in the reply log at the very end is what I think you want. BTW, the video is a little out of date, in that if you get the very latest daily build the MatchMaker tool can match the smaller domains with having to delete part of the structure. --Eric On Nov 23, 2011, at 4:00 PM, WENHE ZHONG wrote: Dear members, I would like to have your ideas if there is any way to identify a rotation centre of domain in two different states using CCP4 or other program. The situation is: the domain of the protein will rotate between two different states (depending on substrate binding) around 8 degree, and it is (nearly) clearly that the domain is rotated around a rotation centrel. So the question is how to identify this rotation centre in this 3D model? The ideal is to identify a region of residues in the domain which are most closed to the rotation centre. The tool I am using right now is the superpose tool in CCP4 package. The output which I think mightbe uesful is: CENTROID OF WORKING MOLECULE : 157.812 152.396 -70.778 CENTROID OF WORKING MOLECULE :(fractional) 157.812 152.396 -70.778 CENTROID OF REFERENCE MOLECULE: 157.251 151.877 -70.874 CENTROID OF REFERENCE MOLECULE:(fractional) 157.251 151.877 -70.874 Distance between CENTROIDS :0.770 Direction cosines of vector between CENTROIDS: 0.729 0.674 0.124 I would say the “CENTROID it mentioned above, such as (157.251 151.877 -70.874), is possibly near to the rotation centre. I would like to have your opinion though. Thank you.
Re: [ccp4bb] Temperature Factor statistics
On Aug 31, 2011, at 4:00 PM, Yuri Pompeu wrote: After i get my output file from baverage containing the average b- factor and rms by residues, How can I calculate and display the average (and or mean) B-factors? Is there a way of calculating it by protein, ligands and solvent separately? Chimera's Render by Attribute tool can depict atoms by their B-factor or residues by their average B-factor (assuming you have a PDB file with a B-factor column). It also shows a histogram of the B-factor values. You can use the Attribute Calculator tool to compute the average B-factor of any part of your structure and write it to a file. Some links: Chimera: www.cgl.ucsf.edu/chimera Render by Attribute: www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/render/render.html Attribute Calculator: www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/calculator/calculator.html a tutorial focused on coloring by B-factor: www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] Defining an ellipse around a protein structure
On May 28, 2011, at 4:00 PM, Vandu Murugan wrote: Dear all, Is there a program or server that would define a ellipsoid around a given protein molecule? I would also like to calculate the axis components of the defined ellipse. Thanks in advance.. Chimera can do this, as per: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006407.html --Eric
Re: [ccp4bb] mutation and minimization
On May 12, 2011, at 4:00 PM, CCP4BB automatic digest system wrote: Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Chimera is pretty good for this. It has a Rotamer tool for making the substitution based on Dunbrack or Richardson libraries, and can screen based on probability / H-bonds formed / steric clashes: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/rotamers/rotamers.html You can then use Chimera's Minimize Structure tool to minimize the side chain and/or the local environment or, if you're feeling frisky, the whole protein: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/minimize/minimize.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu Chimera home page: www.cgl.ucsf.edu/chimera
Re: [ccp4bb] mutation and minimization
On May 13, 2011, at 4:00 PM, Tom J. Brett wrote: On a similar extension to this topic, is there a good software out there for doing these kinds of modifications and minimizations for protein structures with chemicals entities (i.e., protein/inhibitor complexes). What I am looking to do is take a protein/inhbitor complex and add chemical modifications onto the inhibitor and see how they fit. so a little minimization/relaxation of the surrounding protein would be nice. It there a freely available software that will allow something like this, if not what commercial packages are cheapest/best at this? Thanks and sorry for hijacking this thread. Chimera also has a tool (Build Structure) that can be used for simple chemical modifications: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/editing/editing.html It's not as nice as some builders, but it can generally get the job done. Chimera can compute the charges on your modified structure by calling out to AmberTools/antechamber (included with the Chimera download) and then perform minimization. Charge computation might take awhile if the inhibitor is large-ish. This isn't to say that you shouldn't follow the protocol outlined by Saugata Hazra in another posting. It depends on your goals. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] Thermal Ellipsoids pic
On May 9, 2011, at 4:00 PM, Kenneth A. Satyshur wrote: YO! I am making thermal ellipsoid plots of a highly flexibile region of a chromophore using rastep and render from the raster3D package of Merritt el al. But I cannot control the orientation. It obscures the rest of the atoms in the plane of the molecule. Does anyone know a way to orientate molecules AND get a publication quality png file? ccp4mg only produces vague traces. Hey, you can use Chimera to orient the molecule as you like and then use Chimera's Thermal Ellipsoids tool to draw the ellipsoids. That tool lacks rastep's cut-away quadrant depiction but has all the other depictions. More info about Thermal Ellipsoids here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html about Chimera itself here: www.cgl.ucsf.edu/chimera --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] Comparing two proteins
On Apr 13, 2011, at 4:00 PM, Rex Palmer wrote: What is the best program to use for comparing two protein structures which are very similar both structurally and wrt aa sequence? ie to get the rms deviations both generally and in selected regions. Best is kind of subjective, but you can use the MatchMaker tool in Chimera to superimpose the structures and show the superposition. MatchMaker also has an option to show the corresponding sequence alignment. The alignment will have a histogram of the column RMSD values running across the top. You can drag the mouse on the alignment to select/highlight the corresponding parts of the structure and to show the RMSD of the dragged region in the alignment's region- browser window. MatchMaker described here: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/matchmaker.html Chimera obtainable here: http://www.cgl.ucsf.edu/chimera --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] program to calculate electron density at x,y,z
On Apr 1, 2011, at 4:00 PM, Ed Pozharski wrote: I need to calculate the electron density values for a list of spatial locations (e.g. atom positions in a model) using an mtz-file that already contains map coefficients. To write my own code may be easier than I think (if one can manipulate mtz columns, isn't the only problem left how to incorporate symmetry-related reflections?), but I would need an alternative at least for troubleshooting purposes. So, Does anyone know of a software tool that can calculate point electron density for every atom in a structure? If I would have to bring a dependency into this, the best choice for me would be clipper libs. Hi Ed, You'd have to convert the map to ccp4 or XPLOR format, but once you've done that it's pretty straightforward to get the values at atom positions using Chimera, pretty much as described here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-March/006202.html except skipping the part where you average them across a residue. --Eric Eric Pettersen UCSF Computer Graphics Lab
Re: [ccp4bb] Model Building: continuous update of distances as fragment moved
On Feb 14, 2011, at 4:01 PM, Paul McLaughlin wrote:
In doing some model building I want to move a domain of a protein
manually, as a rigid body, and see in real time continuous updates of
some distances from points on the domain to the rest of the protein
(we
have cross linking data).
I dimly remember being able to do with this O,at least a decade ago
(probably more), but it doesn't seem to work in current versions (I
have even dimmer recollections that this might have been a special
feature of a particular graphics card in an SGI)
In any event, does anyone know of anything that might allow us to do
this? { I am not asking about computational ways of exploring
alternate
packing of the domain to satisfy distances ( I know about these) -
rather we want to get a feel for what is possible by seeing it for
ourselves).
DIstance monitors in Chimera (www.cgl.ucsf.edu/chimera) automatically
update as structures are moved. Possibly also of interest, Chimera
can monitor steric clashes/contacts as structures are moved:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
Re: [ccp4bb] rmsd calculation for all atoms
From:Michael Swan Subject: rmsd calculation for all atoms. Dear all, I am having a bit of trouble finding a program to do an rmsd calculation and give me the differences between all the atoms in the structures. I have two structures which are identical in the sense that one is the apo protein and one is the bound structure. I would like to superimpose them using only one domain then output the rmsd values for all the atoms or at least individual residues. The structures are not completely identical as some extra residues were visible in the bound structure so I hope there is a program that can ignore those differences. If anyone knows of a program that will do this calculation I would much appreciate hearing about it. There seem to be many programs that will give an average rmsd over the whole structure or just the region used for alignment but I haven't found anything that will give me distances between atoms or residues that were not used in the alignment. Thanks, Mike. If the domain is an entire chain, you could use Chimera's MatchMaker tool to do the alignment: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/matchmaker.html It will report that RMSD for the atoms used for matching. To get the RMSD for all atoms in common you would have to use the 'rmsd' command and specify the parts in common: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rmsd.html So if all of chain A and residues 12-20 of chain B were in common, then: rmsd #0:.a:12-20.b #1:.a:12-20.b If there were differences in the side chains (say some were incomplete) then you might have to restrict the RMSD measurement to the backbone (which you might want to do anyway): rmsd #0:@c,ca,n:12-2...@c,ca,n #1:@c,ca,n:12-2...@c,ca,n --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] CIF format frustrations
On Jul 29, 2010, at 4:00 PM, CCP4BB automatic digest system wrote: Date:Thu, 29 Jul 2010 13:49:12 +0100 From:Simon Kolstoe s.kols...@ucl.ac.uk Subject: CIF format frustrations Dear all, What's the best way to convert a coordinate cif file to a pdb (without compiling a program, installing new utilities, writing script files...)? You could use Chimera (www.cgl.ucsf.edu/chimera). File..Open to open the CIF file, and then File...Save PDB to write it as PDB (probably after seeing if it looks right in the graphics window). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] How to align a sequence to a know profile
I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Hi Yuan, You can use UCSF Chimera's Multalign Viewer tool to do this. Just open your alignment with that tool and use the Edit-Add Sequence menu item to add your sequence to the alignment. UCSF Chimera: http://www.cgl.ucsf.edu/chimera/ Multalign Viewer tool: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/framemav.html specifically the Add Sequence part: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] programmatic symmetry mate generation
Hi James, The symmetry copies of a molecule asymmetric unit can be saved to a new PDB file using the saveunitcell.py Python script with Chimera. http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts It uses the CRYST1 record in the PDB file to determine the symmetry group. Unfortunately as mentioned in the script you need to use Chimera as the Python interpreter, which you may not be willing to do -- but you can just call out to the command-line version of Chimera (also documented in the script) via os.system() or whatnot. There is also a sym command in Chimera which can generate symmetry mates from a wide spectrum of possible criteria. A Python script to call sym is just: from chimera import runCommand runCommand(sym options you want) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
