Re: [ccp4bb] [ccpem] Making thioester bond in Chimera/ChimeraX

erax-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 > m

Re: [ccp4bb] CCP4BB Digest - 13 Feb 2021 to 14 Feb 2021 (#2021-51)

"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 ###

Re: [ccp4bb] strict structure based alignment

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

r 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

Re: [ccp4bb] Putting Text into Movies

rrent/docs/ContributedSoftware/2dlabels/2dlabels.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

Re: [ccp4bb] residuewise rmsd for multiple chain superposition

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/h

Re: [ccp4bb] secondary structure output

ndary 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 Grap

Re: [ccp4bb] Software for showing crystal packing

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] [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

Re: [ccp4bb] Superpositions: Deviation by Residue

ww.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] Temperature Factor statistics

lator/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://

Re: [ccp4bb] mutation and minimization

o 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] mutation and minimization

ze.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu Chimera home page: www.cgl.ucsf.edu/chimera

Re: [ccp4bb] Thermal Ellipsoids pic

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

Re: [ccp4bb] Comparing two proteins

nable 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

scribed 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

csf.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

Re: [ccp4bb] rmsd calculation for all atoms

...@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] per-residue RMSD calculation for homologous structure

On Nov 19, 2010, at 4:00 PM, Srivastava, Dhiraj wrote: Hi All does anyone know any software that can calculate and print out RMSD of every residue (c alpha will be good) for homologous structures which has only 30-40 % sequence similarity? I looked on the web but all the software tha

Re: [ccp4bb] Protein + DNA volume calculation

e the Voronoi volume of a molecule. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

Re: [ccp4bb] CIF format frustrations

ities, 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 Pett

Re: [ccp4bb] How to align a sequence to a know profile

ally 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] Understanding Conformational Differences

also select representative conformers for each cluster. More information about Chimera and a download link can be found on the Chimera home page: http://www.cgl.ucsf.edu/chimera --Eric Eric Pettersen UCSF Computer Graphics Lab

Re: [ccp4bb] programmatic symmetry mate generation

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 ") --Eric Eric Pettersen UCSF Computer Graphics Lab