July 2014 - Chimera-users - RBVI Mailing Lists

how to connect broken ribbon
by Pu Qian 07 Jul '14

07 Jul '14

Hi there, Sometime, when I use chimera to make a ribbon presentation of protein, the helix region will either broken or does not present properly. Similar thing can be happened in Pymol. But, Pymol provides a command called "alter". When I rebuilt it after altering, broken helix can be repaired. I'm wondering is there similar function in Chimera, or is there a suitable method which can be used to deal with it. Thanks Best regards Pu Qian

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Measure correlation for rotated map positions
by Tom Goddard 03 Jul '14

03 Jul '14

Hi Rakesh, The “measure correlation” rotationAxis option only accepts a specification of two atoms to define the rotation axis. This is explained in the Chimera documentation. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat… Specifying 3 numbers is not enough since you need both a direction and a point on the axis. If you have a center x,y,z position and axis vector ax,ay,az then you could use the “turn” command to do the rotations and the “measure correlation” command without the rotationAxis option as follows. perframe "turn 0,0,1 10 center 0,0,0 coord #1 model #1 ; measure corr #0 #1" frames 36 This does a rotation by 10 degrees about center 0,0,0 and axis 0,0,1 using map #1 coordinates then measures the correlation between map #1 and #0, repeating this 36 times (covering 360 degrees). Results are reported in the reply log. Tom On Jul 3, 2014, at 2:56 PM, Rakesh Ramachandran wrote: > Hi, > > I wanted to know how can I measure correlation starting from a fit and rotating the model around an axis with respect to the map. I tried calculating the centroid of the model and then rotate it using measure correlation but it did not work, the rotationAxis field was not taking the x,y,z position of the centroid of the model. > > Regards > Rakesh

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Structure editing
by George Tzotzos 02 Jul '14

02 Jul '14

I’m dealing with a X-ray model in which some of the residues are shown in two conformations. Is it possible to edit the structure keeping the higher occupancy conformation ONLY? Another question is whether it is possible to delete all waters but the selected ones (e.g. HOH molecules in the binding pocket that are conserved). I’ve been doing this manually using an editor and I wonder if there is better way of doing this. Thanks in advance for your advice Regards George

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suggested improvements
by Dougherty, Matthew T 02 Jul '14

02 Jul '14

1) first suggestion on the sym command the following is defined icosahedral symmetry I[,orientation] around center Example: i,n25 where orientation can be: 222 (default) - with two-fold symmetry axes along the X, Y, and Z axes 2n5 - with two-fold symmetry along X and 5-fold along Z n25 - with two-fold symmetry along Y and 5-fold along Z 2n3 - with two-fold symmetry along X and 3-fold along Z 222r - same as 222 except rotated 90° about Z 2n5r - same as 2n5 except rotated 180° about Y n25r - same as n25 except rotated 180° about X 2n3r - same as 2n3 except rotated 180° about Y In the chimera tool->higher order structure -> the icosahedral structure it defines similar orientations, assume in the same order. It would be helpful on the selections to include the sym syntax as part of the icosahedral structure text ie {222} xyz 2 fold {2n5} x 2 fold z 5 fold 2) second suggestion When reading an MRC file I occasionally see situations that make me question whether the file is EMDB complaint. It would be good to have the means to dump the MRC header, even if chimera refuses to read the file in its entirety. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [Chimera-users] Attaching a Probe to Modify an Existing Amino Acid
by Eric Pettersen 02 Jul '14

02 Jul '14

Hi Shana, Well, you might be able to get away with just setting that atom's "name" attribute to "SD", but since you are writing Python code anyway and residues hold their atoms in a name-indexed structure, it would be better to do it the right way by removing the atom from the residue, renaming it, and putting it back. Assuming you have the CYS residue in a variable named 'cys': s = cys.findAtom("SG") cys.removeAtom(s) s.name = "SD" cys.addAtom(s) --Eric On Jun 19, 2014, at 11:25 AM, Shana Burstein <sburstei(a)haverford.edu> wrote: > Hi Eric, > I was able to move the CN atoms from the CN residue to the CYS residue and call it MSCN. I actually need it to be called MSCN in order for the modified residue to be recognized by a force field in an MD simulation. My only problem now is that the S atom of cysteine is labeled as "SG" and I need it to be called "SD." I know how to do this by going through the Tool menu, but is there a way to automate that? > > Thanks, > Shana > > > On Wed, Jun 18, 2014 at 2:35 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Shana, > If you were starting from scratch, the procedure to add the CN would probably be simpler by using chimera.molEdit.addDihedralAtom() to add the C and then the N at the appropriate bond length, angle and dihedral and then rename the residue with: r.type = "MSCN". Nonetheless, you have come a long way down the road with your script and probably would not prefer to start over from scratch! So let's suppose you have your two relevant Residue instances in variables named 'cys' and 'cn'. The code to do what you want would be: > > for a in cn.atoms: > cn.removeAtom(a) > cys.addAtom(a) > cys.type = "MSCN" > # empty residues are problematic in various parts of Chimera, so... > cn.molecule.deleteResidue(cn) > > If you don't know how to get the 'cys' and 'cn' variables but you know an atom specifier that selects each, you can use this code to set the variables: > > runCommand("sel atom-spec-for-cys") > cys = chimera.selection.currentResidues()[0] > runCommand("sel atom-spec-for-cn") > cn = chimera.selection.currentResidues()[0] > > There's a couple of further relevant things here. Strictly speaking, 4-letter residue names are not legal in PDB format (while there is a column where a 4th character could go, according to the format definition that column is supposed to be blank). Therefore if you export your modified structure to other software programs, they may or may not be able to handle the 4-character residue name without problems. Therefore I recommend you use the same residue name that the PDB uses for this moiety, 4CY (which can be found in the 3or0 entry). > Along the same lines, 4CY can actually be found in the SwissSidechain rotamer library plugin for Chimera (SwissSidechain - A database of non-natural side chains) and therefore if you install that plugin then the entire substitution process becomes a single command: swapnaa 4CY cysteine-atom-spec. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jun 18, 2014, at 6:50 AM, Shana Burstein <sburstei(a)haverford.edu> wrote: > >> Hello, >> I am an undergraduate student at Haverford College and I am attempting to attach thiocyanate probes onto different sites along a protein by first replacing the existing amino acid with a cysteine and then by adding a C and N onto the S- of the Cys residue. I know it is possible to carry this out manually using Tools>Structure Editing>Modify Structure, but I am hoping to automate this process by calling an external .py script that will primarily contain a list of preexisting Chimera commands. >> >> I have been successful at converting the targeted amino acid to Cys using "swapaa," building a CN residue called MSCN (using the createMolecule.py as a guide), combining the two models into one ("combine selected close True") and forming a bond between the Cys S and CN C atoms ("bond"). >> >> At this point, I am seeking help in automating the renaming of the modified residue to MSCN. Currently, Chimera sees this residue as two different separate residues called CYS and MSCN. Is there a way to combine these two structures so that the label corresponds to MSCN and the residue number corresponds to CYS? >> >> Sincerely, >> >> Shana Burstein >> Haverford College '15 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Making a hole in a volume
by Dieter Blaas 01 Jul '14

01 Jul '14

Hi, I am trying to make a small hole in a volume with 'erase octant' but either it cuts away some of the volume at the wrong place or the hole created is much bigger than the green box. Sometimes it does not do anything until I make the box bigger. What might I am doing wrong ? (chimera 1.6.2) Thanks, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Chimera-users July 2014