- Chimera-users - RBVI Mailing Lists

Rendering by arbitrary attributes in external file
by Healey, Joe 03 Jan '19

03 Jan '19

Hi chimera team, I use the Render by Attribute function frequently for models, but to date, I have only ever used it for rendering attributes determined 'internally' by chimera (hydrophobicity, AA conservation from an MSA etc). Is there a way to render residues by an arbitrary set of parameters? Imagine for instance, I have a csv that maps a residue number to a value (between 0 and 1). In my case this is antigenicity. ResNum, Res, Value 1, A, 0.927 2, T, 0.872, 3, W, 0.738 ... Can I read this file in via python/chimera commands and apply these values from an external file? Many thanks Joe Healey M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

2 1

fitting antibody and envelope protein structures to EM map of virus: C3 and icosahedral symmetries
by Kent, Michael S 02 Jan '19

02 Jan '19

I have an EM map for a virus that includes an antibody bound to the envelope proteins. The envelope proteins are trimers of dimers with C3 symmetry that form spikes on the surface of the virus. I fit an atomic model for the spikes to the map using icosahedral symmetry, following the very helpful symmetric fitting video tutorial<http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/>. Now I am trying to fit a model for the antibody into the spike regions of the map. I need to impose C3 symmetry for the antibody for the fit into each spike, in addition to imposing icosahedral symmetry to include all the spikes. How can I impose both of these in the fit? Thanks, ?Mike Kent

2 1

MD animation of electrostatic map
by Bala subramanian 02 Jan '19

02 Jan '19

Dear Chimera users, I have a series of structures (tens of snapshots from MD) for which i have calculated the electrostatic potential (with APBS). I would like to know if there is any way,for instance using MD-movie plugin, to map the elect. potential corresponding to each structure so that i can actually visualize the changes in surface potential. All structures have been already fitted to a reference structure, hence there wnt be any rotation or translation. Any idea or trick to achieve such mapping would be greatly appreciated. Thanks, Bala -- C. Balasubramanian

2 1

Adding Heme ligand to protein pdb
by Yangqi Gu 01 Jan '19

01 Jan '19

Dear Chimera users, I have a pdb file of my protein, but not showing the binding ligand (Heme). I know where the binding motif is and I am wondering is there a way I can add ligand to the binding motif and write out the new pdb file in Chimera? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

3 8

H bonds
by kloe brathon 31 Dec '18

31 Dec '18

Dear Chimera users, I want to calculate H bonds between the ligand of my protein and its nearby residues. Could you give any suggestions on how to select this residues and calculate H bonds between them and the ligand? Kind regards,Kloe

2 3

Visualizing SwissDock clusters.dock4.pdb
by Francesco Pietra 31 Dec '18

31 Dec '18

Hi all I am trying to open sequentially with chimera the various clusters generated by SwissDock (file clusters.dock4.pdb in the output). I was only able to extract clusters from clusters.dock4.pdb and view them, one by one, with chimera. Or a way to highlight the varius pdbs from loading clusters.dock4.pdb and target.pdb, in order to see where they are located. The web gui by SwissDock was much too grob. Thanks for advice francesco pietra

2 1

Re: [Chimera-users] Help on removing ligand on a pdb file with protein in complex with ligand and viewing the conformational change
by Elaine Meng 26 Dec '18

26 Dec '18

Dear Kei Onn, When you open the structure in Chimera, the conformers are already separate submodels, and it looks like they are already superimposed. Also you can delete the ligand residue in all submodels at the same time using the ligand residue name, which is “PKA” according to the the information for this structure at the RCSB PDB: <http://www.rcsb.org/structure/2MGY> I.e.Chimera command: delete :pka However, you need to consider what makes scientific sense. If you just delete the ligand, Chimera is not going to predict the change in the rest of the structure, so it will just look exactly the same as it did before except without ligand. Instead you should search the PDB for a structure of the same or similar (e.g. homolog in different species) protein that has been solved without the ligand. Then you would actually have something different to compare to the structure(s)with the ligand. One way to search is with Blast Protein in the Chimera menu under Tools… Sequence. You have to look through the results and figure out which ones do and don’t have ligand. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/blast.html> I’m sure there are other ways to look for related structures, so you could certainly use other programs or websites to do that. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 24, 2018, at 6:55 PM, #LAI KEI ONN# <KEIONN001(a)e.ntu.edu.sg> wrote: > > Dear Elaine, Eric, Chimera Team and fellow users > > Thank you very much for the great work in developing Chimera! > I was wondering if there's a way in Chimera for me to visualise my protein of interest without the ligand bound to it and for me to visualise it's original unbound conformation ( so that i can compare bound and unbound protein). > > In addition, i realised that the PDB file has 20 conformers of the protein-ligand complex. > Therefore I thought that my steps/strategy would be > • split the 20 conformers into submodels > • del ligand and to do a loop on it for the 20 submodels. > • superimpose all 20 conformers (unbound) vs 20 conformers (bound with ligand) > > Please advice if my steps are right or I am missing something. > > PDB file is 2MGY > > Thank you! > > Once again really appreciate all the work and technical advice provided for Chimera > Best > Kei Onn

2 1

Changes in protein stability
by kloe brathon 25 Dec '18

25 Dec '18

Dear Chimera Users, I am studying on aprotein and its interactions with its ligands and I want to explore what wouldbe the effect on protein thermodynamic stability if some parameters were changed such asaddition, removal of hydrogen bonds or other forces. Any idea on how to dothat? I am new on this. Thank you on advance! Kloe

3 4

Topology error
by Gonzalez Fernandez, Cristina 19 Dec '18

19 Dec '18

Dear Chimera users, I want to perform molecular docking by using Swiss Dock. Therefore, I have used Chimera to remove the molecules that I don't want from the PDB file, add hydrogens and save as mol2. However, when I tried to upload the mol2 file in SwissDock I get this error: "Ligand setup failed. Please check that your structure file has a correct topology. No extra info available". Does anyone know what I am doing wrong? Thank you in advance, C.

2 3

Script to minimise the binding site
by Miro Moman 18 Dec '18

18 Dec '18

Hello, I would like to minimise the binding site including ligands, cofactors and water molecules. I have the following script: ___ runCommand("open " + pdbpath + pdbid + "_chimera.pdb") runCommand("findclash 'ligand | solvent' test '~ligand | ~solvent' overlapCutoff -1.0 hbondAllowance 0.0 intraMol false selectClashes true") runCommand("sel up") runCommand("namesel tomin") runCommand("minimize spec tomin fragment true cache true prep true freeze :@ca cgsteps 0") runCommand("write format pdb #0 " + pdbpath + pdbid + "_min.pdb") runCommand("write format mol2 #0 " + pdbpath + pdbid + "_min.mol2") ___ I am facing two issues: 1) Water molecules are deleted by prep. Is there as way of preventing this. I have tried creating a custom preferences file like: echo "{'AddCharge': {'charge method': 'Gasteiger'}," > ${DIR}/chimera_preferences #echo " 'DockPrep': {'delete solvent': 'false'}," > ${DIR}/chimera_preferences echo " 'DockPrep': {'incomplete side chains': 'rotamers'}}" >> ${DIR}/chimera_preferences However, the second option is not recognised. Does it exist and, if so, what would be the correct syntax? 2) The second problem is that the selection is ignored and every atom except CAs is minimised. Another option I have tried be setting prep to false and running it beforehand: models = chimera.openModels.open(pdbpath + pdbid + "_chimera.pdb") prep(models, delSolvent=False) But, again, if I do this, the selection is also ignored. Best, Miro -- Edelmiro Moman, PhD South Ural State University - SUSU Южно-Уральский государственный университет - ЮУрГУ Phone: +7 902 614 73 77 E-mail: miromoman(a)gmail.com https://www.linkedin.com/in/edelmiro-moman-3a9979a/

3 5