June 2017 - Chimera-users - RBVI Mailing Lists

Hidden water molecules
by Michael Sharkey 11 Apr '19

11 Apr '19

Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike --

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Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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Define Plane
by Catherine Jenifer Rajam Rajendran 01 Jul '17

01 Jul '17

Hi, I am trying to understand how the plane is defined in chimera. Can you please help me with that? "Define a plane for the specified <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> atoms. Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane)." Define a plane for the specified <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> atoms. - specified atoms, i use 'sel protein' Eigenvectors/values are calculated from the atomic coordinates - atomic coordinates, so x,y,z coordinates of all atoms. (Can you please explain a bit more like how and what you read from PDB file to define plane). after subtracting the position of their non-mass-weighted centroid - how is non-mass-weighted centroid is calculated The plane is anchored at the centroid - which centroid is this? Is the protein moved to the origin(0,0,0) position? Thanks, Catherine

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Fwd: pdb-l: EMBL-EBI user survey
by Eric Pettersen 28 Jun '17

28 Jun '17

> Begin forwarded message: > > From: Gerard DVD Kleywegt <gerard(a)xray.bmc.uu.se> > Subject: pdb-l: EMBL-EBI user survey > Date: June 27, 2017 at 3:30:30 AM PDT > To: pdb-l(a)ucsd.edu > Cc: Gerard Kleywegt <gerard(a)xray.bmc.uu.se>, "Gerard Kleywegt \(EBI account\)" <gerard(a)ebi.ac.uk> > > Dear colleagues, > > EMBL-EBI (http://www.ebi.ac.uk/) is running a worldwide survey to understand > usage of its resources (there are several dozen, including UniProt, Ensembl, > ChEMBL, EuropePMC, PDBe, EMDB/EMPIAR and many more). We would like to ask you > to forward this request within your department, company or institution. We are > interested in responses from a wide range of scientists, in particular those > who do not think of themselves as bioinformaticians. The results are extremely > valuable to EBI in helping us to understand our users, and our users' needs. > > Here is the link to the survey: > https://www.surveymonkey.co.uk/r/2017_EBI_survey > > Many thanks! > > --Gerard > > --- > Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK > Head of Molecular and Cellular Structure > gerard(a)ebi.ac.uk pdbe.org emdb-empiar.org > PA: Pauline Haslam pdbe_admin(a)ebi.ac.uk > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo/pdb-l .

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Difference between Chimera and ChimeraX
by Bon Ikwuagwu 26 Jun '17

26 Jun '17

Hello, I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful. Best, Bon Ikwuagwu -- Bon Ikwuagwu PhD Student, Chemical and Biological Engineering Northwestern University

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Libfftw3.so.3
by Robert Waugh 26 Jun '17

26 Jun '17

Hello, I am a Masters Student from Kingston University, I am currently using Chimera as part of a Bioinformatics Project. For this project, I have decided to use IMP to integrate the data I have to make a coarse grained model. Unfortunately, upon using MultiFit I receive the error which I have posted below which states that I cannot open the shared object file libfftw3.so.3. I was wondering if it would be possible if you were to make this file available so that I can complete my Multifit Modelling. https://pastebin.com/kkRW6X3U Thank you, It would be much appreciated, Robert Waugh

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Trying to change dihedrals: ValueError: bond is part of a cycle
by Nikolaos Bismpikos 26 Jun '17

26 Jun '17

Hey, my goal is to change the dihedrals of an already existing pdb template in order to find low-energy protein conformations. The issue I have here is that for some residues the dihedrals phi and psi cannot be changed. That's the error I get: Traceback (most recent call last): File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line 683, in init chimera.openModels.open(a, prefixableType=1) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1929, in open models = func(filename, *args, **kw) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1299, in _openPython loadFunc(sandboxName, fileName, f) File "predictor.py", line 40, in <module> es.main_loop(); File "/home/nick/Python/pdb/AbstractOptimizer.py", line 97, in main_loop self.fs, self.evals, self.terminate = self.eval_pop(self.eval_func,self.pop,self.evals,self.eval_budget,self.extra_par) File "/home/nick/Python/pdb/eval_energy.py", line 20, in eval_energy allR[j].phi = pop[i,j]; File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py", line 98, in setPhi _setAngle(bond, phi, getPhi(res, missingIsError=True), "phi", anchorSide) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py", line 147, in _setAngle br = BondRot(bond) ValueError: bond is part of a cycle Is there a way to determine beforehand which bonds are part of circle and hence which residues' dihedral information cannot be changed? Thank you in advanced for your time, Nikolaos Bismpikos

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Chimera to Excel
by Fábio Pereira 24 Jun '17

24 Jun '17

Good Afternoon, I would like to know if i can to export informations opened in View Dock to Microsoft Excel. If this is possible, how can i do ? great!

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DockPrep sometimes fails with altPos
by Visvaldas Kairys 23 Jun '17

23 Jun '17

Dear Chimera users and developers, I’d like to point out I often have a minor inconvenience when dealing with high resolution Xray structures when trying to add hydrogens via DockPrep. If two consecutive residues have both alternative postions A and B, Chimera in the process of hydrogen addition often gets confused and puts “TER” between the residues, also reporting non-integer charges in the log. I think what is happening, the program picks “A” variant for one residue and “B” for the consecutive residue, and apparently this causes bond detection algorithm to ignore the bond between the residues (due to length I guess). I resolve this by manually editing out one of the AltPos (say, “B”) out of the PDB file for the offending residues, but I guess the program should be able to do it automatically. A PDB example where this happens is 2r3i (or 2r3r). Best regards, Vis

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strand inside and edge color
by Kyle Morris 23 Jun '17

23 Jun '17

Dear Chimera dev, Sorry if I missed this in the documentation and online… Is it possible to make the inside and side edges of strands a color independent of the models coloring? Akin to using ribinsidecolor white to color the inside of helices white, I would like to color the inside and side edges of strands white. Thanks for your help as always! Best wishes, Kyle

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