October 2014 - Chimera-users - RBVI Mailing Lists

Applying settings from one molecule to another
by Oliver Clarke 28 Oct '14

28 Oct '14

Hi, Is it possible (or if not, might it be worth considering in a future version) to apply the display settings (colors, ribbon/stick display etc) from one molecule to another? I’ thinking particularly about a case when one develops a figure with quite complicated coloring and so forth, saves it as a session (potentially with multiple views etc), and then obtains a new, better set of coordinates (from a later refinement, for example). Obviously such a feature would only apply to the atoms in common between the two models (if they are allowed to differ at all), but I feel like this would be a very handy feature to have. Best, Oliver.

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fiting onto density map
by Urszula Uciechowska 28 Oct '14

28 Oct '14

Dear Chimera users, I am trying to fit my protein structure onto an density map. I loaded both the map file and my model coordinates into Chimera. But it looks apparently that they are not in the same size scale. My model is much bigger than the size of my map region where the model is supposed to reside. I suspect the density map size is scaled down somehow. I did a little research on internet but couldn't find a solution. Could you please advice me how to put them to the same size scale? Does anyone can help me here? Best regards Urszula ------------------------- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/

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visualising electron density map
by Neha Gandhi 28 Oct '14

28 Oct '14

Dear Support, I have downloaded pdb file 3j5r and also downloaded corresponding electron density map from EMD (http://www.ebi.ac.uk/pdbe/entry/EMD-5777) The microscopy structure was done in presence of the ligand and the original paper reports electron density for the ligand (Extended figure 7 - http://www.nature.com/nature/journal/v504/n7478/fig_tab/nature12823_SF7.html) However, the authors couldn't model the orientation of ligand in the binding site. I have docked the ligand in the binding site and I am trying to visualize if the docked ligand fits well in the electron density or not. Is there a way to visualise the electron density only for the ligand in UCSF chimera as reported in the above nature paper? Thank you for kind attention, Awaiting your reply, Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate

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Re: [Chimera-users] aligning PDB file
by Eric Pettersen 27 Oct '14

27 Oct '14

openModels.list doesn't necessarily return the currently open models in any particular order. The if/else part of the code is testing whether the first model in the model list has model ID 0. If it does then it assigns the first model to m0 and the second model to m1. Otherwise, it makes the reverse assignment -- so m0 will always contain model 0 (the code assumes there are only two models open). As per the example in that mail, chain A of model 0 had been superimposed on chain B of model 1. That's why the "chains" were set to "[m0.sequence('A'), m1.sequence('B')]" for handing off to makeAlignment -- those were the chains desired in the alignment. Are you saying you don't know which chain from each PDB file to use? How do you know which to superimpose then? --Eric On Oct 27, 2014, at 4:05 PM, Sanjeev Sariya <s.sariya_work(a)ymail.com> wrote: > Thank you Eric for the URL. > Could you please help me understand what is going on here? > from chimera import openModels, Molecule # import > > models = openModels.list(modelTypes=[Molecule]) # array for model- different PDBs > > if models[0].id == 0: # what does this do? > m0, m1 = models > > else: # > m1, m0 = models # why interchanged the m1, mo? > chains = [m0.sequence('A'), m1.sequence('B')] # how do I know how many chains are present in PDB file? > > > > > > > On Monday, October 27, 2014 6:35 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > Hi Sanjeev, > Take a look at this chimera-users message: [Chimera-users] easy way to make alignments in chimera . I think it answers most of your questions. The only change you would need to make is that where it uses "saveStockholm" you would instead use "saveFASTA". > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Oct 27, 2014, at 2:25 PM, Sanjeev Sariya <s.sariya_work(a)ymail.com> wrote: > >> Hi Chimera Developers, >> >> I've used chimera mostly by GUI inerface [click]. >> How do I get the match-align work from command line in a python script? >> I read a good description at: >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html >> >> work flow of the script is: >> take in 2 pdb files and match->align them. >> >> I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ? >> >> How do I get the output saved in a FASTA file without MAV interface? >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > >

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aligning PDB file
by Sanjeev Sariya 27 Oct '14

27 Oct '14

Hi Chimera Developers, I've used chimera mostly by GUI inerface [click]. How do I get the match-align work from command line in a python script?I read a good description at: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html work flow of the script is:take in 2 pdb files and match->align them. I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ? How do I get the output saved in a FASTA file without MAV interface?

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fiting onto density map
by Urszula Uciechowska 27 Oct '14

27 Oct '14

Dear Chimera users, I am trying to fit my protein structure onto an density map. I loaded both the map file and my model coordinates into Chimera. But it looks apparently that they are not in the same size scale. My model is much bigger than the size of my map region where the model is supposed to reside. I suspect the density map size is scaled down somehow. I did a little research on internet but couldn't find a solution. Could you please advice me how to put them to the same size scale? Best regards Urszula ------------------------- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/

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Double structure while loading the pdb file
by Sanjeev Sariya 27 Oct '14

27 Oct '14

Hi Members/Developers, I loaded pdb file 1U19- Bovine Rhodopsin. structure is double the length what is to be. On terminal, on doing color red: 113 I see that 2 residues are colored. Why there are 2 molecules in same file? How do I hide one molecule?

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CASTp
by George Tzotzos 24 Oct '14

24 Oct '14

I’m trying to measure to volume and the solvent-exposed area of the binding site of proteins 4fqt and 3n7h. I’m trying to fetch the structures from CASTp to no avail. CASTp informs that these structures are not in its database. I’ve loaded the structures on Chimera but could not find a way to evoke CASTp. Any suggestions would be most helpful. Best regards George

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Combine maps
by Jian Guan 24 Oct '14

24 Oct '14

Hi all, Can I combine two mrc maps into one? And the two maps are with different pixel size. One is 1.48 A, the other is 2.33 A. I want to combine the two into one with pixel size of 2.33 A. I tried segmentation, and made two maps. But I failed to combine them. Can anybody help me for that? Thanks. Sincerely yours, Jian

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change size of a shape
by Jean-Didier Maréchal 22 Oct '14

22 Oct '14

Dear all, I would like to animate a sphere that grows. But I could alter the dimension of an object created with the shape command? thank you JD

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