- Chimera-users - RBVI Mailing Lists

View Dock plugin
by James Starlight 22 Apr '13

22 Apr '13

Dear Chimera users! I have a question about the View Dock plugin. >From some servers usually I've obtained pdb file of the target protein as well as separate file consisted of all predicted posses which I can visualize in Chimera. So I wounder to know 1- How I could hide hydrogen bonds as well as protein's side chains of the residues which are in contact with the ligands ( on the default both of that two options are turned ON) 2- How I could properly save some poses as the separate pdb models ? E.g when I chose to same target.pdb with the #1_pose from the chimera saving menu I obtain protein and ligand with the surrounded residues as two models in one pdb file ( so I must manually merge it in one model and delete residues from the second model). Does it possible to obtain protein-ligand complex as one model as the output? Thanks for help, James

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multiple volumes' orientation in space
by Yunji Wu 22 Apr '13

22 Apr '13

Dear all -- I am a total newb to Chimera, and I have an issue which I feel like can be easily resolved with your help. I am trying to make a 'structure-based schematic' with the purpose of clarifying the locations of the domains of a complicated crystal structure. There are 12 domains in this structure that I want to represent as 'blobs', and they are oriented in space in a very confusing way, especially if represented as the standard ribbons or cartoons. I used pdb2mrc (in EMAN2) to create 25Å maps from my .pdb files for (with the command e2pdb2mrc.py -R 25 H.pdb K.mrc). These show up fine individually in Chimera, but the separate maps are not oriented properly in space. It looks like the map volume files have no instructions about where to be in space relative to the coordinate files that generated them. If I take a single .pdb file with all 4 chains and generate a single .mrc file, I obviously get something that has the chains correctly oriented. This is less useful and satisfying, since I'd like to make separate chains into separate map volumes so I can color them separately (for example: chains H,K,L,M as H.pdb, K.pdb, L.pdb, M.pdb into H.mrc, K.mrc, L.mrc, M.mrc). When these 4 volumes are plotted in Chimera, they appear to be semi-randomly piled in the middle of the viewing field, with no correlation to the original pdb coordinates (attached screenshot of volumes from 4 chains, calculated from 4 individual pdb files). Is this just a result of a preset in Chimera that I am not aware of that needs to be adjusted? If I plot the original pdb file with the 4 chains from which these volumes were generated, there is no spatial correlation between the structure and the volumes. In trying to solve this, I know that "Fit to Map" will allow the coordinates to be fit into the map volume, but I cannot seem to fit the separately map to the individual chains, which would be a longer way around the issue. Is there some way to do this, or to just create maps that are oriented properly in space relative to each other? Thank you so much for your help, Yunji Wu

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Radius of gyratiion
by George Tzotzos 22 Apr '13

22 Apr '13

Hi everybody, I've search the archive to find a script for measure protein radius of gyration. I came across the following link: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007257.html I'm now trying to find the actual script <radius-of-gyration.py>. Any ideas how to retrieve it? Many thanks in advance George

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euler angle
by Jingchuan Sun 19 Apr '13

19 Apr '13

Hi, After I rotate a volume to a specific orientation, and "save map as" in "volume viewer", the saved volume are still in the original orientation. Could I save it in the new orientation. If I could display the current euler angles, I can rotate it in other software. But how could I display euler angle after rotation? Thanks! Jim

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Doubt
by Víctor J. Gallardo López 19 Apr '13

19 Apr '13

Good Morning Mr./Ms., I have a bit problem with the molecular modeling. I have a dímer (the two chains of this protein are the same sequence) and I want to put 34 residues at the N-terminal in each chain. I load my fasta (with this residues addition) in chimera and I blast a protein structure in the PDB that has the same residues as my protein without this addition. When I modeller (homology) my fasta, the programm only gives me one of the chain with this addition but I need the whole protein (with the two chains and with this residue addition for each chain as well). How can I do it? I hope you resolve my problems. Thanks you for you attention. Sincerely, Víctor J. Gallardo

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Generating trajectory of a user-defined plane
by Lili Peng 18 Apr '13

18 Apr '13

Hi, I am interested in measuring the deviation of an helical segment with respect to the initial structure in a GROMACS trajectory. I have already uploaded my *.tpr and *.trr files into MD Movie and have defined a plane through the helical segment within the initial structure. Is it possible to define another plane through the same helix and track the intersection angle throughout the trajectory? Thank you, Lili

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python script running OUTSIDE chimera possible?
by frederick lee 18 Apr '13

18 Apr '13

hello chimera experts, as far as i know, python scripting for chimera is done within the context of chimera like chimera --nogui myscript.py parameters ... is it possible to run myscript.py without the need of the chimera executable and use import statements of some sort to access the chimera module(s) like python myscript.py parameters best regards, fred

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selecting amino acids and labeling
by Gonzalez, Mireya 18 Apr '13

18 Apr '13

To whom it should concern I am working on some docking structures. Previously I used to have Quimera version 1.7 installed in my computer. Recently I downloaded the version 1.8 but I am having problems identifying the amino acids that are in contact with my compound using the cursor. This function is inactivated. Furthermore if I hold the key Ctrl for selecting them and labeling it is also not doing it at all. Any help with this issue will be greatly appreciated. Mireya Gonzalez

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question
by sunwei_223 18 Apr '13

18 Apr '13

Dear sir I have some question in using your excellent Chimera. How can i set 5 symmetry to a 3 symmetry map? thank you

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AutoDock Vina and hydrogens
by Elaine Meng 16 Apr '13

16 Apr '13

Hello, Users of the AutoDock Vina interface in Chimera 1.7 should be aware of a potential "gotcha": the structures should include hydrogens, at least the "polar" (potentially H-bonding) ones. For the receptor, this is generally taken care of because the "add hydrogens in Chimera" option in the AutoDock Vina interface is turned on by default. However, there is no corresponding option for the ligand in that interface: instead, you need to add hydrogens to the ligand beforehand, for example with Chimera AddH. Polar hydrogens are needed for Vina to correctly recognize the atom types, to correctly calculate docking scores. In the current daily build (and for future releases) we have built in more protections so that if there are no hydrogens and you haven't added them with Chimera, they will still be added by the AutoDock prep scripts before the docking calculation. Recent fixes: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html#bug_fixes> Download the daily build: <http://www.cgl.ucsf.edu/chimera/download.html#daily> Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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