- Chimera-users - RBVI Mailing Lists

Cannot load trajectory in chimers executed through cytoscape
by Natesh Singh 15 Jul '16

15 Jul '16

Dear Sir/Madam, I am not able to load the MD trajectory, either in PDB or XTC in the chimera that was executed from cytoscape. When I define the path for the files, it says 'reading pdb...' but the trajectory never gets loaded into the screen. and this is happening in both linux and windows. Kindly guide me on this that how can I run the trajectory in chimera from cytoscape to analyze the residue interaction network. Best regards, Natesh

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Re: [Chimera-users] error: more than 63 chains; cannot uniquely identify with single characters
by Elaine Meng 15 Jul '16

15 Jul '16

On Jul 15, 2016, at 7:39 AM, Wu, Weimin (NIH/NIAMS) [E] <weimin.wu(a)nih.gov> wrote: > Dear Elaine, > I have a pdb structure with four chains A, B, C, D. and an icoshedral cryo-EM density map. I fit the pdb into the map, and generate 60 copies. I try to merge all these 60 pdbs into a combination, but without renumbering the residues (choose "retain the name" option). I did this operation before without any error, but now it came with the error "more than 63 chains; cannot uniquely identify with single characters". > > If choose renumber the residues, then the merged is not easy to understand, not easy for comparison either. > > Is there any other way to do it? Thank you, > Weimin On Jul 15, 2016, at 8:43 AM, Wu, Weimin (NIH/NIAMS) [E] <weimin.wu(a)nih.gov> wrote: > Or easy to understand, can we add model number into the pdb as done in biological assembly pdb structure 1qgt.pdb1? Hi Weimin, I’m not sure how you made the copies, but if they are atomic structures I think this will work: Similar to what you said in your second message, instead of merging into a single model, simply keep all the models separate. You can still save to a single “multi-model” PDB file with the main menu: File… Save PDB (or just save the Chimera session for later). Then the copies will still all have chain IDs A,B,C,D which may be easier to work with anyway. I tried this with 1pov (which has chains 0,1,3) and with “sym” made the whole assembly with 59 more copies for 60 total. I looked in the model panel and they were models #0 (original) and #1.1-59 (copies). I saved as single PDB file and read it back in, and again had those same 60 models, each with the original chain IDs 0,1,3. It is recommended you send questions to chimera-users(a)cgl.ucsf.edu (CC’d here) instead of just me because I am not the expert on everything. :-) I hope this helps, 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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Distances measurement for NMR ensemble
by James Starlight 15 Jul '16

15 Jul '16

Dear Chimera Users! I wonder to ask whether it possible to calculate distances between two selected atoms by means of the Chimera's Distance measurement tool providing as input NMR-ensemble consisted of 20 snapshots (without any additional files like topology!) or alternatively small md trajectory, obtaining also some elementrary statistics (E.g RMSD etc) Thanks! James

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RMSD of protein-protein interphaces
by James Starlight 12 Jul '16

12 Jul '16

Dear Chimera users! Having several docking poses of 2 proteins I need to estimate RMSD difference between their interphaces (e.g like what I have seen in Capri) Is it possible to do it via some Chimera's plugin e.g in combination with the contact-maps plugin? Thanks! Gleb

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Structural matching of Side-chain selection
by James Starlight 12 Jul '16

12 Jul '16

Dear Chimera users! I need to estimate how the side-chains dynamics are differs in MD compared to X-ray structure. Assuming that I have 2 structures one from md and another from X-ray and I select Sidechains from the both as obj1 and obj02 is it reasonable just to match them using MatchMAker? Thanks! James

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Is it possible to compile python script to an executable file?
by xibei 11 Jul '16

11 Jul '16

Hi, On my computer(debian) I can run "chimera main.py" to run my program. But I also want to submit missions to the server (debian) where only python is installed, chimera is not. Therefore I wonder if it's possible to compile my python script to an executable program so that it can run on another computer without chimera but with python.. Thanks!

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Re: [Chimera-users] Color surface by underlying atom
by Oliver Clarke 08 Jul '16

08 Jul '16

Hi Kyle, Using "Values at Atom Positions" ( http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.h…) will create an atom attribute corresponding to the density value at each atom position. Then you should be able to use "Select by attribute" to select all atoms above/below the desired threshold. Cheers, Oli. Dear Chimera-dev and users, > > Does anyone now of a way to select only the atoms of a PDB that fall inside the displayed density of a volume? > > Thanks in advance! > > Best wishes, > Kyle > >

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select only PDB atoms that fall inside density
by Morris, Kyle 08 Jul '16

08 Jul '16

Dear Chimera-dev and users, Does anyone now of a way to select only the atoms of a PDB that fall inside the displayed density of a volume? Thanks in advance! Best wishes, Kyle

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About findclash in detecting overlap of atoms
by xibei 06 Jul '16

06 Jul '16

Hi, I'm trying to use command "findclash" to check the excluded volume effect by detecting overlaps between atoms. The command I use is "findclash #0 test #0" or "findclash #0 overlapCutoff value test #0", but I found that two close atoms (14C,16C, dis=0.8) are not identified as "overlaped" while another two atoms (11C, 16C, dis=1.8) whose distance is larger are overlaped... Is there anything wrong about understanding the overlap? Example molecular (init.mol2): @<TRIPOS>MOLECULE init.mol2 20 19 20 0 0 NUCLEIC_ACID NO_CHARGES @<TRIPOS>ATOM 1 C 14.7888 10.0072 -5.6663 C.3 1 DA 0.0000 2 C 15.4013 8.5150 -3.5012 C.3 2 DA 0.0000 3 C 13.7388 8.7698 -5.6133 C.3 3 DA 0.0000 4 C 14.6414 7.5770 -3.3654 C.3 4 DA 0.0000 5 C 12.9675 5.9273 -2.0359 C.3 5 DA 0.0000 6 C 13.6457 4.0155 -0.2544 C.3 6 DA 0.0000 7 C 12.8822 2.8588 2.0634 C.3 7 DA 0.0000 8 C 11.7541 3.3958 4.4562 C.3 8 DA 0.0000 9 C 11.2290 4.5854 6.8231 C.3 9 DA 0.0000 10 C 13.8907 4.6510 7.2730 C.3 10 DA 0.0000 11 C 15.5581 5.2490 9.3114 C.3 11 DA 0.0000 12 C 17.8150 4.7800 10.7177 C.3 12 DA 0.0000 13 C 18.0666 2.1205 10.3271 C.3 13 DA 0.0000 14 C 16.9288 4.4119 9.4640 C.3 14 DA 0.0000 15 C 14.9471 3.0788 10.7232 C.3 15 DA 0.0000 16 C 16.7345 3.9070 8.8773 C.3 16 DA 0.0000 17 C 15.5384 2.3512 10.7314 C.3 17 DA 0.0000 18 C 16.0476 1.4159 8.2501 C.3 18 DA 0.0000 19 C 17.5152 1.5369 5.9877 C.3 19 DA 0.0000 20 C 17.5650 3.1811 3.8468 C.3 20 DA 0.0000 @<TRIPOS>BOND 1 1 2 1 2 2 3 1 3 3 4 1 4 4 5 1 5 5 6 1 6 6 7 1 7 7 8 1 8 8 9 1 9 9 10 1 10 10 11 1 11 11 12 1 12 12 13 1 13 13 14 1 14 14 15 1 15 15 16 1 16 16 17 1 17 17 18 1 18 18 19 1 19 19 20 1 @<TRIPOS>SUBSTRUCTURE 1 DA 1 RESIDUE 4 A DA 1 ROOT 2 DA 2 RESIDUE 4 A DA 2 3 DA 3 RESIDUE 4 A DA 2 4 DA 4 RESIDUE 4 A DA 2 5 DA 5 RESIDUE 4 A DA 2 6 DA 6 RESIDUE 4 A DA 2 7 DA 7 RESIDUE 4 A DA 2 8 DA 8 RESIDUE 4 A DA 2 9 DA 9 RESIDUE 4 A DA 2 10 DA 10 RESIDUE 4 A DA 2 11 DA 11 RESIDUE 4 A DA 2 12 DA 12 RESIDUE 4 A DA 2 13 DA 13 RESIDUE 4 A DA 2 14 DA 14 RESIDUE 4 A DA 2 15 DA 15 RESIDUE 4 A DA 2 16 DA 16 RESIDUE 4 A DA 2 17 DA 17 RESIDUE 4 A DA 2 18 DA 18 RESIDUE 4 A DA 2 19 DA 19 RESIDUE 4 A DA 2 20 DA 20 RESIDUE 4 A DA 1 Best Wishes! Jiying Jia

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Color surface by underlying atom
by Tom Zhang 06 Jul '16

06 Jul '16

Hello, I have a question about surface coloring. I've noticed that when I create surfaces in a session for the first time, the surface are colored based on the colors of the underlying atoms. However, after setting the surface colors manually, I couldn’t find a way to change the colors back. I have tried settings in surface attributes, but none of them work. So my question is, how do I change the surface color back so that it is based on the underlying atoms? Many thanks, Tom

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