January 2013 - Chimera-users - RBVI Mailing Lists

Chimera 1.7 for mac
by Pat Heath 08 Jan '13

08 Jan '13

It starts to open and then quits. User was previously running 1.5 fine. Another user on the same machine can open chimera 1.7 just fine. Makes me think there is a file that needs thrown away from the other user that was generated by version 1.5. I deleted the .chimera folder, but that didn't help. Any ideas? Thanks, Pat

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Re: [Chimera-users] Stereo 3D on non-quadro GeForce cards
by Steven Ludtke 07 Jan '13

07 Jan '13

Hmm... Since I get this in digest form, not sure how to post a reply, but it may be worth pointing out that one of the biggest advantages of the passive 3D displays becoming increasingly available is that you can do windowed 3D on Win, Mac and Linux with no drivers and no special setup at all as long as the software supports it (Chimera does). They are inexpensive, and the glasses are dirt cheap (and compatible with movie-theater 3-D). The only disadvantage is the vertical loss of resolution/interpolation, but in my mind it's a very small price to pay for the ease of setup and use. ---------------------------------------------------------------------------- Steven Ludtke, Ph.D. Professor, Dept. of Biochemistry and Mol. Biol. Those who do Co-Director National Center For Macromolecular Imaging ARE Baylor College of Medicine The converse sludtke(a)bcm.edu -or- stevel(a)alumni.caltech.edu also applies http://ncmi.bcm.edu/~stevel

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Front End for NAMD?
by Rudy J. Richardson 07 Jan '13

07 Jan '13

To whom it may concern: First, my profound thanks to the creators of Chimera for a superb research and teaching tool. I am especially grateful for the excellent interface with Modeller for doing such things as creating and optimizing loops to repair chain breaks in X-ray structures; this feature is greatly improved in v. 1.7rc. I am also grateful that Chimera can be used to visualize results of MD simulations with, e.g., NAMD. However, in addition to viewing results, it would be great if Chimera could be developed to serve as an interactive GUI for setting up, running, and analyzing NAMD simulations, including steered MD, as well. There is a real need to make MD more accessible to a wider range of scientists, and it appears that Chimera could be an excellent platform for this. I realize that VMD has co-evolved with NAMD for this purpose, but VMD lacks the integration, polish, and intuitive ease of use of Chimera. Thank you. Sincerely yours, Rudy

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Re: [Chimera-users] Circular DNA minimization
by Eric Pettersen 07 Jan '13

07 Jan '13

On Jan 7, 2013, at 10:10 AM, Damien Larivière wrote: > Dear all, > > I'm still on this subject. > > I tested the command (minimize spec :275-276.E:7-8.F fragment true nsteps 0 cgsteps 1 interval 1) suggested by Conrad or Eric in their reply to the bug I submitted. It works well. > > I attach the original structure to be minimized by Chimera (Chimera_minimization.pdb). This structure poses various problems (too long O3'-P bonds for instance) and that's the reason why I want to minimize it. > > It is interesting to note that the four distorted base rings (275 and 276 chain E, 7 and 8 chain F) occured after the Steepest Descent steps. I attach the structure as it is after 100 Steepest Descent steps (Chimera_minimization_NoConjugate.pdb). > > For your information, the summary of my user experience in this specific case: > - the Steepest descent phase repaired too long O3'-P bonds > - the Steepest descent phase generated four distorted base rings > - the command minimize spec :275-276.E:7-8.F fragment true nsteps 0 cgsteps 1 interval 1 (so just one step of conjugate gradient minimization) repaired the distorted rings. The structure at the end looks like stucturally correct. With the before-minimization structure you provided, I cannot reproduce the ring distortion -- neither with 1.6.2 nor 1.8, and neither on Mac nor Windows 64. 100 steps of steepest descent with no conjugate gradient and default forcefield choices (99SB on 1.6.2; 12SB on 1.8) results in perfectly normal-looking rings in those residues. So if we can't reproduce it, the problem may not be possible for us to solve. We'll see what we can do. > May you tell me how you identified these four distorted rings? thanks to a visual inspection of the base pairs one by one? Well, if you're as familiar with Chimera as I am, you can use the Python layer to directly answer questions that no tool directly addresses. So when I noted that breaking the circularizing phosphate bridges allowed the minimization to proceed, with a big drop in energy but no noticeable movement of the newly-freed ends, I wondered what atoms had moved. Here's how I answered that question: 1) I used MatchMaker to superimpose the structure as best as possible. Since I knew which chains to match up, I used the "specific chain with specific chain" option in MatchMaker to match chain E with E and chain F with F. 2) I opened the IDLE Python interpreter (in Tools/General Controls) so I could interactively execute Python commands. In IDLE I: 2a) Fetched a list of atoms from both models: atoms1, atoms2 = [m.atoms for m in chimera.openModels.list()] 2b) Since one structure had atoms the other didn't, I needed to set up some way of matching up the atoms in one structure to the corresponding atoms (if any) in the other structure. I made a lookup dictionary of the (residue ID + atom name) to atom for one structure's atoms, that I could later use on the other structure's atoms to determine the correspondences: lookup = dict([((a.residue.id, a.name), a) for a in atoms1]) 2c) Then I run through the atoms in the other structure, and for ones that correspond to atoms in the first structure I note the distance between the atoms: dists = [] for a in atoms2: key = (a.residue.id, a.name) if key not in lookup: continue dists.append((a.xformCoord().distance(lookup[key].xformCoord()), a)) Note that since the models have been moved by MatchMaker relative to each other, I need to use xformCoord(). Also, I put the distance first in the 2-tuple, since I know I will want to sort the list next, and sorting works on the first member of a tuple first, only using later parts of the tuple in the event of ties. 2d) Sort the distances. dists.sort() 2e) Since sorting is from smallest to largest, reverse the order. dists.reverse() Then I just examined the list. For instance, "print dists[0]" showed me that the largest movement was ~0.4 angstroms. That seemed significant. "print dists[0][-1]" showed me it was one of the atoms in the four distorted residues. I went and looked at the residue and could immediately see that the distorted ring was the problem. To try to get a handle on how many large movements had occurred (which I arbitrarily decided was 0.2 angstroms) I executed this code: len([a for d, a in dists if d > 0.2]) which told me there were 25 atoms that had moved that much. Since that wasn't an overwhelming number, I just printed them all: for d, a in dists[:25]: print d, a I could see that they were all in those four residues. So that's how I found the problem residues. --Eric > > Many thanks > > Damien > > On 04/01/2013 13:27, Damien Larivière wrote: >> Dear all, >> >> Many thanks for your help on this! >> >> Just one comment about the Steepest Descent steps that did not modify anything (RMSD = 0 as Eric or Conrad said). In fact, the structure I uploaded had already been minimized with through 100 Steepest Descent steps. It resulted in the repairing of several too long O3'-P bonds and other structural deficiencies (but not the distorted base rings). This explains the RMSD equal to 0. >> >> I have a question: >> >> How did Eric or Conrad noticed that some rings were structurally deficient? I also observed these distortions but thanks to a visual inspection and, due to the size of the structure, by chance! One can use the ADIT server to know whether structural deficiencies subsist or not but this requires to make sense of a list of number. In other words, it is not said "your structure poses problem at the sugar rings at position 255 or at base ring at position 266". You were able to tell me that base rings in residues 275 and 276 of chain E and residues 7 and 8 of chain F were deficient: Is there a way in Chimera to notice that "directly" or this is just a matter of expertize? >> >> I can't test the solution before Monday as I am away of my office. If I understand correctly: >> >> - I have to remove the phosphate bridges in order the conjugate gradient phase to start?! >> >> - I have to use the fragment option to accelerate the repair of known distorted rings thanks to the conjugate gradient steps?! >> >> I wish all of you a very happy new year! >> >> Damien >> >> On 03/01/2013 23:04, Eric Pettersen wrote: >>> Okay, the executive summary for those interested is that in a case like this where minimization gets "stuck" on a large structure you may have to minimize badly distorted parts of the structure separately first by using the "fragment" option of the minimize command (not the "freeze" option in the tool or command, which still uses the remainder of the structure in the calculation). >>> >>> --Eric >>> >>> On Jan 2, 2013, at 1:34 PM, Eric Pettersen wrote: >>> >>>> On Dec 29, 2012, at 7:40 AM, Damien Larivière wrote: >>>> >>>>> Dear all, >>>>> >>>>> I'm currently minimizing a circular DNA molecule, relatively large (~11 000 atoms). I use "Minimizing structure" in Structure editing. >>>>> >>>>> The first phase, the Steepest Descent Steps, works fine. >>>>> >>>>> However, the second one, the Conjugate Gradient Steps, looks like blocked with the message "dock prep finished" at the bottom of the screen. >>>>> >>>>> If I remove one base pair so that the molecule is no more cyclized, then the second minimization stage starts as expected. >>>>> >>>>> I'm not versed in the art of minimization. Do you know the reason of this behavior? >>>> >>>> Hi Damien, >>>> I cannot reproduce this behavior. A small circular peptide (attached) minimizes fine with conjugate gradient. I need you to open a bug report (in Chimera, Help->Report A Bug) and attach the circular DNA structure. Thanks! >>>> >>>> --Eric >>>> >>>> Eric Pettersen >>>> UCSF Computer Graphics Lab >>>> http://www.cgl.ucsf.edu >>>> >>>> <circular.pdb>_______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > <Chimera_minimization.pdb><Chimera_minimization_NoConjugate.pdb>

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Edit and UnDo?
by Rudy J. Richardson 07 Jan '13

07 Jan '13

To whom it may concern: Although this would be a departure from the current menu structure in Chimera, would it be possible to add a conventional "Edit" to the menu that would be populated with actions appropriate for editing? In addition, either in a new Edit menu or in the current Actions menu, would it be possible to add a global "Undo" function? Thank you for your consideration. Sincerely yours, Rudy

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average pdb
by edu troche 07 Jan '13

07 Jan '13

Hi chimera users, I was wondering if there is any way to build an average pdb from an Amber MD simulation of a system that doesn't contain any biopolymer. I know there is a script within the Amber suite, to generate an average pdb, but I'm doing the MD in several parts, and then reimaging them, so I wanted to check if the results of the Amber script, that makes an average on the coordinate file (.rst) without centering the system, is the same that I could have after applying the reimaging-centering script. Thank you! -- Eduardo Troche Pesqueira <http://webs.uvigo.es/webqo3/people/eduardo.html> Tel. 986812309 Edificio E, Andar 3º, Laboratorio1 Facultade de Químicas Departamenteo de Química Orgánica Lagoas-Marcosende Universidade de Vigo

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Stereo 3D on non-quadro GeForce cards
by Gökhan Tolun 07 Jan '13

07 Jan '13

Hi, Is Chimera still quadro-only as the stereo-3D goes, and if so, is there ANY way of making it work with a non-quadro card? I have a 560 Ti SLI system with an ACER 27" 3D LCD monitor with active shutter glasses. Thanks. Gökhan

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Announcement: Release of DOCK 6.6
by Scott Brozell 04 Jan '13

04 Jan '13

We are pleased to announce the release of DOCK 6.6. DOCK is a suite of programs for molecular docking. In version 6.6 two new scoring functions are available: Grid-based footprint scoring and SASA-based scoring. The MultiGrid Footprint Score calculates the pair-wise interaction energies over multiple grids. Important receptor residues are initially identified with a reference ligand, and individual grids are generated to model such residues. The SASA score calculates the percent exposure of a ligand, and the percentage of the hydrophobic portion of a ligand and the receptor that are buried in the pocket. In addition, a symmetry corrected RMSD (Hungarian matching) method was added to facilitate pose reproduction studies. For full information on what is new in DOCK 6.6, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.6.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

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3DConnexion Space Navigator dead-zone
by Gökhan Tolun 03 Jan '13

03 Jan '13

Hi, Is it possible to set a dead-zone for the 3DConnexion Space Navigator in Chimera? I tried doing this using its OSX driver, but I cannot find such an option in its control panel. Thanks. Gökhan

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Circular DNA minimization
by Damien Larivière 03 Jan '13

03 Jan '13

Dear all, I'm currently minimizing a circular DNA molecule, relatively large (~11 000 atoms). I use "Minimizing structure" in Structure editing. The first phase, the Steepest Descent Steps, works fine. However, the second one, the Conjugate Gradient Steps, looks like blocked with the message "dock prep finished" at the bottom of the screen. If I remove one base pair so that the molecule is no more cyclized, then the second minimization stage starts as expected. I'm not versed in the art of minimization. Do you know the reason of this behavior? Thanks for your help, Damien ps: I'm working on Windows 7 with a core i5

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Chimera-users January 2013