- Chimera-users - RBVI Mailing Lists

Finding and depicting intermolecular interactions
by Henrique C. S. Junior 27 Mar '16

27 Mar '16

Dear Chimera list, I'm Interested in finding and showing halogen bonds and pi stackings. Is that possible? Attached is an example made using Schrodinger's Maestro. Thanks in advance -- *Henrique C. S. Junior* Químico Industrial - UFRRJ Mestrando em Química Inorgânica - UFRRJ Centro de Processamento de Dados - PMP

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Re: [Chimera-users] resolution distribution on density maps
by onetwo 24 Mar '16

24 Mar '16

Dear Elaine, Thank you very much for your reply. It is really helpful. Thanks and Regards Shivushiv On Fri, 25 Mar 2016 01:38:05 +0530 "onetwo" wrote >Hi All, > > I have seen images in several papers, where the authors present resolution distribution for the density maps obtained by cryo-EM. I wanted to know to how to make these images for a low resolution cryo-EM map in Chimera. > > Thanks and Regards > > Shivushiv Get your own FREE website, FREE domain & FREE mobile app with Company email. Know More >

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resolution distribution on density maps
by onetwo 24 Mar '16

24 Mar '16

Hi All, I have seen images in several papers, where the authors present resolution distribution for the density maps obtained by cryo-EM. I wanted to know to how to make these images for a low resolution cryo-EM map in Chimera. Thanks and Regards Shivushiv

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Fwd: Center of model/volume shifts
by Elaine Meng 23 Mar '16

23 Mar '16

Hi Preeti, It might not be a bug if the models were somehow moved separately. Similar to my previous response on chimera-users to a slightly different question, it may be possible to bring them back into register by by (A) copying the transformation of the original map to the filtered map, e.g. command: matrixcopy #N #M … where N is the model number of the original map and M is the model number of the filtered map (see model numbers by showing the Model Panel from the Favorites menu). or (B) by resetting all model positions, e.g. command: reset If neither of those work, it would be helpful if you would report (to the chimera-bugs email address) which version of Chimera you are using (e.g. from the “version” command) and what series of steps can be used to reproduce the problem. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: Preeti Gipson <gipsonpreeti(a)gmail.com> > Subject: Center of model/volume shifts > Date: March 22, 2016 at 5:39:36 PM PDT > To: chimera-bugs(a)cgl.ucsf.edu > > Hi, > I notice an error in recalling the position/center of the volume map (please see image). > > If I apply a low pass filter/mask etc and open the volume it does not overlay the current map. I never came across this issue with the same operations. I have tried restarting session, chimera & even updating. > > It will be great to have your suggestions to fix this issue, as you can imagine. It basically means redoing an entire session, especially if pdb structures have been fit in the model. > > Thanks, look forward to possible solutions. > > Thanks, > Preeti > -- > ------------------------------------------------------- > Preeti Gipson > Postdoctoral Associate > Howard Hughes Medical Institute > Dept. of Molecular and Cellular Physiology > Stanford University, CA > >

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maintain .seg alignment to .mrc between sessions
by Amy Jobe 23 Mar '16

23 Mar '16

Hello, When I segment an 80S ribosome into individual ribosomal proteins and rRNAs, it takes some time and I often need to close and reopen my session. Whenever I reopen my session, though, my .seg file is no longer aligned to my .mrc map, and I have to spend time manually (and probably slightly inaccurately) re-aligning them. I've tried using the Associate Selected option in the daily build, although I'm not sure if it's meant to maintain alignment, and it hasn't fixed the problem. Can anyone help me with this? I'm using the daily build and the most recent stable version on Mac. Thanks, Amy Jobe -- PhD candidate, Joachim Frank group Department of Biological Sciences Columbia University 2-221 P & S Black Building 650 W. 168th St. New York, NY 10032 Telephone: (315) 879-8192 E-mail: abj2111(a)columbia.edu Lab website: http://franklab.cpmc.columbia.edu/franklab/

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using fitmap with per-frame analysis.
by Bala subramanian 22 Mar '16

22 Mar '16

Friends, I have a task which is as follows; I have done the simulation of a protein, whose EM map is already available. I want to fit the MD snapshots on to the map and to filter out some best frames based on the overlap statistics. I am aware that chimera does only rigid body fitting. I would like to know, for instance, if I can open the EM-map and the MD traj in Chimera and use per-frame analysis to achieve my goal. Also, i need some way to output/write the fitting statistics (eg. overlap value) to a file so that i can later filter out the best frames based on the statistics. Thank you, Bala C. Balasubramanian

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representative fits in chimera fitmap search
by Jan Kosinski 18 Mar '16

18 Mar '16

Hi, In the fitmap command global search, how the unique fit is selected from the cluster of similar fits? Ideally, from each cluster, I would like to obtain the fit the gave the best cross-correlation. But, I think, based on the fit_search code in FitMap/search.py, what is happening is that the first unique fit ever encountered is added to the fit list: close = b.close_transforms(ptf) if len(close) == 0: transforms = [M.multiply_matrices(ptf, mtv) for mtv in mtv_list] stats['hits'] = 1 f = Fit(models, transforms, volume, stats) f.ptf = ptf flist.append(f) b.add_transform(ptf) fo[id(ptf)] = f else: s = fo[id(close[0])].stats s['hits'] += 1 and any subsequent fit that is close to the first, would be discarded, even if it gives better cross-correlation. Do I understand correctly that the unique fit is not necessarily the best scoring fit from the cluster? Thanks in advance for clarification, Jan

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reset positions
by Dougherty, Matthew T 18 Mar '16

18 Mar '16

I have two positions set, p1 & p3. When I do "reset p1; reset p3 100" I have a trajectory problem with the camera crashing through a structure in between p1 & p3. I would like to create a new position p2 to avoid the crash, going from p1 to p2 to p3. I can get close to the crash by a freeze command. How can I determine the frame number being executed by the reset command when I freeze? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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opening large models
by benoit.zuber＠ana.unibe.ch 17 Mar '16

17 Mar '16

Hello Opening a model of the 80S ribosome takes about 30 minutes on my computer (chimera version 1.10.2 build 40686). Is it normal? Is there any way to speed up this step (for example, can the task be parallelized)? Thanks in advance Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2 Postfach 922 3000 Bern 9 Switzerland benoit.zuber(a)ana.unibe.ch +41 31 631 84 40 http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

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opening huge models
by benoit.zuber＠ana.unibe.ch 17 Mar '16

17 Mar '16

Hello Opening a model of the 80S ribosome takes about 30 minutes on my computer (chimera version 1.10.2 build 40686). Is this normal? Is there any way to speed up this step (for example, could the task be parallelized)? Thanks in advance Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2 Postfach 922 3000 Bern 9 Switzerland benoit.zuber(a)ana.unibe.ch +41 31 631 84 40 http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

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