March 2015 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Query on morph command in Chimera
by Elaine Meng 22 Mar '15

22 Mar '15

On Mar 22, 2015, at 9:38 AM, vinothkumar <vkumar(a)mrc-lmb.cam.ac.uk> wrote: > Dear Elaine, > I have three different volumes/maps of the same protein but differing in conformation. I am able to use the command line - ‘vop morph #0,1,2 constantVolume True model #3 frames 200’ which then interpolates and I could produce a movie. However, by default the threshold for the volumes and level goes to 4. Is there a way to insert in the command line to tell that all the volumes be set to level (1) and a certain threshold. > Thank you > Regards > Vinoth Dear Vinoth, You should adjust the threshold of the maps before the morphing. This could be done with the “volume” command if you are not using GUIs, e.g. command: volume all level 1 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> Actually, my own experiments suggest it is only the threshold of the first input map that matters in setting the starting level of the morph. If you use the “constantVolume” morphing option, however, the threshold will be adjusted to keep the enclosed volume constant. If you really wanted to keep it exactly at 1 through the whole morph, you would not use that option. I hope this helps! For future questions, we recommend you send them to chimera-users(a)cgl.ucsf.edu (CC’d here) instead of to me or other individuals directly, unless you are including private data. 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

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problem related to open the chimera file by Coot
by Smith Liu 21 Mar '15

21 Mar '15

Dear All, I have fit a PDB file with a MRC by the Chimera. I saved both the fitted PDB file and the fitted MRC file by coot. When I open the fitted PDB file and the fitted MRC file by Chimera at the same time, they still fit perfectly. However when I open the Chimera fitted PDB file and the Chimera fitted MRC file by coot, the protein backbone (and the sidechains) does not fit the MRC file anymore. Will you please tell me what should I do in order to have the Chimera fitted PDB file and the Chimera fitted MRC file still fit in Coot? I am looking forward to getting your reply. Smith

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Constraining map-to-map fitting based on symmetry?
by Oliver Clarke 20 Mar '15

20 Mar '15

Hi, If I have two maps of the same symmetry (say C4), and I align them using fit in map, is there any way to force chimera to keep the rotation axes of the two maps aligned, and to only search rotation around (and translation along) that axis, rather than arbitrary rotations? Cheers, Oliver.

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Contour levels
by Nicholas Michelarakis 20 Mar '15

20 Mar '15

Hello all, Forgive me if this is a silly question but I was under the impression that when you opened two density maps in volume viewer and used the Fit in Map tool, with the Use only data above contour level option ticked, the correlation would change according to the contour level you selected in the volume viewer. In my case this does not happen. If this is indeed a bug, I would be happy to provide further information. Atm, I'm using Chimera 1.10. Thank you very much in advance. Best, Nick

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Total number of atoms in all submodels
by Cruz, Phil (NIH/NIAID) [C] 19 Mar '15

19 Mar '15

Dear Chimera users, When I fetch a biological unit into Chimera from PDB, the symmetry related units are placed into separate submodels. I would like to find the total number of atoms in all submodels that make up the biological unit within a python script. Constructs (and variations that I've tried) such as the following only give the number of atoms in each sub model: numAtoms = len(openModels.list(modelTypes=[Molecule])[0].atoms) Is there some way to get the grand total of atoms? Alternatively, if the script could find the total number (or list) of the submodels, I could probably still handle it. My example is the virus capsid 1ej6. Thanks for any suggestions. -- Phillip Cruz, Ph.D. Contractor, Medical Science & Computing Computational Structural Biologist Computational Biology Section Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Dr., Room 3B62 Bethesda, MD 20892-0485 Office: 301-451-1089 http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH) http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Interaction interface between two residues and measure buriedArea
by ms 19 Mar '15

19 Mar '15

Dear all, I am trying to understand what is the area buried between two residues (or between one residue and two other ones) in several structures. It seemed to me the best way to do this was to use the command "measure buriedArea :res1 :res2" on the full structure (once all non-protein components have been cleaned out of it). The overall trend of these measures seems consistent with visual inspection. However I have a couple of questions about it: 1) I am unsure about what value is best to use/compare, buriedSAS and buriedSES. It seems to me that the difference between the two is essentially in the geometrical protocol used. Is there any general wisdom about what do they physically mean and how should I approach each value? 2) In some cases I receive *negative* values for buriedSAS and/or buriedSES. Looking on the ML it seems that it is a symptom of a buggy or failed area calculation (e.g. http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005119.html ). However it also says that I should see a "fallback" warning on the Reply Log -I see nothing of the sort. How do I troubleshoot this? Also in cases where the calculated value is positive, how can I be sure that the values are indeed meaningful? Any other feedback on the kind of measurement I am trying to do is more than welcome. Thanks a lot, Massimo

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how to convert mtz file to a file which can be openne by Chimera
by Smith Liu 19 Mar '15

19 Mar '15

Dear All, Will you please tell me how to convert mtz file to a file which can be openne by Chimera? Smith

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Chimera service unavailable
by SA 18 Mar '15

18 Mar '15

Dear developer, I am using Chimera PDB2PQR module. However, it is failed. The error message is below: self.backend = Backend(service, url) File "/soft/chimera/Chimera64-1.10.1/share/WebServices/opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:pdb2pqr_1.8' is unavailable. See Reply Log for more details. For your indormation, I am using the latest linux version of Chimera. Thank you. Siti Postdocs UCSD

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How to get prmtop file corresponding to a pdb file
by Mahendra B Thapa 18 Mar '15

18 Mar '15

Dear Chimera users, To get *Amber prmtop file* corresponding to a *pdb file using Chimera*, I did the following steps: 1] tools -> Amber -> write prmtop 2] In a pop-up window 'save file in chimera', I gave file name, say, aa.prmtop, then clicked save. 3] No charges message appeared, then I clicked 'Assign charges'. 4] In a pop-up window 'Add charge', I selected 'AM1-BCC' in other residues, then clicked ok. 5] In a pop up window 'specify net charge', I selected 'AMI-BCC' in charge method 6] I got 'chimera error' - failure running ANTECHEMBER for residue HIS. Check reply log for details. 7] In reply log, '*Failure running ANTECHEMBER for residue HIS*' seen. Any help in this issue will be a good help for me. Thank you. Mahendra Thapa University of Cincinnati,OH

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visualization of electrostatic potential
by Christos Deligkaris 18 Mar '15

18 Mar '15

Dear Chimera Users, I am interested in visualizing the electrostatic potential calculated by the APBS tool Chimera provides and I have several questions regarding this. 1) We have been having troubles running the PDB2PQR/APBS tools (I am not sure if we had trouble with both, it has been a few weeks) that Chimera provides, and I believe we fixed this by changing the version number at the very end of the web server address. Is there anything else we could have done to fix this? 2) I noticed that the numbers that are displayed when I visualize the APBS-calculated potential on the MSMS are very different from the numbers shown when I use the volume viewer (I mapped the values to atoms and then displayed those as labels). Why are those numbers not the same? Is it because the volume data will map the potential near the atoms and display that, whereas the potential on the surface (or actually 1.4 Angstroms from the surface) will display the potential value on the surface? Should I assume that the units are the same? 3) I am interested in finding the "patches" of the molecular surface the have fairly positive potential. I am familiar with the PatchFinderPlus server but I am interested in finding several patches, not just the largest one. I have not found any tool related to this in Chimera, please let me know if I am wrong. So,I found the redarea.py script avalaible from Chimera's website and I am thinking about modifying it in order to do this. The script iterates over all surface pieces. Is it possible to calculate the distance between vertices and atoms? Is it possible to obtain the potential value at a vortex? I think this would help me get started... Thank you very much, Christos Deligkaris, PhD Assistant Professor of Physics, Drury University 900 N Benton Ave, Springfield MO, 65802 Office Phone: (417) 873-7234 www2.drury.edu/christos <http://www2.drury.edu/christos/index.html> @DeligkarisGroup <https://twitter.com/DeligkarisGroup> +ChristosDeligkaris <http://google.com/+ChristosDeligkaris>

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Chimera-users March 2015