- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] morphing
by Elaine Meng 31 Mar '12

31 Mar '12

Hello Francesco! First make sure you are hiding the input conformations, so that you are seeing only the morph (for example, you could show Model Panel from Favorites menu, then uncheck the S(hown) boxes for everything except the morph results). I say that because if you see something not moving, it might be the original structure. As explained here, the morph should contain all of the atoms in the protein chain that are included in all of the input structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#p…> Since your input structures are the same protein, if each one includes the sidechain atoms, the morph should contain all the same sidechains and they should move from one position to the other during the morph. They may not be displayed automatically, however. Try displaying all atoms (again better to hide the other structures first) to make sure of what is there. About the ion: even if the ion is in both structures, it may not be in the morph if you are using an older version of Chimera. However, there have been some fixes, and I believe if you are using Chimera 1.6 or newer, the ion should be included. The fix I'm thinking of was 6 months ago and is described here: <http://plato.cgl.ucsf.edu/trac/chimera/ticket/9886> If you try Chimera 1.6 and the suggestions above but you believe there is a bug, you could use Help... Report a Bug in the menu and describe how to reproduce the problem, attaching session file if necessary. 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 On Mar 31, 2012, at 5:24 AM, Francesco Malatesta wrote: > Hello from Rome! > I'm trying to morph 2 different conformations of the same protein. I get a very very nice movie, but I can't get amino acid side chains or heteroatoms (heme iron) to move also. > Is there any way to do this? > thank you for help > Francesco

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How to save VIPER transformation matrix
by snoze pa 30 Mar '12

30 Mar '12

Dear Chimera Users, Is it possible to save the coordinates after the VIPER transformation (xyz-2 fold symmetry) in Chimera. I can create a multiscale biological molecule in chimera but it is not saving the viper matrix in pdb file. Please note that this pdb is a model not the crystal structure and I am trying to save the viper matrix for this pdb. Thank you, S

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Chimera is not loading properly
by Andrea Edwards 27 Mar '12

27 Mar '12

I have not used Chimera in awhile. I just downloaded the new version for Mac-OSX-64-bit and when I open it, none of the buttons on the gui are visible. There are ovals and things where there should be buttons, but not words on them. How can I fix this? attached is a screenshot. Thanks, Andrea

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PDB model merging
by Nikolay Igorovich Rodionov 27 Mar '12

27 Mar '12

Hi all, I'm working on a project that requires me to merge models created through PDB BIOMT records. I have been using the copy&combine feature in the model panel to merge all of my models, and then writing a new PDB of only the combined model. I've noticed that this method deletes a large amount of information about the structure, including secondary structure records. Is there a way to merge models without losing such data? If it is relevant, I am merging 90+ models.

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Trajectory analysis: hbond
by George Tzotzos 26 Mar '12

26 Mar '12

I'm wondering if there's a way to determine hbond formation during a trajectory in a similar way to the way the Plot distances tool in MD Movie/Analysis works. Or dumb values to a file. Many thanks in advance for any suggestions Regards George

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Re: [Chimera-users] Electrostatic Potential using APBS .dx file
by Tom Goddard 26 Mar '12

26 Mar '12

Hi Soca, Sounds like you are doing everything right. That makes me suspect that something is wrong with your APBS file -- like all the potential values are zero. To see what the distribution of the potential values are, open the APBS file and then use menu Tools / Volume Data / Volume Viewer, and click on the histogram (empty rectangle in the middle of the volume dialog). That will show a histogram of the potential values. You can move the vertical bar on the histogram to see what the potential value is at that position. Check if -5 to 5 is a reasonable range. Tom > Hello, > > I have been attempting to generate a electrostatic surface map in > chimera using an external potential file generated from APBS (.dx). > > I understand that Chimera has an internal surface calculation protocol > via Coulombic Surface Coloring, however, I would like to use the > Electrostatic Surface Coloring. > > However, when I open my molecule (PDB), show surfaces, and choose its > MSMS main surface to color by electrostatic potential using the .dx > file, the surface map is not the red, white, blue that I have set in > my parameterts under Surface color. Everything turns to grey. My other > parameters include: > > red -5, white 0, blue 5. Colors 3. Palette Red-Blue. Surface offset 1.4. > > I feel as though I am missing something trivia that would allow me to > generate the surface image I want, however I am lost after may > searches for advice through the forums and tutorials. > > Please let me know what I am missing. > > Thanks > > Soca > > -- > Ardian Soca Wibowo, Ph.D. > Postdoctoral Associate > Dann Research Group > Department of Chemistry > Indiana University

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Dimethyl Sulfoxide Electromagnetic Absorbance
by Nancy 25 Mar '12

25 Mar '12

Hi All, I would greatly appreciate it if anyone could provide a reference or information on the electromagnetic absorbance characteristics of dimethyl sulfoxide, especially in the region of 800-1400nm. Thank you, Nancy

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RMSD plot
by lecan 23 Mar '12

23 Mar '12

Hi everybody. I am interested in plotting RMSD values vs time from molecular dynamics. Is there a way to extract the RMSD values from a the RMSD map in the analysis tool of MD movie. Or maybe exists another way to do this with Chimera. Thank you in advance Luis L.

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how to measure the volume of the active site
by Thomas Evangelidis 23 Mar '12

23 Mar '12

Dear UCSF Chimera developers, I am interested in measuring the volume of the active site of a kinase. I have searched through the documentation and the only thing I found was how to measure the enclosed volume of a surface object. Is it possible to do what I want with UCSF Chimera? Could you please point me towards the relevant commands? Thanks in advance for any help. Thomas -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

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Multi-PDB fitting question
by Tom Goddard 21 Mar '12

21 Mar '12

> Dear Tom, > > ... > Currently we are trying to use a lot of PDBs (hundreds!) to fit one > density map and trying to find out the best fitted PDB, and we found > that fitting the PDBs one by one manually was very time-consuming and > low-efficiency. So we are wondering that if there is any advanced way > or batch file that can speedup this process? > > Thank you so much and we are looking forward your reply. > > Best Regards, > Lei > Hi Lei, Ok, I added a new "eachModel" option to the Chimera fitmap command so that one command can independently fit many molecules in the same map. For example, fit #1-50 #0 resolution 13.5 eachModel true listFits true will fit PDB models with id numbers 1 to 50 into map with id #0 and list the fits in a dialog. Each of the fits is done independently (no account for clashes between molecules). Details on each fit are given in the Reply Log dialog (menu Favorites / Reply Log). This will be in tonight's Chimera daily builds (run at midnight) if they succeed: http://www.cgl.ucsf.edu/chimera/download.html#daily Here is the fitmap command documentation which will be updated later this week or next week. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html You will probably find that you can't open hundreds of PDB molecules in Chimera because it takes too much memory. But you can fit them in a few batches if this happens. Tom

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