March 2010 - Chimera-users - RBVI Mailing Lists

file format conversion using chimera
by snoze pa 12 Mar '10

12 Mar '10

Dear Chimera Users, I want to save/convert a pdb file into .mrc or .ccp4 format using chimera I think I did it before using chimera but don't remember exactly how! I will highly appreciate your help. Thank you S

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Re: [Chimera-users] Chimera: Display map around atoms
by Elaine Meng 12 Mar '10

12 Mar '10

Hi Greg, That "bv" shortcut creates a new, larger map (periodically extended as needed to cover the atoms), which sounds like the opposite of what you want. You can limit the density display to a zone around selected atoms. Choose "Zone" from the "Features" menu in the Volume Viewer dialog to add the relevant controls to the dialog. The zone feature is described here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… > For future questions, it's better to send Chimera questions to the chimera-users(a)cgl.ucsf.edu list rather than to me directly. That way it won't fall through the cracks if I'm on vacation, or sick, or don't know the answer. I hope this helps, ----- 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 12, 2010, at 1:24 PM, Greg Friedland wrote: > Hi Elaine, > Thanks for your earlier help with Chimera. I'm currently have > difficulty displaying a density map. I'd like to only display the > density around protein atoms, not the full symmetry density. I tried > the shortcut 'bv' according to http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/003002.html > but the new map still contains lots of the symmetric molecule > density. Is there another way? > Thanks, > Greg > > Greg Friedland > Postdoc > Sandia National Lab > Joint BioEnergy Institute

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Recording trajectory
by Francesco Pietra 11 Mar '10

11 Mar '10

Hi: I am interested in following the pathway of a ligand forced to leave a protein. I can follow that path with the movie (NAMD format) but I would be interested to also have a trace of the pathway recorded. I would like to show around the protein the various traces for different pathways of exit of the same ligand. thanks francesco pietra

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Re: [Chimera-users] Recording trajectory
by Eric Pettersen 09 Mar '10

09 Mar '10

On Mar 9, 2010, at 2:17 PM, Francesco Pietra wrote: > Hello Eric: > I have seen your later correction mail. > > I had a bad day, that is little time for chimera and with little > success. Please try to guess were I was faulty. > > francesco@tya64:~$ chimera --version > chimera alpha version 1.5 (build 30193) 2010-03-06 09:27:34 GMT > francesco@tya64:~$ > This is amd64, at the moment I have no 32bit computer. > > <select ligand> selects too much. > > <select :residue.number> > <select :residue.name> > do select exactly what I want (which is a small ligand of HEME ligand > of the protein. > > The problem was with <define> command > > MD-movie...Per-Frame "define centroid :residue.number" ... Apply > > then activating the movie gave the same view as not going through the > Per_Frame, i.e., the small ligand does not leave any sphere on the > path. I did not investigate if the sphere are too small to be seen at > the magnification I used, ore have the same color as the background > (black). Very likely, I did some other major mistake. Not sure what to say. Works for me. I've appended an image of centroids tracing the motion of a small ligand in an RNA binding site. I used a step size of 10 and this 'define' command: define centroid raiseTool false radius 1.0 color goldenrod sel "raiseTool false" prevents 'define' from trying to bring up the Axes/ Planes/Centroids tool (and update that tool's table) for every centroid created. The other options control the size and color of the centroid. I had the small ligand selected so 'sel' is my atom spec. I tried it a second time with ":35" (which also selects the small ligand) and that worked too. FYI, "~define" will get rid of all the centroids. I hope this helps somehow. Are you sure you had the "Interpret script as" part of the per-frame dialog set to "Chimera commands"? I can't imagine that you didn't, since you would have gotten some kind of error if it had been interpreted as Python. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] Scripting to write / save multiple models into single pdf file
by Elaine Meng 09 Mar '10

09 Mar '10

On Mar 7, 2010, at 5:12 AM, Sumitro Harjanto wrote: > Hi Meng, > I would like to use chimera to help me with a process of combining > receptors and ligands that were modelled separately (in separate > files) > > So here is my intended framework: > > For each iteration: > • open “template.pdb” template file (which contains the receptor/ > ligand complex) I used to model the receptor and ligand > • open the receptor_model.pdb > • open the ligand_model.pdb > • match receptor to template > • match ligand to template > • close template.pdb > • save the models in their current position into a single new pdb > file. > > I was exploring the feasibility of using the command “write” but I > am not too sure if it will allow me to save the complex as a single > pdb file..? > > On a side note, if it’s possible, any suggestion on how to optimise > the run time since I might be running this for a large number of > iterations ..? I read somewhere about switching off the GUI to save > time, does it help..? > > Thanks! > Cheers, > Sumitro Hi Sumitro, You can't save multiple models in one file with the "write" command, but you can use "write" multiple times, one for each model you want to save. If you make sure to save each model "relative" to the same model, they will be in the correct positions with respect to each other when you reopen the files. See the "relative" keyword: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> Or, if you really need to have them in a single file, you can use the "combine" command to create a new single model from multiple models. You would do that after the matching, but before saving the PDB file. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> I can't answer about how to script for multiple models, or how much faster it might be to use noGUI, so I'm sending this to the chimera- users list. In the future, please send Chimera questions to the chimera-users(a)cgl.ucsf.edu list, because I might be away from work or (like now) others may be better able to answer the question. I hope this helps, ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Problem with energy minimization
by Bill McIntire 05 Mar '10

05 Mar '10

I used Dock Prep for my modeled structure, and get no error comments. However, when I try to energy-minimize, I get the following message: No MMTK name for atom "HN1" in standard residue "PRO" PRO is at the N-terminus. I cannot find any help in manual. Please help with this problem. Thanks Bill McIntire

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cap color from command line
by Jean-Paul Armache 05 Mar '10

05 Mar '10

Hello, Thank you for all your previous answers. I would like to ask you whether there is a way to change the cap color not only from the Surface capping tool, but the command line as well and declare it maybe in a script (like for example coloring of the maps and models). Thanks, Jean-Paul

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make one chain from two chains ID in PDB
by Dong, Jianbo 04 Mar '10

04 Mar '10

Hello, I'm working with a PDB file, in this file, one protein peptide was recognized as two chains (B and C), I want to make it as one chain, so it will be easier to do some interface analysis and modeling. I guess I can open the file as WORD file and change all the C to B one by one, but it's too much work to edit it that way. May I get some help for this? Is there a easier way to do this? Many thanks, Jianbo

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positive and negative overlaps
by Kshatresh Dutta Dubey 04 Mar '10

04 Mar '10

Dear all, Can anyone tell me the significance of positive and negative overlaps results in structure analysis module of chimera, as i got 140 contacts that contains both positive and negative overlap values? Any help is appreciated. Thanks in advance Kshatresh Dutta Dubey

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show axis ?
by Stefan Bäckström 03 Mar '10

03 Mar '10

Hi. It is possible to show the box of a volume, and I wonder if it is possible to show the X, Y and Z axis as lines ? Best, Stefan Bäckström Medical Biochemistry Göteborg University Sweden

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