- Chimera-users - RBVI Mailing Lists

Bond change
by Bruno Cramer 30 Nov '09

30 Nov '09

Hi After getting the conformations as *.sdf (or *.pdb) files with Macromodel (from Shroedinger) and/or Vconf(VeraChem) I use Chimera to add missing H's and add charges with amber 99. After these steps are completed, I split the sdf conformations-file into single *.mol2 files. All works fine except for the last step, that changes a single bond into a double bond in each molecule. I am correcting this manualy opening the *.mol2 file with Texd editors and changing the double bond into single bond the the benzene rings. Opening a chosen conformation from the *.sdf file it looks correct.So, the problem happens during conversion/splitting process. Question: How can this arbitrary bond change be avoided? Attached zip file with *.mol2 examples of one compound after splitting process. Thank you Regards Bruno

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missing ribbon loop
by klumpler＠sci.muni.cz 30 Nov '09

30 Nov '09

Hallo, please, can you tell me how to create missing part of ribbon representation of loop? Using "ball and stick" representation is peptide chain complete without gap, but in "ribbon" representation is one residue missing and forms the gap. Thank you very much

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structure manupulation
by Haixin Sui 24 Nov '09

24 Nov '09

Tom and Elaine, Is there a simple way to manipulate part of a protein structure in Chimera? What I would like to do is the following. Let's say I have a molecular compose 8 helixes. 7 of them fit in the cryo-EM map perfectly but one short helix is off probably owing to conformational change. I would like to move the short helix into the density map manually. The difficult part is how to make a smooth transition for loop regions at both ends of the helix. Would you please give me some advice on this? Thanks! Haixin -- Haixin Sui, Ph.D. Wadsworth Center NYS Dept. of Health Empire State Plaza P.O. Box 509 Albany, NY 12201-0509 (518)474-4235 (office) (518)473-0309 (lab) IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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Question regarding saving PDB in Chimera
by Pancera, Marie (NIH/VRC) [E] 24 Nov '09

24 Nov '09

Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie

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Display of double-bond in Chimera
by J H 24 Nov '09

24 Nov '09

Dear Chimera, Is there a way to display a molecule's double bond as double-bond (i.e., two lines between the atoms instead of one) in chimera? Thanks a lot. Best, Jules.

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Moving PDB between 3 orientations
by Thomas Goddard 23 Nov '09

23 Nov '09

Hi Chris, To show a molecular model moving between three orientations you would use Chimera commands savepos and reset and matrixcopy. Here's how I'd go about it. First put copies of the molecular model at all 3 positions. If you have saved these in 3 Chimera session files I would open all 3 sessions telling Chimera not to close the previous session when I open each new session. Now open a 4th copy of the molecule. Suppose the original 3 copies are model numbers #0, #1, #2 and the 4th copy is model #5. To align the 4th copy with #0 use matrixcopy #0 #5 (The matrix being copied is the positioning matrix, the rotation and shift that places the molecule in the scene.) Record the positions of all the models now with savepos p0 The name p0 could be anything. We'll use it later with the reset command. Also save positions with the 4th model in the other 2 states: matrixcopy #1 #5 savepos p1 matrixcopy #2 #5 savepos p2 Now to move the 4th model pack to position 0: reset p0 and to move it from position 0 to 1 over 50 frames reset p1 50 and then from 1 to 2 reset p2 50 In a movie recording command script remember to put a "wait 50" between these two commands so they don't both try to run simultaneously. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html There is a movie making tutorial that explains some of this: http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html Tom -------- Original Message -------- Subject: Re: [Chimera-users] how to link three EM confirmations in morph map From: Chris Arthur To: Thomas Goddard Date: 11/23/09 1:40 PM > Hi Tom, > I have one other question. I have a pdb (the same pdb loaded into > chimera 3 times), that I have docked into three distinct EM maps. I > would like to make a movie showing the rotation of the pdb as it goes > from one docked state to the next, to the next. I guess this would be > similar to the morph command but for pdb's instead of EM maps. Any > suggestions? > Thanks, > Chris > > > The Scripps Research Institute

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Make volume have mean 0, standard deviation 1
by Thomas Goddard 23 Nov '09

23 Nov '09

Hi Terry, Chimera does not automatically scale density maps. You can use a command like vop scale #0 shift -8.0 factor 0.2 to shift map #0 values by -8.0 and then scale by 0.2. If the mean were 8.0 and standard deviation were 5.0 then this would normalize to mean 0 and SD 1.0. This creates a new volume data set. There is no capability to shift and scale an existing map without making a new volume data set. The Volume Filter dialog (menu Tools / Volume Data) can do the same thing. Python code to do the shift/scale is in chimera/share/VolumeFilter/scale.py There is a menu entry Tools / Volume Data / Volume mean, SD, RMS that reports the mean and SD and RMS about zero of the highlighted map in the volume dialog. There is no command equivalent (I should make the measure command do this). The Python code that does this is in chimera/share/VolumeStatistics/__init__.py Tom -------- Original Message -------- Subject: question about ccp4 formatted map density From: Terry Lang To: Tom Goddard Date: 11/23/09 11:39 AM > Hey Tom, > > I am looking into some new schemes for scaling electron map > density. I know you said that the scaling to a mean of zero and > standard deviation of 1.0 is implemented in the current release. > However, I can't seem to find where the code is located. I am really > interested in figuring out where exactly scaling happens and if it's > automatic or needs to be requested. Any input you can provide would be > greatly appreciated! > > Sincerely, > Terry >

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Re: [Chimera-users] [chimera-dev] Rotation about the axis of symmetry
by Elaine Meng 23 Nov '09

23 Nov '09

On Nov 23, 2009, at 2:06 AM, Liam Browne wrote: > I want to rotate a model by 90 degrees about the axis of symmetry, > but I seem to be having problems setting the axis correctly. > After two identical models are superimposed I use measure rotation > and get the following: > > Matrix rotation and translation > -0.04092271 -0.36724445 0.92922379 -82.20183653 > -0.91203666 0.39354649 0.11537022 -54.21831923 > -0.40806183 -0.84276490 -0.35104539 11.47082481 > Axis -0.55288898 0.77167664 -0.31437070 > Axis point -56.22800779 0.00000000 25.47389901 > Rotation angle (degrees) 119.94780111 > Shift along axis 0.00338820 > > What should I do to rotate the model at the same axis but by 90 > degrees? > > Many thanks, > Liam Hi Liam, You can just use the reported values -- the tricky part is remembering to indicate that they are in the coordinate system of the first model in the "measure rotation" command, and also using the reported axis point as the center of rotation. Let's say you used the command "measure rotation #0 #1". Then the values in the Reply Log are for the transformation of #1 relative to #0 expressed in the coordinate system of #0. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation > Now you can use the values in the Reply Log to rotate #1 further. Keep in mind that this transformation will be applied on top of any existing transformations. If you want only the new rotation and not prior transformations, you would need to "reset default" first. To rotate model #1 90 degrees about the reported axis and use the reported axis point as the center, the command would be: turn -.55288898,.77167664,-.31437070 90 center -56.22800779,0,25.47389901 mod #1 coord #0 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> 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

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question
by Laura Packer 20 Nov '09

20 Nov '09

To whom it may concern: I am not sure if I am sending this inquiry to the correct e-mail address. If not, I apologize for any inconvenience. I am looking to acquire a list of atoms that are within a certain distance of a set other atoms. I have googled this question and have learned how to select these atoms: bfsdjf select <description of atoms/residues> z<5.0 # or zr<5.0 or select <description of atoms/residues> za<5.0 What I would like to know is how to get a list of these results. It is not appearing in my reply log as I thought it might. Thank you for your time. Sincerely, Laura Packer packer(a)bu.edu

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how to link three EM confirmations in morph map
by Chris Arthur 19 Nov '09

19 Nov '09

I am wondering what would be the best way to link three EM maps using Morph Map? I have three sequential conformations of a protein and I would like to show a movie morphing from 1 to 2 to 3 if possible. Thanks in advance for any tips. Regards, Chris Christopher Arthur Ph.D. Staff Scientist Milligan/Unwin Lab The Scripps Research Institute carthur(a)scripps.edu 858-784-7073

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