- Chimera-users - RBVI Mailing Lists

isosurface
by Bala subramanian 09 Dec '09

09 Dec '09

Friends, I have calculated the electrostatic-potential map using APBS program. I can use the 'electrostatic colouring' to colour my protein but i want to display the +ve and -ve isosurface. Kindly write me how to do the same. Thanks, Bala

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chimera help - calmodulin
by roach a.p.l. (aplr1g08) 07 Dec '09

07 Dec '09

Hi, I am a student trying to do a project on the protein calmodulin. I have just started using chimera and have gone though your tutorials and understood everything as it is very clear but i don't know how i would select the protein calmodulin and put it in the chimera display to make my images. I realise this is probably a simple step but this is all new to me and i would much appreciate your help. Thank you Annabel Roach

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Maximizing performance with large volume data maps
by Ryan Rochat 07 Dec '09

07 Dec '09

Hello, I was wondering how much video memory Chimera is capable of accessing. I currently have a 898Mb videocard that begins to slow down with a 550x550x550 map (at step size 1). This map is actually a downsample of the true 1100x1100x1100 map coming in at 5GB. I was contemplating going for a much larger video card at 4GB, however I was curious to what extent I could expect to see acceleration using Chimera with such a massive dataset (600+MB) and video card. Thank you, Ryan H. Rochat MS MD/PhD Candidate (Baylor College of Medicine) Graduate Student SCBMB (Baylor College of Medicine) Chiu Lab One Baylor Plaza N420 Alkek Houston Texas 77030

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Re: [Chimera-users] To consult the Morph conformation
by Elaine Meng 07 Dec '09

07 Dec '09

Dear Jiraporn, Sorry, Morph Conformations only includes parts that are in both structures in the morphing trajectory. In your situation, I suggest text-editing one of the input PDB files (more details below). Morph Conformations maps residues in the starting structure to residues in the ending structure by creating a sequence alignment. Where the residue in the starting structure is aligned with the same type of residue in the ending structure, the whole residue will be included. Where the residue in the starting structure is aligned with a different type of residue, only the parts that are the same will be included, which will include the backbone and sometimes part of the sidechain. Where there are backbone atoms, you can show a ribbon. If the residue is aligned with a gap, it will not be included. Here is the explanation in the manual: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#p… > Currently Morph Conformations will only use the sequence alignment it figures out itself. A future improvement will be to allow the user to provide the sequence alignment (perhaps avoiding some of the gaps), but that is not available yet. I took a look at your proteins, 3DRR and 3DRS. They are the same protein, and the only difference is that the 3DRR crystal structure has more residues at the C-terminal end, forming a helix. 3DRR ends at 557 and 3DRS ends at 548. I guess you want that end part shown in the morphing trajectory. The structures look nearly the same in the residues before the difference, so to do this I would just use a text- editor and add the end residues from 3DRR onto the 3DRS structure. For example, make a copy of the 3DRR PDB file, then edit it to replace 543-end with 543-end from the 3DRS PDB file. Then you would just open the new edited 3DRR with the longer tail and then morph from that to 3DRS. 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 Dec 5, 2009, at 1:29 AM, Nok :p wrote: > Dear Chimera teme, > > First of all, I would like to introduce myself. My name is Jiraporn > Yongpisanphop. Now, I am a master student of KMUTT university in > Bioinformatics field. > > My thesis topic involve in drug design. A part of my work is > concerning about overaly binding pocket of single mutant enzymes > (PDB file: 3DRR and 3DRS). And, I > > use Morph Conformation method. It is good but it not complete for my > work. Because the intermedate structure was generate from compare of > same amino acid > > of both structures. However, the difference amino acid was kept only > reference model. Therefore, I would like to consult you how I will > keep amino acid that > > differece of both structures into intermediate structure. > > Thank you very much for your kind. > > Best regards, > > Jiraporn

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Movie spinning and slicing a density map
by Thomas Goddard 06 Dec '09

06 Dec '09

Hi Andy, I've added an example movie spinning and slicing a virus EM density map to the Chimera Animations page. See the bacteriophage phi6 entry. There is also a link to the movie script. http://www.cgl.ucsf.edu/chimera/animations/animations.html Tom -------- Original Message -------- Subject: making a movie From: Anindito Sen To: Thomas Goddard Date: 12/2/09 5:50 PM > Hi Tom > > I am not sure if this email can be out on the general Chimera wiki. THe > following movie is from a published work of mine. Can you help me > getting the script for generating such a movie. There is a Chimera session in the > webpage but I think its a bit too much for me to understand. > > Please feel free to reframe the question and put it in the Chimera wiki > email list which may prove helpful to others. > > Thanks for your help. > > Best > > Andy > > > > http://emnavi.protein.osaka-u.ac.jp/emnavi_detail.php?id=1500 > > Dr. Anindito Sen (Ph.D) > >

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drawing elipsolids
by Keren Lasker 03 Dec '09

03 Dec '09

Dear Chimera team, Is there a way to draw ellipsoids in Chimera. The ellipsoid is defined by its center and 3 radii. Thanks for your help. Best, Keren.

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How to clip surface using mclip
by Marhoefer, R (Richard) 03 Dec '09

03 Dec '09

Dear Chimera Team and Users, I like to clip the surface of a model (but not the model itself) using the command mclip. Unfortunately, this command apparently is waiting for a model number and therefore works on the surface as well as the model itself. On the other hand, the interactive tool "Per Model Clipping" allows to clip the surface only. Because I like to use clipping in a movie, using the interactive interface is not an option. Does anybody know how this could be acomplished using the command line? Kind regards, Richard Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

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Re: [Chimera-users] missing ribbon loop
by klumpler＠sci.muni.cz 03 Dec '09

03 Dec '09

Dear Elaine, I think PDB is alright, I send it as a attachment. Could you help me with the editing? Thank you very much Tomas > Hello, > My guess is there is something strange about the structure or the format of the input file -- for example, maybe the residues don't all have the same chain ID, or the backbone atoms do not have the expected names (N,CA,C,O). If Chimera does not show a ribbon at that position even though you told it to show ribbons for everything, it is probably necessary to edit the input file to fix the problem. I couldn't be more specific without seeing the file. > Best, > 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 Nov 27, 2009, at 2:16 AM, klumpler(a)sci.muni.cz wrote: > >> 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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keyboard input gone
by Zhou, Wei 02 Dec '09

02 Dec '09

Hi, Yesterday I installed the latest 1.4 32bit linux version of chimera into my opensuse 11.1. Soon after I fetched some pdb files and started to use it, at some point, I can no longer input any text into the program, such as typing another pdb id, or typing a command line, or type a file name to save it. I can still use mouse. Please help. I'm here at mission bay, rock hall. My extension is 60421. Thanks, Wei Zhou

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phenix map not reading in chimera
by Geoffrey Feld 02 Dec '09

02 Dec '09

Greetings, I'm trying to make a figure showing off my best density from a 2Fo-Fc map I generated using phenix.refine. The output file has a .map suffix. However, Chimera gives an error about the header, which I've included: MRC header value nsymbt (538976288) is invalid. How do I give Chimera a map with a header it can read? Thanks, -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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Chimera question with Mac
by Durga Velukumar 30 Nov '09

30 Nov '09

Hello, I'm an undergraduate student at the University of Georgia and I'm using your system, UCSF Chimera, for my powerpoint presentation. I'm having some problems with trying to create a movie. I have a MacBook Pro, which I just got this recent August, and downloaded the latest Chimera version for the Mac. I'm trying to save the commands in a separate file, like TextEdit, but I don't know what type of file to save it as. I'm hoping to be able to open the file through Chimera to play the movie. I tried saving the commands as "movie.cmd" but TextEdit is not allowing me to save that type of file. Any help would be greatly appreciated. Thank you, Durga

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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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<< Versions to download >>
by Hatuey Hack 18 Nov '09

18 Nov '09

Hello, I would like to know if it is possible to put the version number of Chimera in the download or to add it to the file name. Regards and keep the good work!, Hatuey ___ Mike Ditka <http://www.brainyquote.com/quotes/authors/m/mike_ditka.html> - "If God had wanted man to play soccer, he wouldn't have given us arms."

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control of scale in STL output files
by Jonathan Schaefer 18 Nov '09

18 Nov '09

Hi- I've got a question about controlling the scale of protein models in .stl files generated by Chimera under File/Export Scene in the GUI. I'm trying to print a 3D model of two interacting proteins with a rapid prototyping machine that takes .stl files as input. The two proteins are co-crystalized and contained in one .pdb file (1nbf). I want the two proteins to be printed at the same scale so that I could fit them together like legos. Can I achieve this by getting a scale set, then showing just the first chain and exporting the data to a .stl file, followed by showing just the other chain and exporting the data to a second .stl file? I'm a novice to Chimera, so I might be missing something obvious. Any help you offer will be appreciated. Jonathan Schaefer Morgan Lab UCSF

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making a movie in Chimera
by Victor Padilla-Sanchez 18 Nov '09

18 Nov '09

Hi, my name is Victor and I would have a question about a problem that I have making movies. I record the movie in MPEG 4 format and everything seems fine but when I want to play the movie in Quicktime I obtain just a black screen playing just that. Could you help me with this problem. Thank you very much Victor

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capping surface with a VRML model
by Damien Larivière 18 Nov '09

18 Nov '09

Dear all, It is possible in Chimera to cap the clipped surface of an isosurface made with the Multiscale Model tool. However, if the isosurface is exported in VRML and then reopened in Chimera, it is no more possible to cap the clipped surface. This function (surface capping) is very interesting in particular when the scene is crowded by many proteins. Is it a way to cap VRML model? Many thanks for your help! Damien

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