- Chimera-users - RBVI Mailing Lists

model loop in chimera
by Mikolajek H. 11 Dec '12

11 Dec '12

Hi, I am trying to model a protein in chimera using the model loop command. I get this error: Modeller temporary directory: c:\users\admini~1\appdata\local\temp\modellerjtn4xd Unable to run modeller: [Error 2] The system cannot find the file specified Do you know where I am going wrong? Best wishes Halina

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surface calculation
by Anton Vila Sanjurjo 11 Dec '12

11 Dec '12

Hi, I have seen posts regarding this problem before. Here is the log I got after attempting to render a surface representation of the 50S ribosomal subunit (rcsb ID: 3CPW). #0, chain 0: 23S ribosomal rna #0, chain 1: L35E #0, chain 2: 50S ribosomal protein L44E #0, chain 4: 5'-R(*cp*cp*ap*(phe)*(aca))-3' #0, chain 9: 5S ribosomal rna #0, chain A: 50S ribosomal protein L2P #0, chain B: 50S ribosomal protein L3P #0, chain C: 50S ribosomal protein L4P #0, chain D: 50S ribosomal protein L5P #0, chain E: 50S ribosomal protein L6P #0, chain F: 50S ribosomal protein L7AE #0, chain G: HS6 #0, chain H: 50S ribosomal protein L10E #0, chain I: 50S ribosomal protein L13P #0, chain J: HMAL13 #0, chain K: 50S ribosomal protein L15P #0, chain L: 50S ribosomal protein L15E #0, chain M: 50S ribosomal protein LC12 #0, chain N: 50S ribosomal protein L18E #0, chain O: 50S ribosomal protein L19E #0, chain P: 50S ribosomal protein L21E #0, chain Q: HL31 #0, chain R: 50S ribosomal protein L23P #0, chain S: 50S ribosomal protein L24P #0, chain T: 50S ribosomal protein L24E #0, chain U: HL21/HL22 #0, chain V: 50S ribosomal protein L30P #0, chain W: 50S ribosomal protein L31E #0, chain X: 50S ribosomal protein L32E #0, chain Y: HL5 #0, chain Z: 50S ribosomal protein L37E C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface calculation failed, mscalc returned code 5. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface 3CPW.pdb, category ligand, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 989.35 Total solvent accessible surface area = 1473.85 In this case, I am not interested in splitting the file into its individual chains. I have also unsuccessfully played with the probe-radius and vertex parameters. I should mention that I was able to get this to work with previous versions of Chimera (1.5.something) and that small proteins can be successfully rendered with the latest versions. best, Antón -- Antón Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Química Fundamental Facultade de Ciencias Universidade de A Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s(a)gmail.com

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placing models on the same plane
by Bala subramanian 10 Dec '12

10 Dec '12

Friends, I open two pdb files. When i visualize them, one model is far away from the viewer and another is closer. I want to put both models on the same plane in order to make a figure. Is there any way to do this without doing a fitting. Thanks, Bala -- C. Balasubramanian

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Re: [Chimera-users] [chimera-dev] Hello~ how to make a 3D structure for a number of family genes
by Elaine Meng 10 Dec '12

10 Dec '12

Hi Tao Zhao, Chimera does not do homology modeling directly, but it can connect to a web server running the Modeller program. To use this feature, you would first need to go to the Modeller web site and sign up for a license key <http://www.salilab.org/modeller/registration.html> -- it is free for noncommercial use. A full explanation of homology modeling is not feasible for this mailing list (there are probably several books and thousands of papers on this topic), but for a description of the Modeller interface in Chimera, see: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> ... and for more about how to get the input ready... it sounds like you are "Starting with a structure already known to be a suitable template": <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> There is also a tutorial, but be aware that it is only one example, and the process may be different depending on your protein of interest and what is known about it. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.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 P.S. better to send questions about using Chimera to chimera-users(a)cgl.ucsf.edu (CC'd on this message), not chimera-dev(a)cgl.ucsf.edu which is meant for programmers On Dec 2, 2012, at 10:21 PM, tao zhao wrote: > Hello, > I am new to chinmera, this tool seems really powerful. Here is my question, I want to build a structure for a number of peptide sequences, all belongs to the AP2 family. > It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next. > > Could you please give me some instruction? > Thank you very much. > > Tao Zhao > Northwest A&F University,Yangling, China

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Re: [Chimera-users] Disulfide bonds
by Elaine Meng 06 Dec '12

06 Dec '12

On Dec 5, 2012, at 1:20 AM, Moritz Bitzhenner wrote: > Hi Elaine, > You are a lifesaver. Thank you very much, it all worked perfectly. Now I have a nice colourful ribbon structure protein with disulfide bonds. The middle of the bond is coloured in yellow, the rest of the sidechain is coloured in light grey. Can I change the colour of the grey sidechain without changing the colour of the AA in the ribbon structure? But it´s not that important. > > I also created a movie of the rotating protein. (Command line: roll). Can I decrease the speed of the rotation? > > With best regards from Germany and many thanks for your help. > Moritz Hi Moritz, Greetings to you in Germany! You can specify that coloring should apply only to atoms/bonds (not ribbons, surfaces, etc.) using the Color Actions dialog. Menu: Actions... Color... all options, and then in that dialog see the "Coloring applies to" section. The same thing can be done in the command line, for example: color goldenrod,a :cys ...means to make atoms-only of Cys residues the color named goldenrod. Each command has a manual page, which you can see with the "help" command (e.g. commands "help roll" "help color") so I recommend looking at those for more details such as how to control the speed of roll. See also the general information on making movies: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.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 P.S. best to send to chimera-users(a)cgl.ucsf.edu so that others can benefit

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Disulfide bonds
by Moritz Bitzhenner 04 Dec '12

04 Dec '12

Dear Chimera Users I am fairly new to the program and I have a particular problem with the display of disulfide bonds. I have an amino acid sequence, I created a pdb-file with Expasys Swiss Model Workspace. I opened the pdb file with Chimera and coloured the ribbon structue (it looks amazing), I even did a movie of my rotating protein. But I cannot display the three disulfide bonds. Is my pdb file lacking the CONECT information? How can I include them? With Swiss PDB Viewer (Deepviewer) I can show the bonds, but somehow I cannot transfer the information to the pdb file and Chimera. I also tried manually bonding the closest cysteins by selecting Cystein residues and "bond" in the command line. How do I select the two single atoms that I want to connect? I read through former similar questions in the list server but nothing helped so far. If you can find any time helping my case, it would be greatly appreciated. With best regards from Germany, Moritz Here is the AA sequence: GEIDNNQCQICELLVKDIIEGLTANQSVEVIEHGLNLICDHIPLHVRVCKQFVDSNFQKIVQFIENHDDPQEICEKCGVC

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stick representation after selection / DNA helical axis
by Damien Larivière 03 Dec '12

03 Dec '12

Dear all, I used the command sel @N1 @N3 to select the N1 and N3 atoms of a nucleic acid structure (like 1bna). when I do "show only" in Actions / Atoms&Bonds, a specific representation is displayed as in the image below: sticks connect N1 atoms of one strand and N3 atoms of the other strand. May you tell me the meaning of this representation and how can I modify it (I mean, how to change the type of atoms to be connected)? In fact, I would like to visually apprehend the helical axis. Is there a way to calculate and display this axis in Chimera? Many thanks for your help Damien

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Fwd: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
by Francois Berenger 30 Nov '12

30 Nov '12

-------- Original Message -------- Subject: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them) Date: Fri, 26 Oct 2012 10:25:10 +0900 From: Francois Berenger <berenger(a)RIKEN.JP> Reply-To: Francois Berenger <berenger(a)RIKEN.JP> To: CCP4BB(a)JISCMAIL.AC.UK Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.

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(no subject)
by Richard Sibout 28 Nov '12

28 Nov '12

Dear users of Chimera, I can't find the definition of ACT, DTV, EDO...in the residue (non standard) section. Can someone help me to find these definitions ? Thanks Richard

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Help... Report a Bug
by amna khan 27 Nov '12

27 Nov '12

hi, when i minimize my structure it gives the following error for my pdb file. that prolone residues is missing and about integral charges. please help me to remove this error #0, chain D: dna (5'- D(*ap*gp*ap*tp*gp*gp*gp*gp*ap*ap*tp*cp*cp*cp*cp*tp*A P*gp*A)-3') #0, chain P: nuclear factor κ-B (nf-kb) Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records Chain-initial residues that are actual N terminii: DA 1.D Chain-initial residues that are not actual N terminii: PRO 43.P Chain-final residues that are actual C terminii: DA 19.D Chain-final residues that are not actual C terminii: GLU 353.P 321 hydrogen bonds Removing spurious proton from 'C' of GLU 353.P Hydrogens added No incomplete side chains Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records Chain-initial residues that are actual N terminii: DA 1.D Chain-initial residues that are not actual N terminii: PRO 43.P Chain-final residues that are actual C terminii: DA 19.D Chain-final residues that are not actual C terminii: GLU 353.P 188 hydrogen bonds Removing spurious proton from 'C' of GLU 353.P Hydrogens added Charge model: AMBER ff99SB Total charge for #0: -15.624 The following residues had non-integral charges: DA 1.D -0.3079 DA 19.D -0.6921 PRO 43.P 0.376 1 model(s) had non-integral total charge Details in reply log Residue #0:43.P (PRO/proline) is missing atoms H_3 and H_2 No incomplete side chains Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records Chain-initial residues that are actual N terminii: DA 1.D Chain-initial residues that are not actual N terminii: PRO 43.P Chain-final residues that are actual C terminii: DA 19.D Chain-final residues that are not actual C terminii: GLU 353.P 188 hydrogen bonds Removing spurious proton from 'C' of GLU 353.P Hydrogens added Charge model: AMBER ff99SB Total charge for #0: -15.624 The following residues had non-integral charges: DA 1.D -0.3079 DA 19.D -0.6921 PRO 43.P 0.376 1 model(s) had non-integral total charge Details in reply log Residue #0:43.P (PRO/proline) is missing atoms H_2 and H_3 regards amna khan

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