January 2010 - Chimera-users - RBVI Mailing Lists

Rename atoms...
by Yasser Almeida Hernández 25 Jan '10

25 Jan '10

Hi.. How can i rename atoms? How would be the script python syntax? Thanks Best regards -- Lic. Yasser Almeida Hernández Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 246 ---------------------------------------------------------------- Correo FENHI

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Fitting a structure to a DAMMIN/SAXS model/volume
by Byrd, Robert A. (NIH/NCI) [E] 25 Jan '10

25 Jan '10

Chimera Team & users, We have been using SAXS data and the DAMMIN software from the Svergun group. The bead model that DAMMIN produces approximates the shape and volume of the molecule. If one has a three dimensional structure of the molecule, then it becomes valuable to do a best superposition of the structure into the bead-model shape. Chimera is our preferred molecular display & analysis software, and we would like to perform this fitting in Chimera. Do you have any experience in how to display the bead-model output of DAMMIN and to fit or superimpose the bead model with a known structure? Thanks Andy Byrd

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Re: [Chimera-users] Failed surface calculation
by Elaine Meng 25 Jan '10

25 Jan '10

Hi Ibrahim, First, make sure you set the New Surfaces preference value before showing the surface for the first time -- it would not affect a surface that already exists (even if it is hidden when you set the preference). If the surface already exists, you could change it to single-component by changing its attributes, such as with the command given in my previous message. However, if the Reply Log says there is only one component of the surface in both sets of parameters, I think it is still possible for a surface area to decrease when the VDW radii increase. I'm imagining a case where there is a lot of concavity. Similar to the situation of an inside bubble shrinking or disappearing, a concave part of the surface could become shallower or much less extensive as the VDW radii are increased. This is just a case I'm imagining. If you feel there is an error, please use "Help... Report a Bug" in the Chimera menu and be sure to describe exactly what you did to get the two area measurements, what two values you are comparing, and attach the PDB file of the structure (or just include the PDB ID in your description if it is taken directly from the Protein Databank). 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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Failed surface calculation
by Ibrahim Moustafa 23 Jan '10

23 Jan '10

Dear Chimera, I¹m trying to calculate the surface for a protein but I get an error ²Surface calculation failed, mscalc returned code 5². I tried to change the probe size from 1.4 to 1.5 or 1.7 but still getting the same error. I know there is some issue with The code that calculates the surface (if I¹m not wrong) but I wonder if there is a way to get around this. For some smaller pdb files I don¹t have this problem. I¹m not sure if the size of the protein is a factor here. The protein having the problem is a single chain protein with 880 amino acids. Any advice? Thanks for help. Ibrahim

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Compatibility of Chimera with MacOS 10.4.11. PPC
by Arwid.Bierbach 23 Jan '10

23 Jan '10

Ldies and Gentlemen, The Chimera version Mac OS X (Aqua, PowerPC) chimera-alpha-osx_ppc_aqua.dmg Size: 73241868 bytes MD5: 39623fa9e0d9f4a869a4c985d45223bb Jan 22, 2010 is not compatible with G4 PPC Mac OS 10.4.11. Do you plan to quit the G4 PPC OS 10.4.11. - Compatibility ???? With best regards, Dr. Arwid Biebach, Germany

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Massive superposing...
by Yasser Almeida Hernández 22 Jan '10

22 Jan '10

Hi... I'm performing a massive superposing of aminoacids in different conformations. The first model is a arginine "template" reference structure that is the fixed model in all matching iterations. I've loaded 236 models and i want to match the arginine guanidine group on the template guanidine. In each iteration i execute two matching, with different atoms selections. The first selection is the "right" selection: CD,NE,CZ,NH1,NH2 and the second is the "inverse" selection: CD,NE,CZ,NH2,NH1. I run the two superpositions, and i want to show that with the minimal RMSD between the guanidine groups. This is the code: import chimera from chimera import runCommand right = "@CD,NE,CZ,NH1,NH2" inverse = "@CD,NE,CZ,NH2,NH1" for i in range(2,328): print "Superposing..." runCommand("match #"+str(i)+right+" #0"+right+"; close 1") right_rmsd = runCommand("rmsd #"+str(i)+right+" #0"+right+"; close 1") runCommand("match #"+str(i)+right+" #0"+right+"; close 1") inverse = runCommand("rmsd #"+str(i)+inverse+" #0"+right+"; close 1") if right < inverse: print "Minimum RMSD =",right,"\n\n" runCommand("match #"+str(i)+right+" #0"+right+"; close 1") elif right > inverse: print "Minimum RMSD =",inverse_rmsd,"\n\n" runCommand("match #"+str(i)+right+" #0"+right+"; close 1") In principle this script should show the matching with the minimum RMSD, but it doesn't work. Please, help... Thanks -- Yasser Almeida Hernández, BSc Center of Molecular Inmunology (CIM) Nanobiology Group P.O.Box 16040, Havana, Cuba Phone: (537) 271-7933, ext. 246 ---------------------------------------------------------------- Correo FENHI

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Measuring Distances in Chimera
by Beale, John 21 Jan '10

21 Jan '10

Hello, I am trying to measure distances between atoms using the Tools -> Structure Analysis -> Distances routine. Chimera is requesting that two atoms must be selected in the main graphics window for this to work. I can't figure out how to select the atoms. Can someone help me? John

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Ligand Binding to Homodimeric Proteins
by Nancy 18 Jan '10

18 Jan '10

Hi All, I am performing molecular docking simulations of a ligand binding to a homodimeric protein, to determine a potential binding site(s). Due to the symmetrical nature of a homodimer, I would expect that the binding site(s) on one protomer would be identical on the other protomer. Therefore, a ligand should bind with equal probability and affinity to both sides of the protein. However, when I perform a molecular docking simulation (using an X-Ray crystal structure), the ligand preferentially binds to one side of the homodimer. Is this outcome likely the result of errors inherent in the X-Ray crystal structure, as one would expect identical binding to both sides? Thank you very much. Nancy

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adding hydrogens and charges
by Elaine Meng 18 Jan '10

18 Jan '10

> 1 how can i calculate the charges for molecular. > to calculate the charges both for ligand and receptor > individually. > if i want to do docking,if i must calculate charges. > 2 how can i add hydrogen for HIS. Maybe , no exact position for HIS. > how can i add hydrogen directly? > thank you very much! > Hello, Use the Dock Prep tool (in menu, Tools... Structure Editing... Dock Prep). It can do several things to prepare a structure, including adding hydrogens and charges. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html> 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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Re: [Chimera-users] [chimera-dev] Calculating RMSD
by Elaine Meng 15 Jan '10

15 Jan '10

Hi Victor, I'll CC the chimera-users(a)cgl.ucsf.edu list -- that address is better for general Chimera "user" questions, while chimera-dev is more for "programmer" questions, i.e. involving python or other code. The "rmsd" command does not automatically use serial number to pair the atoms. You can control the order by specifying the residues and their atoms in the command. Of course, that can be painful if you want to include very many atoms in the calculation. If the order is not given in the command, "the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number" as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> You can see command manual pages using the "help" command, e.g.: help rmsd What approach is best depends on your particular case -- whether these are multi-residue macromolecules or single-residue small molecules, and how many atoms you want to include in the calculation. If they are single-residue small molecules, you might just modify the mol2 files so that the atoms you want to pair have the same names in the two structures (but unique within a structure). 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 Jan 15, 2010, at 2:11 AM, Victor Muñoz wrote: > Hi, > I want to calculate the RMSD between two mol2 structures in place. > The two structures are different forms of the same structure. I > haver modified the mol2 so that the two of them have the same > serialNumber in their respective atoms. The problem is that when I > use the command rmsd #model1 #model2, it return an incorrect value > of the rmsd, as the value showed is too high, about 5, when it > should be about 1 (the two structures are very similar). Is there > any way to calculate the RMSD value in place correctly or I am > doing anything wrong? > Thanks for your help. >

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