December 2009 - Chimera-users - RBVI Mailing Lists

help in installation of chimera-1.4-linux_x86_64.exe
by Dr Muhammad Nadeem Kardar 14 Dec '09

14 Dec '09

chimera-1.4-linux(2).exe chimera-1.4-linux.exe chimera-1.4-linux_x86_64.exe I have three files of chimera but unable to execute chimera kindly help Kardar -- M. Nadeem Kardar, PhD Assistant Professor Department of Chemical Engineering COMSATS Institute of Information Technology Defence Road Off Raiwind Road, Lahore, Pakistan Cell# +92-300-2414231 Email: drmnkardar(a)ciitlahore.edu.pk Website: http://www.ciitlahore.edu.pk/researchgroups/bcrg/page/kardar.html

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File conversion question
by Miriam Gochin 12 Dec '09

12 Dec '09

I have a series of docked ligands produced by AutoDock (as .dlg files, containing more than one conformer per ligand) and I would love to be able to view these ligands using the ViewDock utility in Chimera. Is there a file conversion protocol? Thanks so much, Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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image size
by Bala subramanian 11 Dec '09

11 Dec '09

Friends, What is the best way to generate an image of fixed size. Say i want to create an image of 4,4 (width, height) at 300dpi. I tried the following windowsize 1200 1200 When i go to save image--> I saw the pixel width and height changed as *1200, 618* ( I dnt understand why this changes although i set as 1200 1200). So i set the print unit as 'inches', then i entered width and height as 4,4. The final image that it produced has different width and height (4, 6.13). Thanks, Bala

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Curves+ output files
by David Chenoweth 10 Dec '09

10 Dec '09

Problem solved! Sorry, but it seems all I needed to do was show the atoms and bonds. Chimera is reading the file it just doesn't show anything until you tell it to show atoms and bonds. Another surprise with the new Chimera version is that it automatically displays my nucleic acid files with slab bases, filled sugars, and a backbone ribbon. Is there anyway to shut this off so I don't have to go in and manually do it each time I open a nucleic acid structure? Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Curves+ output files
by David Chenoweth 10 Dec '09

10 Dec '09

Hi! I have been using a program called Curves for analyzing nucleic acid crystal structures for quite a while and I have always used Chimera to visualize the output pdb. One file shows the backbone splines and the vectors defining the nucleic acid groove widths (r+bdna_b.pdb) and the other file shows the nucleic acid helical axis (r+bdna_X.pdb). Chimera has always been able to read both of these files until the recent production release where it is no longer able to read the r+bdna_b.pdb file. I have attached the two files and the actual DNA pdb file. Can you please help me fix the problem with reading the r+bdna_b.pdb file in the new production release? Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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creating additional coordinates to save from BIOMT records
by Irene Newhouse 09 Dec '09

09 Dec '09

I'm working with a pdb structure that's icosahedral. The surface is tiled with hexamers and pentamers of its single chain. The unit cell contains 4 chains, 3 from a hexamer and 1 from a pentamer. I need to compare the pentamer inter-chain contacts to those in the hexamer, so I immediately thought of Chimera. I can generate a pretty picture of hexamers & pentamers on screen, but what I can't seem to figure out how to do is to save additional coordinates for the other units of the pentamer, analogous to saving additional coordinates when you fill out a unit cell using the "Higher-order Structure" utilities. Thanks for your help! Irene Newhouse Res. Corp. U of Hawaii _________________________________________________________________ Windows 7: Unclutter your desktop. Learn more. http://www.microsoft.com/windows/windows-7/videos-tours.aspx?h=7sec&slideid…

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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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Chimera-users December 2009