To whom it may concern, I'm using the chimera to visualize a protein ligand docking, but I want to save the best model as a PDB file that I can use anywhere to perform other analysis, is it possible? For example, the pdb that I saved by the chimera do not open in PyMol viewer... Can you help me? Nathalia
Dear Nathalia, We have been careful to make PDB files saved from Chimera follow the official PDB format description, so that other programs that read PDB should be able to read them without problems. I assume you are using "File… Save PDB" from the Chimera menu, or the "write" command. Can Chimera open the file? If not, please just start Chimera and use menu "Help… Report a Bug" and attach the PDB file (the bugreport dialog allows attaching a file) so that we can take a look at it. If Chimera can read it, I really can't say why Pymol or other programs wouldn't like the file. Maybe some users that also use both Chimera and Pymol can send some comments on this issue. 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 Sep 19, 2013, at 5:10 AM, Nathalia Varejão <varejaon@gmail.com> wrote:
To whom it may concern,
I'm using the chimera to visualize a protein ligand docking, but I want to save the best model as a PDB file that I can use anywhere to perform other analysis, is it possible? For example, the pdb that I saved by the chimera do not open in PyMol viewer...
Can you help me? Nathalia
Dear Nathalia, 1) How do you save your pdb file (ligand and receptor included). Did you select the "single file" option at the bottom the save menu? 2) How looks your pdb file in a text editor (worpad for windows or gedit in Linux)? I'm not sure, somebody correct me if I'm wrong, when you are trying to merge two pdb files Chimera introduces some legends ("model") into the pdb file to indicate who is the pdb 1 and pdb 2, respectively. You should try (using your text editor) to find those legends and removing them from the pdb file, save the changes, then, you should be able to open your file in Pymol. Best regards, Aldo -- ========================================= Aldo Segura-Cabrera Postdoctoral Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blood Diseases Institute Cincinnati Children's Hospital Medical Center 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229 e-mail: Aldo.Segura-Cabrera@cchmc.org <asegurac@ipn.mx>; aldosegura@gmail.com =========================================
Dear All, I have generated a movie that shows the rotation of a domain of the protein molecule in Chimera. I want to prepare a figure which shows that trajectory of the domain movement between the 2 states (probably using lines instead of the ribbons). How can I do that in Chimera. Thanks. Andy Anindito Sen (Ph.D)
Department of Cell Biology & Anatomy Graduate School of Medicine University of Tokyo Tel & fax: +81-3-5841-3339
Hi Andy, It sounds like you made a morph trajectory that is being displayed with the MD Movie tool. You can save the whole trajectory to a single PDB file (using main menu: File... Save PDB, and choosing only the morph model and other appropriate settings including saving "all frames" instead of "current frame"). Then maybe save the session so you won't lose your work, but then close session. Open the new single PDB file to see all the different steps at the same time. Then you can color, change display style, etc. For example, commands: rainbow models ribscale licorice ~disp ... to rainbow-color the different steps, make ribbon into a thin tube, and hide atoms. There is also a nice "ViewMotions" web server from the Kantrowitz group that does basically all of this stuff including the morphing, and includes a Chimera session in the output so you can change the orientation etc. as desired before saving an image: <http://viewmotions.bc.edu/> 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 Sep 26, 2013, at 8:10 PM, Anindito Sen wrote:
Dear All, I have generated a movie that shows the rotation of a domain of the protein molecule in Chimera. I want to prepare a figure which shows that trajectory of the domain movement between the 2 states (probably using lines instead of the ribbons). How can I do that in Chimera. Thanks. Andy
participants (4)
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Aldo Segura -
Anindito Sen -
Elaine Meng -
Nathalia Varejão