Editing Category:FAQ (section)

===Startup===
Q: I've installed PyMol_0_98 correctly but I can't open my files in .mol2 or .pdb format from the menubar. Instead I can open them with the program. I can't even save the images I create in PyMol and obviously the mivie too.

Could you help me to solve these problems.
Thanks
Vittorio

A1: Vittorio, if I understand you correctly, then you need to (a) make sure you have the PDB file on your machine, say Desktop (or home directory, for *nix), then in the GUI click on, "File"->"Open" then use the dialog to find the file you want to load.  You can save time if you know where the file is by just using PyMol's "load" command
 load fileName, objectName
loads the fileName into a new object called objectName, for example,
 load /tmp/1ggz.pdb, 1ggz

See [[Cmd load|load]], 

A2: To save images you have a couple options.  First, to save a quick raw screen dump type, "png fileName" to save a PNG image (IE and other programs can view these files).  Or, secondly, if you prefer a higher quality image with ray-traced shadows and textures you can do, "ray" then, the above "png" command.

See [[Cmd ray|ray]], [[Cmd png|png]], [[:Category:Using_Pymol|Using PyMol]]

Hope this helps.  If it didn't please restate your question to make it more clear.
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Q: Hi I have a problem. For some reason PyMOl do not display certain areas (several loops) of my .pdb file (1DAN) when in cartoon. When I display the structure in "lines" or "sticks" everything is ok. Furthermore, other .pdb viewers dont have this problem. I have tried several things:
1. Upgraded to the newest version og PyMol.
2. Redefined secondary structure using the "alter command".
3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl.

None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!)
Cheers
Kasper

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Q: Can the startup settings be edited so that MacPyMol starts with a One-Button Mouse mode? Please advise.
A: echo "config_mouse one_button" >> ~/.pymolrc

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Q: What I should write into the .pymolrc (Mandriva Linux) to be able open PyMol with .pdb or .pml from shell? I was able to run pymol *.pdb with old 0.99rc6 version, but then I upgraded Mandriva Linux and this option is not working anymore.