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Please post your FAQs here. I suggest you write a Q&A style list with a short answer. More involved answers should link to its own page. Just my suggestion. Should we have topics?

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 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 ray, png, Using PyMol

Hope this helps. If it didn't please restate your question to make it more clear.

Q: I've installed PyMol_0_98, and recently my structures have stopped displaying. I've tried uninstalling PyMol_0_98 and installing PyMol_0_97, and yet i've ran into the same .pdb files no longer display, although it is evident that they are being loaded and I can edit them.

Does anybody have any clue as to what might be the problem? Thanks, shebsmehr

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