https://wiki.pymol.org/api.php?action=feedcontributions&user=Kasperrand&feedformat=atomPyMOL Wiki - User contributions [en]2024-03-28T23:52:04ZUser contributionsMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=Category:FAQ&diff=3989Category:FAQ2005-10-14T08:56:36Z<p>Kasperrand: </p>
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<div>==FAQ==<br />
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===Overview===<br />
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?<br />
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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.<br />
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Could you help me to solve these problems.<br />
Thanks<br />
Vittorio<br />
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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<br />
load fileName, objectName<br />
loads the fileName into a new object called objectName, for example,<br />
load /tmp/1ggz.pdb, 1ggz<br />
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See [[Cmd load|load]], <br />
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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.<br />
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See [[Cmd ray|ray]], [[Cmd png|png]], [[:Category:Using_Pymol|Using PyMol]]<br />
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Hope this helps. If it didn't please restate your question to make it more clear.<br />
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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 problem...my .pdb files no longer display, although it is evident that they are being loaded and I can edit them.<br />
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Does anybody have any clue as to what might be the problem?<br />
Thanks, shebsmehr<br />
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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:<br />
1. Upgraded to the newest version og PyMol.<br />
2. Redefined secondary structure using the "alter command".<br />
3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl.<br />
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None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!)<br />
Cheers<br />
Kasper</div>Kasperrandhttps://wiki.pymol.org/index.php?title=User_talk:Kasperrand&diff=10798User talk:Kasperrand2005-10-14T08:53:58Z<p>Kasperrand: </p>
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<div>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:<br />
1. Upgraded to the newest version og PyMol.<br />
2. Redefined secondary structure using the "alter command".<br />
3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl.<br />
<br />
None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!)<br />
<br />
Cheers<br />
Kasper</div>Kasperrand