[PyMOL] Hetatm Problems
Hi All, There are some questions to which I could not find the answer by myself : 1) I can select till 4 atoms by mouse (Ctrl+M_Click) from a surface.But I will be interested in moving them - as a group - to another place (i.e. changing their coordinates). How can I do this with the mouse and Ctrl/Shift keys ? 2) I would be interested to select more than 4 atoms from a surface. Take for ex. the following pdb file : HETATM6 H00 NON A 1 12.457 10.370 5.554 1.00 0.00H HETATM7 H00 NON A 1 12.457 0.837 5.554 1.00 0.00 H HETATM8 H00 NON A 1 15.209 5.603 5.554 1.00 0.00 H HETATM9 H00 NON A 1 17.961 10.370 5.554 1.00 0.00H HETATM 10 Au00 NON A 1 8.240 4.758 0.045 1.00 0.00Au HETATM 11 Au00 NON A 1 10.993 9.524 0.045 1.00 0.00 Au HETATM 12 Au00 NON A 1 13.745 14.291 0.045 1.00 0.00 Au HETATM 13 Au00 NON A 1 13.745 4.758 0.045 1.00 0.00 Au HETATM 14 Au00 NON A 1 16.497 9.524 0.045 1.00 0.00 Au HETATM 15 Au00 NON A 1 19.249 14.291 0.045 1.00 0.00 Au HETATM 16 Au00 NON A 1 19.249 4.758 0.045 1.00 0.00 Au HETATM 17 Au00 NON A 1 22.001 9.524 0.045 1.00 0.00 Au HETATM 18 Au00 NON A 1 24.753 14.291 0.045 1.00 0.00 Au HETATM 19 Au00 NON A 1 5.465 4.748 0.058 1.00 0.00 Au HETATM 20 Au00 NON A 1 8.217 9.515 0.058 1.00 0.00 Au I can not build a selection based on residue name or residue number (it is 1 for the entire file). I can however have a selection based on the residue id select myselect, id 7+14+15+16+18+19 My question is : having in face the surface how do I know what is the residue id of an atom ? Ctrl+L/M/R_Click display only : You clicked /ex//A/NON`1/Au00 . Nothing about id or atom coordinates which are the only unique in my case. I am working with PyMol v 0.97 on a Windows XP system Thanks for any help, Ed __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
[PyMOL] newbie: converting sdf to png (or other image format)
Sorry for the total newbie question, but I have to start somewhere. I'm trying to help someone convert a number of sdf files (1000s) to image files to be used on a web page. I don't know much about chemistry or pymol, but from googling around this seemed like a good place to start my investigation. I have several 1000 sdf files to convert so working manually through the gui would be prohibitive. I'd like to either generate the images on the fly as needed or do all of them once in a batch. If someone knows of a (preferably free) tool for doing this already I'd appreciate being pointed in the right direction. Otherwise any hints on how this might be done in pymol would be great. I've been googling around and browsing thru the documentation but still not clear to me how to do the above. Seems like there is a way to script pymol. Are there some examples of simple scripting that shows how to open a file and then save as a given format? Seems like that would get me most of the way there. thanks, -- Dustin Lee qhfgva=rot13(dustin)
Subject: [PyMOL] newbie: converting sdf to png (or other image format)
Shameless PyMolWiki plug time: We PyMol frequenters have setup a PyMolWiki and you can get lots of information and newbie hints/tips there. Already over 100 pages; topics varying from simple commands & scripts to more complicated 3D information. (Feel free to add what you know!) Your specific question may be answered (or assisted) by browsing to: http://www.pymolwiki.org/index.php/Category:Scripting_Script_Library Also use the search function to look for more scripting examples. There's convient Python line numbering and coding for scripts. I'm guessing you can also learn more by checking out the load, save and png (as well as ray) commands. Windows shell scripting I think allows a FOR command so you can loop through files. Otherwise, just write a Python script. HTH, -- Jason On Sun, 2005-03-06 at 20:18 -0800, pymol-users-requ...@lists.sourceforge.net wrote: > Subject: [PyMOL] newbie: converting sdf to png (or other image format) > -- Jason Vertrees BSCB Graduate Student @ UTMB, Galveston javer...@utmb.edu :: http://www.bscb.utmb.edu
