[email protected] wrote on 11/28/2006 05:25:15 AM:
> Hi all, > I'm new to this list and I'm a newbie of Pymol. > I'm trying to do some morphing movies between different complexes (same > protein but different ligands). I'm having troubles cause the morphed > structures (pdbs generated by lsqman (procedure taken by this page > http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html )) partially > lost the informations about the ligands (only the core of the similar > portion of each ligand is mantained, but the substituent are lost). Do > you know if there is a way to solve/overcome this problem? > Another related question is if was possible to set a ray resolution > (let's say ray 2400, 2400) for the creation of all the frames of the > movie (multiple png). I've been able to do that for one frame at time, > manually...is there the possibility to set a different resolution > recursively for all the image creation processes? > Many thanks in advance and sorry for the long message > Andrea > > Dear Andrea - You should try using the Gerstein Morph Server: http://www.molmovdb.org/molmovdb/morph/ The core algorithm uses CNS, so if your structure is parsed properly by CNS, it should emerge from the server looking OK. You'll get a small movie back from the server, and you can also ask it to send you the PDB files used for each frame, so you can make your own movies in Pymol. For making movies in complicated situations like this, I've usually used script files to explicitly define each frame of the movie: load file1.pdb (rendering commands) ray 2400,2400 png frame1.png delete file1 load file2.pdb etc... You get a long script file, but you can use a text editor to copy & paste the text blocks. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
