I would try the volume visualization tools in PyMOL: http://pymol.org/volume
Also, you probably want to be careful about "cross-posting" in two separate forums at the same time... Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. On 5/31/12 9:42 AM, "Bishwa Subedi" <bps...@utu.fi> wrote: >Hi all, > >I would like to make a figure of my protein-ligand complex for >publication. I would like to clearly show the density for the ligand in >the binding cavity. I tried to show it as mesh but the figure is not very >informative. Can anyone help me with clear steps how to get such >informative figure with clear density map for the interacting residues >and with different color for the electron density of ligand. > >Any help with coot would also be helpful. (I could not obtain publication >quality figure with coot in white background, also the representation of >ball and sticks just for binding residues avoiding other non interacting >residues were difficult.) > >Thanx in advance > >Best regards, >Bishwa >-------------------------------------------------------------------------- >---- >Live Security Virtual Conference >Exclusive live event will cover all the ways today's security and >threat landscape has changed and how IT managers can respond. Discussions >will include endpoint security, mobile security and the latest in malware >threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >_______________________________________________ >PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
