Re: [PyMOL] Viewing cavities?
Marcus, Here is one way (courtesy Kyle Lassila): Check out VOIDOO: http://xray.bmc.uu.se/usf/voidoo.html Then: Use VOIDOO to make a map of the cavity. That gives a map in one of the electron density formats, .ezd. Then use MAPMAN (also found as Uppsala Software Factory) to convert to .ccp4 so that pymol can read it. Load the map with load filename.ccp4. View the map with isomesh msh1,filename,1.0 mapman input file: RE m1 cavity_1.ezd NEWEZD WR m1 cavity_1.ccp4 CCP4 QU sample voidoo input file: c n voidoo_etc/cavity.lib design.pdb 0.75 1.2 20 1.05 1 y 49.1 32.7 46.5 n cavity.log y 10 o 0.90 15 0.05 0.05 n y cavity 0.2 n Eric Marcus Collins wrote: Hello all, The surface rendering in PyMOL is quite nice, but I cannot separate the branches of the surface. That is, I would like to view a large cavity inside of a protein independently from the outer, solvent accessible surface. Is anyone aware of a means to do this? Marcus Collins * Marcus D. Collins Gruner Biophysics Group, Cornell University Dept. of Physics, LASSP (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650 You have opened a new door, and I share this with you, for I have been where you are now. * --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] wild card
Anyone who works with nucleic acids will certainly prefer the current situation. From the PDB format guidelines: * The asterisk (*) is used in place of the prime character (') for naming atoms of the sugar group. The prime was avoided historically because of non-uniformity of its external representation. Eric David A. Horita wrote: Warren, Personally, I'd much rather have wild-card selections in atom names and have to deal individually with the ill-conceived PDB files than the other way around. Regards, David Horita -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren DeLano Sent: Wednesday, February 18, 2004 10:56 AM To: 'John Berrisford'; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] selecting multiple atoms ie oxygen John, color red, 5paa and elem o The problem with using asterices as wildcards in atom names is that some ill-conceived PDB files actually use them in atom names. However, PyMOL does support the use of a terminal wildcard in some cases, such as with the delete command... create obj01, none create obj02, none delete obj* And with residue names color red, as* color blue, gl* color pink, hi* Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of John Berrisford Sent: Wednesday, February 18, 2004 3:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] selecting multiple atoms ie oxygen I wish to select multiple oxygens (labelled O1, O2 etc.. within my pdb file) and colour them red for example. Is there any easy way of doing this other than typing out a list of all the oxygens I wish to select? eg. color red, (5paa and (name o1+o1a+o2+o3+o4+o5+o1p+o2p+o3p)) I know in molscript its posible to use a o* label to select all oxygens, is such a switch possible in pymol. It doesn't work, or I am using the wrong syntax if its possible. Any thoughts would be appreciated. John --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id56alloc_id438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] save molecule format
All- When using the Pymol ability to save a structure as a PDB file it appears that the "standard" PDB format is changed in at least one instance. When a sidechain has more than one conformation in the crystal structure (A, B), the saved PDB file will have the two conformations before the amide of the group instead of after. Doing nothing more than loading and then saving a structure to a new file yields the following results. Original file: ATOM 87 N SER A 13 2.735 9.167 21.169 1.00 9.31 N ATOM 88 CA SER A 13 2.455 9.048 19.752 1.00 10.35 C ATOM 89 C SER A 13 1.623 10.233 19.278 1.00 9.48 C ATOM 90 O SER A 13 1.775 10.681 18.144 1.00 10.31 O ATOM 91 CB ASER A 13 1.719 7.737 19.462 0.34 10.21 C ATOM 92 CB BSER A 13 1.705 7.743 19.467 0.66 14.26 C ATOM 93 OG ASER A 13 2.552 6.621 19.728 0.34 11.15 O ATOM 94 OG BSER A 13 0.474 7.699 20.166 0.66 22.03 O After saving to pdb: ATOM 87 CB ASER A 13 1.719 7.737 19.462 0.34 10.21 C ATOM 88 OG ASER A 13 2.552 6.621 19.728 0.34 11.15 O ATOM 89 CB BSER A 13 1.705 7.743 19.467 0.66 14.26 C ATOM 90 OG BSER A 13 0.474 7.699 20.166 0.66 22.03 O ATOM 91 N SER A 13 2.735 9.167 21.169 1.00 9.31 N ATOM 92 CA SER A 13 2.455 9.048 19.752 1.00 10.35 C ATOM 93 C SER A 13 1.623 10.233 19.278 1.00 9.48 C ATOM 94 O SER A 13 1.775 10.681 18.144 1.00 10.31 O As far as I can tell it only happens with those sidechains with multiple conformations. Anyone else have this problem? Is there a quick fix? Pymol 0.93 on Fedora Core 1. Thanks. Eric Zollars