From: Michael G. L. <ml...@um...> - 2004-08-17 23:42:58
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Hi, I have a file which contains a protein and a bunch of ligands. The ligands come from a Monte Carlo simulation where they were allowed to talk to the protein, but not to eachother. So, lots of the ligands overlap. When PyMOL sees this, it draws bonds between the ligands. Every time I load up one of these structures, I have to unbond things with something like for i in range(160,660):cmd.do('unbond resi %s, not resi %s'%(i,i)) which takes a *really* long time. Is there a faster way to do this? I once hacked up the PyMOL source so that HETATMS with resi > N didn't get bonded to anything else in the first place, but that's obviously a bad way to do things (and I can't seem to compile things myself on our SGIs, so it doesn't work there anyway). Thanks, -michael -- This isn't a democracy;| _ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mlerner@umich |
From: Kaushik R. <kx...@ps...> - 2004-08-18 08:40:07
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If you have a PDB file of the ligands and know the number of atoms in each ligand, then you could introduce a TER card after the each ligand. That way PyMOL will not draw bonds between the ligands. If you want to visualize it one after the other then MODEL and ENDMDL cards before and after each ligand would work too. -Kaushik On Tuesday, August 17, 2004, at 01:02 PM, Michael George Lerner wrote: > > Hi, > > I have a file which contains a protein and a bunch of ligands. The > ligands come from a Monte Carlo simulation where they were allowed to > talk > to the protein, but not to eachother. So, lots of the ligands overlap. > When PyMOL sees this, it draws bonds between the ligands. Every time I > load up one of these structures, I have to unbond things with something > like > > for i in range(160,660):cmd.do('unbond resi %s, not resi %s'%(i,i)) > > which takes a *really* long time. Is there a faster way to do this? I > once hacked up the PyMOL source so that HETATMS with resi > N didn't > get > bonded to anything else in the first place, but that's obviously a bad > way > to do things (and I can't seem to compile things myself on our SGIs, so > it doesn't work there anyway). > > Thanks, > > -michael > > -- > This isn't a democracy;| _ |Michael Lerner > it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan > -Torrence, Bring It On| - against HTML email X | Biophysics > | / \ | mlerner@umich > > > ------------------------------------------------------- > SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media > 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 > Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift. > http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Michael G. L. <ml...@um...> - 2004-08-18 16:30:44
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[Kaushik Raha] > If you have a PDB file of the ligands and know the number of atoms in > each ligand, then you could introduce a TER card after the each ligand. > That way PyMOL will not draw bonds between the ligands. That's not quite enough; PyMOL still draws bonds for me. I seem to recall something about PyMOL wanting non-consecutive residue IDs to ensure that things don't get bonded together, but that's still not enough: select nonprot, resi 160-660 alter (nonprot),resi=str(int(resi*2)) save thing.pdb delete all load thing.pdb still produced the unwanted bonds (and I made sure that there were still TER cards) [Kristian Rother] > Did you try to split up the file into smaller ones? This should do it. I wrote a cool script that split a file up into chunks on the fly and used read_pdbstr to load the chunks separately. Unfortunately, PyMOL was really slow when dealing with so many objects (it was faster to do the cmd.do('unbond...')). any other ideas? thanks, -michael > On Tuesday 17 August 2004 17:02, Michael George Lerner wrote: > > to the protein, but not to eachother. So, lots of the ligands overlap. > > When PyMOL sees this, it draws bonds between the ligands. Every time I > > load up one of these structures, I have to unbond things |