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Re: [PyMOL] Pymol recolour B factors
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From: Robert C. <rob...@qu...> - 2019-03-22 13:39:00
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Hi Mark, In that data2bfactor.py script (which I wrote) you need to provide the molecular object name, not a file name. In other words in your example you should load the 1d3z.pdb file as an object (defaults to 1d3z as object name). Then after using the run command to load the script into your pymol session then you can type: data2b_res 1d3z, shift_to_b.txt The other script you mention works the same way. The pdb file needs to be loaded into PyMOL as a molecular object first. Cheers, Rob On Fri, 2019-03-22 11:36 +0000, Dr Mark Bostock <mj...@ca...> wrote: > Hello, > > I'm trying to recolour the B factors in a pymol file with chemical > shift differences (from NMR data). There's a nice script here for > this http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ > (data2bfactor.py) and also a simpler one here > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffigshare.com%2Farticles%2FPymol_script_loadBfacts_py%2F1176991&data=02%7C01%7Crobert.campbell%40queensu.ca%7C664f1bfa0c934c52f40108d6aebdf161%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636888528158871468&sdata=jDmJ4NSc%2F%2BXy5IG%2BRCCsQOmqh1Xj9l4j6gTMEmJB6Zc%3D&reserved=0. > > In both cases after loading the script with the run command, when I > execute the script I get the following error > > data2b_res 1d3z.pdb, shift_to_b.txt > Selector-Error: Invalid selection name "1d3z.pdb". > ( 1d3z.pdb )<-- > > The pdb file and list of new b-factor values are in the same > directory and can be filled in with tab-completion. I've also tried > using the full file path but get a similar error. I've tried with a > couple of different pdb files as well so it's not just a problem with > that particular pdb file. > > I'd be grateful if anyone has any experience with this or suggestions > as to what is going wrong. > > Thanks in advance, > > Mark > > > > _______________________________________________ > PyMOL-users mailing list > Archives: > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=02%7C01%7Crobert.campbell%40queensu.ca%7C664f1bfa0c934c52f40108d6aebdf161%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636888528158871468&sdata=rhUIX1kYhGF0ax1YHrbOBvO5agrVsRdkuUKYJA9A26w%3D&reserved=0 > Unsubscribe: > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=02%7C01%7Crobert.campbell%40queensu.ca%7C664f1bfa0c934c52f40108d6aebdf161%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636888528158881482&sdata=rsNyC33RqUJbXDKsWpMVagHLOXVUH4bM8vo3cdmTtlE%3D&reserved=0 -- Robert L. Campbell, Ph.D. Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |