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 Post subject: CIF File?
PostPosted: Sat Jan 29, 2011 12:50 am 
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Hi forum,

I found some CIF file at internet. Can I use them within ePMV and how can I read them?
Source of the CIF file is http://www.crystallography.net

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Highlander2000


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 Post subject: Re: CIF File?
PostPosted: Sat Jan 29, 2011 1:19 am 
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hi Highlander2000,

PMV is supposed to support the cif format.So ePMV hsould as well.
try to load it using the browse button, If nothing happen, well the cif file your trying to load cant be read by PMV.
I will try to have a look at this next week see if we can make the cif parser more robust.

Btw You can also try to fecth cif file from the PDB directly using their ID (click the pulldown menu next to the fecth button to see the different option/serer currently supported)

Ludovic


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 Post subject: Re: CIF File?
PostPosted: Sat Jan 29, 2011 11:46 am 
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hi Ludovic,

I see, PMV is the stand alone version. Perhaps, if it is able to read cif-file, I could use it and after loading the file, I could save it as pdb?
Is there a known problem, to have the ePMV plugin installed and then installing the MGLTools?
Can I find PMV within the directory of MGLToolsPckgs I already have with ePMV?

By the way, I'm not able to unzip MGLToolsPckgs.zip (62MB) which can be found here http://mgltools.scripps.edu/downloads. Winzip says it might be no archive?

Thanks
Highlander2000


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 Post subject: Re: CIF File?
PostPosted: Sat Jan 29, 2011 4:31 pm 
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hi Highlander2000,

what I mean is that if ePMV can't load it is because PMV can't as well as ePMV and PMV are the same thing. So If you can get your Cif file you need to use another software for that or wait until we get a more robust cif parser.
You can try chimera (http://www.cgl.ucsf.edu/chimera/) that seems to read mostly any kind of file, and then write as pdb.

btw since you have ePMV installed and you are using windows, i will not recommand installing PMV as it will install a different python version, and could bring some problem using ePMV.

hope this help
Ludovic


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 Post subject: Re: CIF File?
PostPosted: Sat Jan 29, 2011 6:28 pm 
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hi Ludovic,

thanks for the great tip with chimera. This works good for me at the moment, until cif parser is more robust in ePMV.

Highlander2000


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 Post subject: Re: CIF File?
PostPosted: Sat Jan 29, 2011 7:32 pm 
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Highlander2000 wrote:
By the way, I'm not able to unzip MGLToolsPckgs.zip (62MB) which can be found here http://mgltools.scripps.edu/downloads. Winzip says it might be no archive?

Thanks for the info. I couldn't open it either. I removed the zip file link. Please use the one from http://mgltools.scripps.edu/downloads/nightly which works fine. Thanks!

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 Post subject: Re: CIF File?
PostPosted: Tue Feb 01, 2011 4:47 pm 
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hi Highlander2000,

sargis work out our cif parser to handle theses files. You should be able to open it in ePMV using the new parser. But you cant use all representations. Seems that only point cloud line, CPK and coarse surface are working, the other will produce an error.
You can find the new parser here :
http://mgldev.scripps.edu/cgi-bin/viewv ... .1&view=co
download this file and paste it in MGLToolsPckgs/MolKit/


Ludovic


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