alpha values
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Dmitry Ziolkovskiy
Feb 21, 2013, 4:54:08 AM2/21/13
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Dear Hans,
when I create pharmacophore with PyMol plugin alpha values for f.e. HYBL (about 1.4) differs from command line ones (0.7 as described in manual). Is it by design or I have to change something?
Hans De Winter
Feb 21, 2013, 5:30:47 AM2/21/13
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Hi Dmitry,
could you please edit the 'align-it.py' script and comment-out lines 98 and 99? Then rerun the plugin and send me the '/tmp/_tmp_AlignIt.pdb' and '/tmp/_tmp_AlignIt.phar' files?
Thx,
Hans
On 21 Feb 2013, at 10:54, Dmitry Ziolkovskiy <ziod...@gmail.com> wrote:
Dear Hans,when I create pharmacophore with PyMol plugin alpha values for f.e. HYBL (about 1.4) differs from command line ones (0.7 as described in manual). Is it by design or I have to change something?
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Dmitry Ziolkovskiy
Feb 21, 2013, 5:59:07 AM2/21/13
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Hans,
thank you for response,
I've attached temp files and they're seems OK. But saved file (temp.phar) has alpha 1.42857142857
Also in more complex case I've catched nan for some of normals. Is it normal behavior?
Dmitry Ziolkovskiy
Feb 21, 2013, 6:05:36 AM2/21/13
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sorry, have error340 during uploading files, so can't post them here.
Hans De Winter
Feb 21, 2013, 6:06:34 AM2/21/13
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Difficult to say without examples …
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