Re: [PyMOL] Problem with finding polar contacts

Hi,
I am running version 1.7.2.1 from the svn (revision 4088) and the bug 
with dynamic_measures persists. Unsetting it as in that link corrects 
that issue though.

I can send you my files that find the error if you would like.

Matt

On 08/27/2014 11:19 AM, Thomas Holder wrote:
> Hi Matt,
>
> this was a bug with the dynamic_measures setting. It was fixed in PyMOL 1.7.0. So please upgrade PyMOL or read this old post for workarounds:
>
> http://sourceforge.net/p/pymol/mailman/pymol-users/thread/501...@us.../
>
> Cheers,
>    Thomas
>
> On 27 Aug 2014, at 10:30, Matthew Baumgartner <mp...@pi...> wrote:
>
>> Hi,
>> I ran into a bug with the find polar contacts function (distance with
>> mode=2) today. The problem arises when I was trying to find the hydrogen
>> bonds between a ligand and a receptor that had been processed with
>> reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A
>> bug/feature of reduce is that when it adds hydrogens, it gives all of
>> the newly added hydrogens a 0 as the atom index in the pdb file.
>> So what happens is when you try to find the polar contacts between the
>> ligand and the receptor, it draws a bond between a ligand atom and the
>> last hydrogen (which happens to be non-polar) which is 12 A away. I'm
>> guessing it is because pymol is using the atom index from the pdb.
>> One possible alternative would be to index based on the set of the atom
>> id, atom name, residue name, chain id, and residue ID, but I don't know
>> how feasible that is.
>>
>> The work around that I have found is to pass the receptor through babel
>> after processing with reduce. babel prot.pdb prot2.pdb , which
>> re-indexes the atom ids.
>>
>> Matt Baumgartner