[Chimera-users] findclash distance measurements

[Jozef Lewandowski]

Hi Elaine,
Thank you for the response. However, neither
findclash #0.265:7 at c  test H overlap -8 hbond 0 ignoreIntraRes false log 
true bondSeparation 0
nor
findclash #0.265:7 at c  test "H" overlap -8 hbond 0 ignoreIntraRes false 
log true bondSeparation 0
yields no contacts in the situation where the same without the test 
option yields hundreds of contacts. I have also tried to just put 
atom-spec that definitely should be picked up e.g. test  #0.265:7 at ca, 
but that also reports no contacts. If that does not work, does it mean 
that it is a bug?

Józef

On 3/3/10 6:36 PM, Elaine Meng wrote:
> Hi Jozef,
> Looks like your command is exactly right except for the specification 
> of the hydrogens.  I think you just want "H" instead of "@H" to 
> specify element hydrogen.  The "@" signifies atom name -- maybe none 
> of the hydrogens are named H?
>
> Somebody else would have to answer the other part, however, as I'm not 
> a Python coder either.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Mar 3, 2010, at 9:25 AM, Jozef Lewandowski wrote:
>
>> Hi everybody,
>>
>> I am trying to get a list of all hydrogen atoms within certain 
>> distance from a specific atom. I found an old thread suggesting using 
>> findclash for that. When I use:
>> findclash #0.265:4 at c  overlap -8 hbond 0 ignoreIntraRes false log 
>> true bondSeparation 0
>> everything works fine and I get the list of all the atoms within the 
>> desired distance limits. However, I get all types of atoms.
>> To select only for contacts to hydrogens, I have tried to add the 
>> "test" option but when I type:
>> findclash #0.265:4 at c  overlap -8 hbond 0 ignoreIntraRes false log 
>> true bondSeparation 0 test @H
>> the procedure does not report on any contacts. Am I misunderstanding 
>> the syntax? What is the way to get only the distances between :4 at c 
>> and all hydrogens within ~10A?
>>
>> Moreover, I am ultimately interested in the sum of all reported 
>> distances (or more specifically sum of (1/r)6 where r is the 
>> distance). Is there simple way to get this value calculated in 
>> Chimera (e.g. simple script)? Unfortunately, I have no idea about 
>> Python coding, so right now I have to import the list to Excel and 
>> calculate what I need in there (which is fine for a few atoms but 
>> slightly tedious  when you have to check several hundred of them...). 
>> Any help would be appreciated.
>>
>> Thanks,
>> Józef
>
>