[Chimera-users] findclash distance measurements

[Jozef Lewandowski]

Beautiful. After upgrading to the daily build everything works as 
advertised. Thank you.
Józef


On 3/3/10 6:57 PM, Elaine Meng wrote:
> Hi Jozef,
> I tried almost exactly the same command (only with different atom 
> specs because I don't have the same structure) before sending the 
> reply to make sure it worked.  Now I think maybe you are using an 
> older version of Chimera.  You need version 1.5 (daily builds) to be 
> able to use "test H" (by the way, you don't need the "" in the command).
>
> I thought you were looking at this previous reply, which mentions that 
> the improvement is in 1.5:
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004826.html> 
>
>
> In general it is impossible for us to tell if it is a bug without 
> using the same data file you are using (you should use Help...Report a 
> Bug and attach the data file or say what the PDB ID is), but in this 
> case it really sounds like you just need to get a newer version of 
> Chimera.
>
> Best,
> 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 9:47 AM, Jozef Lewandowski wrote:
>
>> 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
>>>
>>>
>>
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>
>