Hi Elaine, Thank you for the response. However, neither findclash #0.265:7@c test H overlap -8 hbond 0 ignoreIntraRes false log true bondSeparation 0 nor findclash #0.265:7@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@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@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@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@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