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
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 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, 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:
On Mar 3, 2010, at 9:25 AM, Jozef Lewandowski wrote:
Hi Jozef, I appended a script that if you've created pseudobonds for the contacts (which is the default) will sum the inverse of the sixth power of their lengths and print the result to the reply log. Run the script by opening it with File...Open or with the "open" command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Elaine Meng -
Eric Pettersen -
Jozef Lewandowski