Hi group, So I am struggling with hydrogens in proteins. I have neutron data which shows H-atom positions. Well, Deuterons, but here are the issues. If I open a pdb in Chimera with old school hydrogen names like HG1, how can I get it to write out the new ones (like HG11) without explicitly adding the hydrogens in Chimera? I don't want the atom positions to change. Also, I notice Chimera doesn't seem to handle deuterons optimally. Writing out the pdb moved the atom name column to the left one space and changed the atom type in the last column back to H. The problem is caused by Coot, which we use to perform real space refinement of atom positions, but to quote George Sheldrick, "I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle." Unfortunately, the point of my project is to see the hydrogens!!!! Thanks for any help you can offer, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405
Hi Wally, I believe Chimera keeps the input atom names, and there is no option to translate hydrogen names from one version of PDB format to another. For this, I recommend using another program such as the MolProbity server (more on this below). Can anyone suggest other utilities/servers for translating hydrogen names between different programs and/or versions of PDB format? A separate issue is that you have encountered bugs in writing out deuterium: - names such as D1,D2,D3 displaced one column to the left - D in rightmost column changed to H I will file a bug report on writing out deuterium and add you to the notification list for when these problems are fixed. I should also mention there was a bug in writing the new-format hydrogen names, fixed mid-July (4-char hydrogen names were "wrapped" like 1HG1 instead of HG11). For hydrogen name translation, you might try the MolProbity (Richardson lab) server: <http://molprobity.biochem.duke.edu/> It can do a ton of things to fix up the structure, but I believe it can read in and write out v2.3 or v3.0 as instructed. It may be tedious if you need to process very many structures, however. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 13, 2008, at 6:31 AM, Walter Novak wrote:
Hi group, So I am struggling with hydrogens in proteins. I have neutron data which shows H-atom positions. Well, Deuterons, but here are the issues. If I open a pdb in Chimera with old school hydrogen names like HG1, how can I get it to write out the new ones (like HG11) without explicitly adding the hydrogens in Chimera? I don't want the atom positions to change. Also, I notice Chimera doesn't seem to handle deuterons optimally. Writing out the pdb moved the atom name column to the left one space and changed the atom type in the last column back to H.
The problem is caused by Coot, which we use to perform real space refinement of atom positions, but to quote George Sheldrick, "I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle."
Unfortunately, the point of my project is to see the hydrogens!!!!
Thanks for any help you can offer, Wally
Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405
Hi Elaine, I have tried Molprobity and it doesn't work. I think because Coot isn't even writing the 2.3 hydrogen names correctly, so it doesn't assume they are 2.3 names and won't upconvert them either. I may have to abandon Coot for my real space refinement! Thanks, Wally On Aug 13, 2008, at 1:59 PM, Elaine Meng wrote:
Hi Wally, I believe Chimera keeps the input atom names, and there is no option to translate hydrogen names from one version of PDB format to another. For this, I recommend using another program such as the MolProbity server (more on this below). Can anyone suggest other utilities/servers for translating hydrogen names between different programs and/or versions of PDB format?
A separate issue is that you have encountered bugs in writing out deuterium: - names such as D1,D2,D3 displaced one column to the left - D in rightmost column changed to H I will file a bug report on writing out deuterium and add you to the notification list for when these problems are fixed.
I should also mention there was a bug in writing the new-format hydrogen names, fixed mid-July (4-char hydrogen names were "wrapped" like 1HG1 instead of HG11).
For hydrogen name translation, you might try the MolProbity (Richardson lab) server: <http://molprobity.biochem.duke.edu/> It can do a ton of things to fix up the structure, but I believe it can read in and write out v2.3 or v3.0 as instructed. It may be tedious if you need to process very many structures, however.
Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Aug 13, 2008, at 6:31 AM, Walter Novak wrote:
Hi group, So I am struggling with hydrogens in proteins. I have neutron data which shows H-atom positions. Well, Deuterons, but here are the issues. If I open a pdb in Chimera with old school hydrogen names like HG1, how can I get it to write out the new ones (like HG11) without explicitly adding the hydrogens in Chimera? I don't want the atom positions to change. Also, I notice Chimera doesn't seem to handle deuterons optimally. Writing out the pdb moved the atom name column to the left one space and changed the atom type in the last column back to H.
The problem is caused by Coot, which we use to perform real space refinement of atom positions, but to quote George Sheldrick, "I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle."
Unfortunately, the point of my project is to see the hydrogens!!!!
Thanks for any help you can offer, Wally
Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405
Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405
participants (2)
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Elaine Meng -
Walter Novak