Re: [Chimera-users] Chimera-users Digest, Vol 173, Issue 3
Dear Chimera developers, I'm using Chimera to estimate molecular weight from cryo-em map through volume viewer/tools/measure volume and area/ The value of the volume I got is in e3 unit. What dies this e3 mean. This e3 unit is used for area as well, which confused me. The version I'm using is 1.12. It seems that the e3 equals nm3, but I'm not sure. It would be a great appreciated if you could help me to make it clear. Thanks Best regards Qian On 7 September 2017 at 16:44, <chimera-users-request@cgl.ucsf.edu> wrote:
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Today's Topics:
1. COX inhibitor demo discrepancy (simon chapman) 2. longbond command documentation? (Oliver Clarke) 3. Re: Batch mode for Chimera (Elaine Meng) 4. Re: COX inhibitor demo discrepancy (Elaine Meng) 5. Re: longbond command documentation? (Elaine Meng) 6. Re: COX inhibitor demo discrepancy (simon chapman)
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Message: 1 Date: Wed, 6 Sep 2017 12:17:56 +0100 From: simon chapman <rowanlodge19@gmail.com> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] COX inhibitor demo discrepancy Message-ID: <CAJPu8_4y4xVjZiXnT3TRXOj7XDnAtg2D7T-VuOQ7BTV3NdVteQ@mail. gmail.com> Content-Type: text/plain; charset="utf-8"
Hi, I'm very impressed with Chimera as a user of only 3 weeks so far
Trying out the various facilities has been a very useful exercise for completing my Masters in MedChem.
However, when I emulated the tutorial covering COX 1 and 2 inhibition, inputting the molecules fluribrofen and SC558 I generated via DS Visualiser bind at the outside edge of the enzymes. Not centrally as displayed in the video.
I also noted the molecular data in ViewDock, ie: energies etc, is missing. The table is blank other than the molecule number. Selecting 'Column' etc has no effect. The 'H-bonds' option does display however.
I've probably done something wrong, hey ho...but can you enlighten me?
Best wishes Simon
Hi Qian, The e3 just means exponent, in other words, multiply by 10**3 (thousands). It is not the units. The units are based on whatever length scale the data are in, usually angstroms, so the volume would be cubic angstroms and the area square angstroms. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 8, 2017, at 1:01 AM, Pu Qian <p.qian@sheffield.ac.uk> wrote:
Dear Chimera developers, I'm using Chimera to estimate molecular weight from cryo-em map through volume viewer/tools/measure volume and area/ The value of the volume I got is in e3 unit. What dies this e3 mean. This e3 unit is used for area as well, which confused me. The version I'm using is 1.12. It seems that the e3 equals nm3, but I'm not sure. It would be a great appreciated if you could help me to make it clear. Thanks Best regards Qian
Hi Elaine, Thanks. Understood. Qian On 8 September 2017 at 17:22, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Qian, The e3 just means exponent, in other words, multiply by 10**3 (thousands). It is not the units. The units are based on whatever length scale the data are in, usually angstroms, so the volume would be cubic angstroms and the area square angstroms. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 8, 2017, at 1:01 AM, Pu Qian <p.qian@sheffield.ac.uk> wrote:
Dear Chimera developers, I'm using Chimera to estimate molecular weight from cryo-em map through volume viewer/tools/measure volume and area/ The value of the volume I got is in e3 unit. What dies this e3 mean. This e3 unit is used for area as well, which confused me. The version I'm using is 1.12. It seems that the e3 equals nm3, but I'm not sure. It would be a great appreciated if you could help me to make it clear. Thanks Best regards Qian
participants (2)
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Elaine Meng -
Pu Qian