Hi-
Is it possible to differentiate between chain ID’s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6).
Thanks, Melissa
Hi Melissa, This is already done. Although chain-ID capitalization is ignored when the file has only capitalized IDs, when both are present, the upper- or lower-case that you type is honored. I tested by opening 5GM6, and making sure that the following give different results:
sel :.a sel :.A
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 Sep 27, 2016, at 4:24 PM, Melissa Jurica mjurica@ucsc.edu wrote:
Hi- Is it possible to differentiate between chain ID’s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). Thanks, Melissa
Hmm. If I have a command file with the following, both chains end up being called smb1_b. Am I missing something? Prior to running this I used the “split” command to separate the chains into sub-models.
setattr m name Brr2_B #0:.B setattr m name smb1_b #0:.b
Melissa
On Sep 28, 2016, at 9:43 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Melissa, This is already done. Although chain-ID capitalization is ignored when the file has only capitalized IDs, when both are present, the upper- or lower-case that you type is honored. I tested by opening 5GM6, and making sure that the following give different results:
sel :.a sel :.A
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 Sep 27, 2016, at 4:24 PM, Melissa Jurica mjurica@ucsc.edu wrote:
Hi- Is it possible to differentiate between chain ID’s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). Thanks, Melissa
Hi Melissa, After you use split, there is no a longer a model with both upper- and lower-case chain IDs (since each model is now only one chain) and so the case is ignored. After splitting you would have to specify by model number instead, e.g. #0.25. It is only in models with both upper- and lower-case chain IDs that the case you type matters. Elaine
On Sep 28, 2016, at 9:53 AM, Melissa Jurica mjurica@ucsc.edu wrote:
Hmm. If I have a command file with the following, both chains end up being called smb1_b. Am I missing something? Prior to running this I used the “split” command to separate the chains into sub-models.
setattr m name Brr2_B #0:.B setattr m name smb1_b #0:.b
Melissa
On Sep 28, 2016, at 9:43 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Melissa, This is already done. Although chain-ID capitalization is ignored when the file has only capitalized IDs, when both are present, the upper- or lower-case that you type is honored. I tested by opening 5GM6, and making sure that the following give different results:
sel :.a sel :.A
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 Sep 27, 2016, at 4:24 PM, Melissa Jurica mjurica@ucsc.edu wrote:
Hi- Is it possible to differentiate between chain ID’s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). Thanks, Melissa
OK- thanks. M
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Melissa S. Jurica, Ph.D. Professor, Molecular, Cell & Developmental Biology Center for Molecular Biology of RNA University of California, Santa Cruz 1156 High Street Santa Cruz, CA 95064
Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 http://www.mcd.ucsc.edu/faculty/jurica.html ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
On Sep 28, 2016, at 2:12 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Melissa, After you use split, there is no a longer a model with both upper- and lower-case chain IDs (since each model is now only one chain) and so the case is ignored. After splitting you would have to specify by model number instead, e.g. #0.25. It is only in models with both upper- and lower-case chain IDs that the case you type matters. Elaine
On Sep 28, 2016, at 9:53 AM, Melissa Jurica mjurica@ucsc.edu wrote:
Hmm. If I have a command file with the following, both chains end up being called smb1_b. Am I missing something? Prior to running this I used the “split” command to separate the chains into sub-models.
setattr m name Brr2_B #0:.B setattr m name smb1_b #0:.b
Melissa
On Sep 28, 2016, at 9:43 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Melissa, This is already done. Although chain-ID capitalization is ignored when the file has only capitalized IDs, when both are present, the upper- or lower-case that you type is honored. I tested by opening 5GM6, and making sure that the following give different results:
sel :.a sel :.A
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 Sep 27, 2016, at 4:24 PM, Melissa Jurica mjurica@ucsc.edu wrote:
Hi- Is it possible to differentiate between chain ID’s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). Thanks, Melissa
participants (2)
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Elaine Meng -
Melissa Jurica