update readme

README.md

@@ -5,7 +5,7 @@
 #### This is the first release for paper [High-resolution de novo structure prediction from primary sequence](https://www.biorxiv.org/content/10.1101/2022.07.21.500999v1).
 
 We will continue to optimize this repository for more ease of use, for
-instance, reducing the GRAM required to inference long proteins and 
+instance, reducing the GRAM required to inference long proteins and
 releasing possibly stronger models.
 
 ## Setup
@@ -18,10 +18,8 @@ pip install -r requirements.txt
 
 should get you where you want.
 Even if this failed, since we use minimal 3rd party libraries, you can
-always just install
-[PyTorch](https://pytorch.org)
-and
-[biopython](https://biopython.org)
+always just install the latest
+[PyTorch](https://pytorch.org) and [biopython](https://biopython.org)
 (and that's it!)
 yourself.
 
@@ -36,7 +34,13 @@ python main.py INPUT_FILE.fasta OUTPUT_DIRECTORY
 And voila!
 
 The `INPUT_FILE.fasta` should be a normal fasta file with possibly many
-sequences.
+sequences with a comment line starting with `>` or `:` above the amino
+acid sequence itself.
+
+This command will download the weight
+from https://helixon.s3.amazonaws.com/release1.pt
+to `~/.cache/omegafold_ckpt/model.pt`
+and load the model
 
 However, since we have implemented sharded execution, it is possible to
 
@@ -53,6 +57,8 @@ For more information, run
 python main.py --help
 ```
 
+where we provide several options for both speed and weights utilities.
+
 ## Output
 
 We produce one pdb for each of the sequences in `INPUT_FILE.fasta` saved in
@@ -65,9 +71,7 @@ If this is helpful to you, please consider citing the paper with
 
 ```tex
 @article{OmegaFold,
-	author = {Wu, Ruidong and Ding, Fan and Wang, Rui and Shen, Rui and 
-       Zhang, Xiwen and Luo, Shitong and Su, Chenpeng and Wu, Zuofan and Xie, 
-       Qi and Berger, Bonnie and Ma, Jianzhu and Peng, Jian},
+	author = {Wu, Ruidong and Ding, Fan and Wang, Rui and Shen, Rui and Zhang, Xiwen and Luo, Shitong and Su, Chenpeng and Wu, Zuofan and Xie, Qi and Berger, Bonnie and Ma, Jianzhu and Peng, Jian},
 	title = {High-resolution de novo structure prediction from primary sequence},
 	elocation-id = {2022.07.21.500999},
 	year = {2022},

pipeline.py

@@ -112,7 +112,7 @@ def fasta2inputs(
     for line in lines:
         if len(line) == 0:
             continue
-        if line.startswith(">"):
+        if line.startswith(">") or line .startswith(":"):
             name = True
             chain_ids.append(line.strip(">").strip("\n"))
         else: